Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
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2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
We envisage the introduction of a secondary structure predictor in module one shortly.
[ "43", "47", "35" ]
86
9,800
0
false
We envisage the introduction of a secondary structure predictor in module one shortly.
[]
We envisage the introduction of a secondary structure predictor in module one shortly.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
For larger systems, i.e.
[ "43", "47", "35" ]
24
9,801
0
false
For larger systems, i.e.
[]
For larger systems, i.e.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
those containing more than 100 amino acid residues and those with more than three secondary structural elements, we conceive the introduction of loop filters to control the combinatorial explosion in the number of trial structures.
[ "43", "47", "35" ]
231
9,802
0
false
those containing more than 100 amino acid residues and those with more than three secondary structural elements, we conceive the introduction of loop filters to control the combinatorial explosion in the number of trial structures.
[]
those containing more than 100 amino acid residues and those with more than three secondary structural elements, we conceive the introduction of loop filters to control the combinatorial explosion in the number of trial structures.
false
true
true
true
false
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
We have utilized two biophysical filters presently in module three for trial structure selection and plan to utilize a few more such as hydrophobicity and packing fraction at later stages.
[ "43", "47", "35" ]
188
9,803
0
false
We have utilized two biophysical filters presently in module three for trial structure selection and plan to utilize a few more such as hydrophobicity and packing fraction at later stages.
[]
We have utilized two biophysical filters presently in module three for trial structure selection and plan to utilize a few more such as hydrophobicity and packing fraction at later stages.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
Also one could profitably employ constraints on strands for sheet formation, constraints on metal ions to cluster residues and disulphide bridges as filters for reducing the number of trial structures.
[ "43", "47", "35" ]
201
9,804
0
false
Also one could profitably employ constraints on strands for sheet formation, constraints on metal ions to cluster residues and disulphide bridges as filters for reducing the number of trial structures.
[]
Also one could profitably employ constraints on strands for sheet formation, constraints on metal ions to cluster residues and disulphide bridges as filters for reducing the number of trial structures.
true
true
true
true
true
1,559
2
DISCUSSION
1
35
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
The all atom empirical energy function utilized in module six was tested previously and was seen to separate native from the decoy structures in 67 of the 69 protein sequences from among 61 640 decoys studied (35).
[ "43", "47", "35" ]
214
9,805
1
false
The all atom empirical energy function utilized in module six was tested previously and was seen to separate native from the decoy structures in 67 of the 69 protein sequences from among 61 640 decoys studied.
[ "35" ]
The all atom empirical energy function utilized in module six was tested previously and was seen to separate native from the decoy structures in 67 of the 69 protein sequences from among 61 640 decoys studied.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
The scoring function calculates the non-bonded energy of each trial structure as a sum of the electrostatics, van der Waals and hydrophobicity.
[ "43", "47", "35" ]
143
9,806
0
false
The scoring function calculates the non-bonded energy of each trial structure as a sum of the electrostatics, van der Waals and hydrophobicity.
[]
The scoring function calculates the non-bonded energy of each trial structure as a sum of the electrostatics, van der Waals and hydrophobicity.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
There is scope for improvement in the scoring function particularly in describing the hydrophobicity component.
[ "43", "47", "35" ]
111
9,807
0
false
There is scope for improvement in the scoring function particularly in describing the hydrophobicity component.
[]
There is scope for improvement in the scoring function particularly in describing the hydrophobicity component.
true
true
true
true
true
1,559
2
DISCUSSION
1
43
[ "b43", "b47", "b35" ]
17,090,600
NA|NA|pmid-4124164|pmid-11226239|pmid-15215442|pmid-16166519|pmid-15980581|pmid-15980571|pmid-14507680|pmid-16294329|pmid-15980489|pmid-9005434|pmid-16363875
Work on the above mentioned lines as also on a Flexible Monte Carlo simulation strategy to bring down the RMSD < 3 Å of the native is in progress.
[ "43", "47", "35" ]
146
9,808
0
false
Work on the above mentioned lines as also on a Flexible Monte Carlo simulation strategy to bring down the RMSD < 3 Å of the native is in progress.
[]
Work on the above mentioned lines as also on a Flexible Monte Carlo simulation strategy to bring down the RMSD < 3 Å of the native is in progress.
true
true
true
true
true
1,559
3
DISCUSSION
0
null
null
17,090,600
null
The individual modules of Bhageerath are web enabled for free access.
null
69
9,809
0
false
null
null
The individual modules of Bhageerath are web enabled for free access.
true
true
true
true
true
1,560
3
DISCUSSION
0
null
null
17,090,600
null
These include the four biophysical filters (persistence length, radius of gyration, hydrophobicity ratio and packing fraction), a protein structure optimizer, an all-atom empirical energy based scoring function and ProRegIn utility.
null
232
9,810
0
false
null
null
These include the four biophysical filters (persistence length, radius of gyration, hydrophobicity ratio and packing fraction), a protein structure optimizer, an all-atom empirical energy based scoring function and ProRegIn utility.
true
true
true
true
true
1,560
3
DISCUSSION
0
null
null
17,090,600
null
These are listed in Table 5 along with their corresponding URL's.
null
65
9,811
0
false
null
null
These are listed in Table 5 along with their corresponding URL's.
true
true
true
true
true
1,560
0
INTRODUCTION
1
1
[ "b1" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
The inability of DNA polymerases to start de novo DNA synthesis imposes in most organisms the necessity of an RNA molecule to provide the 3′-OH group needed to initiate DNA elongation.
[ "1" ]
184
9,812
0
false
The inability of DNA polymerases to start de novo DNA synthesis imposes in most organisms the necessity of an RNA molecule to provide the 3′-OH group needed to initiate DNA elongation.
[]
The inability of DNA polymerases to start de novo DNA synthesis imposes in most organisms the necessity of an RNA molecule to provide the 3′-OH group needed to initiate DNA elongation.
true
true
true
true
true
1,561
0
INTRODUCTION
1
1
[ "b1" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
This requirement creates a dilemma for the replication of the ends of linear genomes since, once the last RNA primer for the lagging strand synthesis is removed, a portion of ssDNA at the end of the genome will remain uncopied.
[ "1" ]
227
9,813
0
false
This requirement creates a dilemma for the replication of the ends of linear genomes since, once the last RNA primer for the lagging strand synthesis is removed, a portion of ssDNA at the end of the genome will remain uncopied.
[]
This requirement creates a dilemma for the replication of the ends of linear genomes since, once the last RNA primer for the lagging strand synthesis is removed, a portion of ssDNA at the end of the genome will remain uncopied.
true
true
true
true
true
1,561
0
INTRODUCTION
1
1
[ "b1" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
In order to avoid the continuous shortening of the linear genomes in subsequent replication rounds, several mechanisms have evolved, most of them making use of the presence of repetitive sequences at the ends of the chromosomes that allow to create long concatemers, to circularize, or to form hairpin loops to fill the ...
[ "1" ]
339
9,814
0
false
In order to avoid the continuous shortening of the linear genomes in subsequent replication rounds, several mechanisms have evolved, most of them making use of the presence of repetitive sequences at the ends of the chromosomes that allow to create long concatemers, to circularize, or to form hairpin loops to fill the ...
[]
In order to avoid the continuous shortening of the linear genomes in subsequent replication rounds, several mechanisms have evolved, most of them making use of the presence of repetitive sequences at the ends of the chromosomes that allow to create long concatemers, to circularize, or to form hairpin loops to fill the ...
true
true
true
true
true
1,561
0
INTRODUCTION
1
1
[ "b1" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
In higher eukaryotes, telomerase prevents chromosome ends shortening by elongating the 3′-OH group of the ssDNA end using as template its own RNA (1).
[ "1" ]
150
9,815
1
false
In higher eukaryotes, telomerase prevents chromosome ends shortening by elongating the 3′-OH group of the ssDNA end using as template its own RNA.
[ "1" ]
In higher eukaryotes, telomerase prevents chromosome ends shortening by elongating the 3′-OH group of the ssDNA end using as template its own RNA.
true
true
true
true
true
1,561
1
INTRODUCTION
1
2
[ "b2" ]
17,071,961
NA|pmid-8969297|pmid-11006291
Several phages, animal viruses as adenovirus and hepadnaviruses, mitochondrial plasmids, and linear chromosomes and plasmids of Streptomyces have solved such a quandary by using a protein as primer, called terminal protein (TP).
[ "2" ]
228
9,816
0
false
Several phages, animal viruses as adenovirus and hepadnaviruses, mitochondrial plasmids, and linear chromosomes and plasmids of Streptomyces have solved such a quandary by using a protein as primer, called terminal protein (TP).
[]
Several phages, animal viruses as adenovirus and hepadnaviruses, mitochondrial plasmids, and linear chromosomes and plasmids of Streptomyces have solved such a quandary by using a protein as primer, called terminal protein (TP).
true
true
true
true
true
1,562
1
INTRODUCTION
1
2
[ "b2" ]
17,071,961
NA|pmid-8969297|pmid-11006291
The OH group of a specific serine, threonine or tyrosine of TP is used by the replicative DNA polymerase to start DNA synthesis from both ends of the linear genome, the TP remaining covalently linked to such 5′ ends (2).
[ "2" ]
220
9,817
1
false
The OH group of a specific serine, threonine or tyrosine of TP is used by the replicative DNA polymerase to start DNA synthesis from both ends of the linear genome, the TP remaining covalently linked to such 5′ ends.
[ "2" ]
The OH group of a specific serine, threonine or tyrosine of TP is used by the replicative DNA polymerase to start DNA synthesis from both ends of the linear genome, the TP remaining covalently linked to such 5′ ends.
true
true
true
true
true
1,562
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The development of in vitro replication systems with purified proteins, mainly in the case of bacteriophage φ29 and adenovirus, has allowed the elucidation of the general bases of the protein-priming mechanism of DNA replication (2–4).
[ "2", "4", "5", "9", "2" ]
235
9,818
0
false
The development of in vitro replication systems with purified proteins, mainly in the case of bacteriophage φ29 and adenovirus, has allowed the elucidation of the general bases of the protein-priming mechanism of DNA replication.
[ "2–4" ]
The development of in vitro replication systems with purified proteins, mainly in the case of bacteriophage φ29 and adenovirus, has allowed the elucidation of the general bases of the protein-priming mechanism of DNA replication.
true
true
true
true
true
1,563
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
Specific initiation proteins interact with the replication origins at both 5′ ends of the genome, partially opening the double helix, exposing a region of ssDNA.
[ "2", "4", "5", "9", "2" ]
161
9,819
0
false
Specific initiation proteins interact with the replication origins at both 5′ ends of the genome, partially opening the double helix, exposing a region of ssDNA.
[]
Specific initiation proteins interact with the replication origins at both 5′ ends of the genome, partially opening the double helix, exposing a region of ssDNA.
true
true
true
true
true
1,563
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The complex formed by a free TP and the replicative DNA polymerase interacts with the replication origins at both ends of the genome by specific recognition of the parental TP and DNA sequences.
[ "2", "4", "5", "9", "2" ]
194
9,820
0
false
The complex formed by a free TP and the replicative DNA polymerase interacts with the replication origins at both ends of the genome by specific recognition of the parental TP and DNA sequences.
[]
The complex formed by a free TP and the replicative DNA polymerase interacts with the replication origins at both ends of the genome by specific recognition of the parental TP and DNA sequences.
true
true
true
true
true
1,563
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
DNA polymerase catalyses the incorporation of a specific dNMP onto the priming OH group of the TP, in a reaction directed by an internal dNMP in the template strand (initiation reaction).
[ "2", "4", "5", "9", "2" ]
187
9,821
0
false
DNA polymerase catalyses the incorporation of a specific dNMP onto the priming OH group of the TP, in a reaction directed by an internal dNMP in the template strand (initiation reaction).
[]
DNA polymerase catalyses the incorporation of a specific dNMP onto the priming OH group of the TP, in a reaction directed by an internal dNMP in the template strand (initiation reaction).
true
true
true
true
true
1,563
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The initiation complex thus formed slides-back (in the case of bacteriophages φ29, GA-1, PRD1 and Cp1) or jumps-backs (as in adenovirus) to recover the terminal nucleotides, by virtue of the presence of repetitive sequences at the replication origins (5–9).
[ "2", "4", "5", "9", "2" ]
257
9,822
0
false
The initiation complex thus formed slides-back or jumps-backs (as in adenovirus) to recover the terminal nucleotides, by virtue of the presence of repetitive sequences at the replication origins.
[ "in the case of bacteriophages φ29, GA-1, PRD1 and Cp1", "5–9" ]
The initiation complex thus formed slides-back or jumps-backs (as in adenovirus) to recover the terminal nucleotides, by virtue of the presence of repetitive sequences at the replication origins.
true
true
true
true
true
1,563
2
INTRODUCTION
1
2
[ "b2", "b4", "b5", "b9", "b2" ]
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
Finally, the same DNA polymerase catalyses chain elongation via a strand displacement mechanism to fulfil TP-DNA replication (2).
[ "2", "4", "5", "9", "2" ]
129
9,823
1
false
Finally, the same DNA polymerase catalyses chain elongation via a strand displacement mechanism to fulfil TP-DNA replication.
[ "2" ]
Finally, the same DNA polymerase catalyses chain elongation via a strand displacement mechanism to fulfil TP-DNA replication.
true
true
true
true
true
1,563
3
INTRODUCTION
1
10
[ "b10" ]
17,071,961
pmid-2498321|pmid-4336040|pmid-2838173
In addition, the protein-priming mechanism of replication of the linear genomes solves the requirement of a functionally asymmetric replisome, as the placement of the two replication origins at both ends of the duplex DNA allows both strands to be replicated continuously (10) by two molecules of DNA polymerase in a pro...
[ "10" ]
371
9,824
1
false
In addition, the protein-priming mechanism of replication of the linear genomes solves the requirement of a functionally asymmetric replisome, as the placement of the two replication origins at both ends of the duplex DNA allows both strands to be replicated continuously by two molecules of DNA polymerase in a processi...
[ "10" ]
In addition, the protein-priming mechanism of replication of the linear genomes solves the requirement of a functionally asymmetric replisome, as the placement of the two replication origins at both ends of the duplex DNA allows both strands to be replicated continuously by two molecules of DNA polymerase in a processi...
true
true
true
true
true
1,564
4
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
Bacteriophage φ29 DNA polymerase is the only member of the protein-priming subgroup of DNA polymerases whose structure has been crystallographically solved, giving the insights into the structural basis that confer both processivity and strand displacement capacities to the enzyme (11).
[ "11", "12", "13", "14", "11", "15" ]
287
9,825
1
false
Bacteriophage φ29 DNA polymerase is the only member of the protein-priming subgroup of DNA polymerases whose structure has been crystallographically solved, giving the insights into the structural basis that confer both processivity and strand displacement capacities to the enzyme.
[ "11" ]
Bacteriophage φ29 DNA polymerase is the only member of the protein-priming subgroup of DNA polymerases whose structure has been crystallographically solved, giving the insights into the structural basis that confer both processivity and strand displacement capacities to the enzyme.
true
true
true
true
true
1,565
4
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
The main structural difference with respect to other family B DNA polymerases is the presence of two new subdomains corresponding to the two sequence insertions specifically present in the protein-priming DNA polymerases subgroup, called Terminal Protein Region 1 and 2 (TPR1 and TPR2) (12,13).
[ "11", "12", "13", "14", "11", "15" ]
294
9,826
0
false
The main structural difference with respect to other family B DNA polymerases is the presence of two new subdomains corresponding to the two sequence insertions specifically present in the protein-priming DNA polymerases subgroup, called Terminal Protein Region 1 and 2 (TPR1 and TPR2).
[ "12,13" ]
The main structural difference with respect to other family B DNA polymerases is the presence of two new subdomains corresponding to the two sequence insertions specifically present in the protein-priming DNA polymerases subgroup, called Terminal Protein Region 1 and 2.
true
true
true
true
true
1,565
4
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
The specific TPR2 insertion, together with the exonuclease, thumb and palm subdomains, forms two tunnels capable of interacting with DNA.
[ "11", "12", "13", "14", "11", "15" ]
137
9,827
0
false
The specific TPR2 insertion, together with the exonuclease, thumb and palm subdomains, forms two tunnels capable of interacting with DNA.
[]
The specific TPR2 insertion, together with the exonuclease, thumb and palm subdomains, forms two tunnels capable of interacting with DNA.
true
true
true
true
true
1,565
4
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
The major one would encircle upstream duplex DNA, conferring the DNA binding stability required to replicate processively.
[ "11", "12", "13", "14", "11", "15" ]
122
9,828
0
false
The major one would encircle upstream duplex DNA, conferring the DNA binding stability required to replicate processively.
[]
The major one would encircle upstream duplex DNA, conferring the DNA binding stability required to replicate processively.
true
true
true
true
true
1,565
4
INTRODUCTION
1
14
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
In addition, this tunnel also surrounds the priming domain of TP during the first phases of TP-DNA replication, confirming that both TP and DNA occupy, in a sequential manner, the same binding cleft (14).
[ "11", "12", "13", "14", "11", "15" ]
204
9,829
1
false
In addition, this tunnel also surrounds the priming domain of TP during the first phases of TP-DNA replication, confirming that both TP and DNA occupy, in a sequential manner, the same binding cleft.
[ "14" ]
In addition, this tunnel also surrounds the priming domain of TP during the first phases of TP-DNA replication, confirming that both TP and DNA occupy, in a sequential manner, the same binding cleft.
true
true
true
true
true
1,565
4
INTRODUCTION
1
11
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
The narrow dimensions of the minor tunnel would preclude the passage of dsDNA through it, enclosing exclusively the downstream template and forcing the unwinding of both strands before the template enters such a tunnel (11).
[ "11", "12", "13", "14", "11", "15" ]
224
9,830
1
false
The narrow dimensions of the minor tunnel would preclude the passage of dsDNA through it, enclosing exclusively the downstream template and forcing the unwinding of both strands before the template enters such a tunnel.
[ "11" ]
The narrow dimensions of the minor tunnel would preclude the passage of dsDNA through it, enclosing exclusively the downstream template and forcing the unwinding of both strands before the template enters such a tunnel.
true
true
true
true
true
1,565
4
INTRODUCTION
1
15
[ "b11", "b12", "b13", "b14", "b11", "b15" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
These hypotheses have recently been demonstrated by biochemical characterization of a φ29 DNA polymerase mutant lacking the TPR2 insertion (15).
[ "11", "12", "13", "14", "11", "15" ]
144
9,831
1
false
These hypotheses have recently been demonstrated by biochemical characterization of a φ29 DNA polymerase mutant lacking the TPR2 insertion.
[ "15" ]
These hypotheses have recently been demonstrated by biochemical characterization of a φ29 DNA polymerase mutant lacking the TPR2 insertion.
true
true
true
true
true
1,565
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
Bacteriophages Nf and GA-1 belong to the group of phages that infect Bacillus.
[ "2", "16", "6", "17" ]
78
9,832
0
false
Bacteriophages Nf and GA-1 belong to the group of phages that infect Bacillus.
[]
Bacteriophages Nf and GA-1 belong to the group of phages that infect Bacillus.
true
true
true
true
true
1,566
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
This group has been subclassified into three serological classes (2).
[ "2", "16", "6", "17" ]
69
9,833
1
false
This group has been subclassified into three serological classes.
[ "2" ]
This group has been subclassified into three serological classes.
true
true
true
true
true
1,566
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
The first class includes phages φ29, PZA, φ15 and BS32; the second one comprises phages B103, Nf and M2Y; and the third one contains phage GA-1 as the only member.
[ "2", "16", "6", "17" ]
163
9,834
0
false
The first class includes phages φ29, PZA, φ15 and BS32; the second one comprises phages B103, Nf and M2Y; and the third one contains phage GA-1 as the only member.
[]
The first class includes phages φ29, PZA, φ15 and BS32; the second one comprises phages B103, Nf and M2Y; and the third one contains phage GA-1 as the only member.
true
true
true
true
true
1,566
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
As in the case of φ29, these phages possess a double-stranded linear DNA with a TP covalently linked at both 5′ ends (TP-DNA) that is replicated by a protein-priming mechanism.
[ "2", "16", "6", "17" ]
176
9,835
0
false
As in the case of φ29, these phages possess a double-stranded linear DNA with a TP covalently linked at both 5′ ends (TP-DNA) that is replicated by a protein-priming mechanism.
[]
As in the case of φ29, these phages possess a double-stranded linear DNA with a TP covalently linked at both 5′ ends (TP-DNA) that is replicated by a protein-priming mechanism.
true
true
true
true
true
1,566
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
As in φ29, the product of bacteriophages Nf and GA-1 gene 2 is the replicative DNA polymerase.
[ "2", "16", "6", "17" ]
94
9,836
0
false
As in φ29, the product of bacteriophages Nf and GA-1 gene 2 is the replicative DNA polymerase.
[]
As in φ29, the product of bacteriophages Nf and GA-1 gene 2 is the replicative DNA polymerase.
true
true
true
true
true
1,566
5
INTRODUCTION
1
16
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
Nf DNA polymerase contains 572 amino acids (66.4 kDa), showing 81.8% of sequence identity with respect to φ29 DNA polymerase (91.3% similarity) (16).
[ "2", "16", "6", "17" ]
149
9,837
1
false
Nf DNA polymerase contains 572 amino acids, showing 81.8% of sequence identity with respect to φ29 DNA polymerase (91.3% similarity).
[ "66.4 kDa", "16" ]
Nf DNA polymerase contains 572 amino acids, showing 81.8% of sequence identity with respect to φ29 DNA polymerase.
true
true
true
true
true
1,566
5
INTRODUCTION
1
2
[ "b2", "b16", "b6", "b17" ]
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
DNA polymerase is a polypeptide of 578 amino acids (67.1 kDa) which shares 54% of sequence identity and 67.3% of similarity when compared with φ29 DNA polymerase (6,17).
[ "2", "16", "6", "17" ]
169
9,838
0
false
DNA polymerase is a polypeptide of 578 amino acids which shares 54% of sequence identity and 67.3% of similarity when compared with φ29 DNA polymerase.
[ "67.1 kDa", "6,17" ]
DNA polymerase is a polypeptide of 578 amino acids which shares 54% of sequence identity and 67.3% of similarity when compared with φ29 DNA polymerase.
true
true
true
true
true
1,566
6
INTRODUCTION
0
null
null
17,071,961
NA|NA|pmid-2498321|pmid-3081736|pmid-1655759|pmid-7918621|pmid-9135160|pmid-9108156
In this work, we describe the catalytic properties of the Nf and GA-1 DNA polymerases responsible for efficient and accurate synthesis of full-length TP-DNA.
null
157
9,839
0
false
null
null
In this work, we describe the catalytic properties of the Nf and GA-1 DNA polymerases responsible for efficient and accurate synthesis of full-length TP-DNA.
true
true
true
true
true
1,567
6
INTRODUCTION
0
null
null
17,071,961
NA|NA|pmid-2498321|pmid-3081736|pmid-1655759|pmid-7918621|pmid-9135160|pmid-9108156
In addition, we present data showing GA-1 DNA polymerase as the first example of a protein-primed DNA polymerase whose structure is specifically adapted to use exclusively its corresponding TP as primer of polymerization.
null
221
9,840
0
false
null
null
In addition, we present data showing GA-1 DNA polymerase as the first example of a protein-primed DNA polymerase whose structure is specifically adapted to use exclusively its corresponding TP as primer of polymerization.
true
true
true
true
true
1,567
0
DISCUSSION
1
32
[ "b32", "b33", "b34" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
Extensive studies performed both in vitro and in vivo, mainly using bacteriophage φ29 and adenovirus, have provided the general insights about the mechanism of protein-primed DNA replication (32,33).
[ "32", "33", "34" ]
199
9,841
0
false
Extensive studies performed both in vitro and in vivo, mainly using bacteriophage φ29 and adenovirus, have provided the general insights about the mechanism of protein-primed DNA replication.
[ "32,33" ]
Extensive studies performed both in vitro and in vivo, mainly using bacteriophage φ29 and adenovirus, have provided the general insights about the mechanism of protein-primed DNA replication.
true
true
true
true
true
1,568
0
DISCUSSION
1
32
[ "b32", "b33", "b34" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
Both 5′ ends of the linear genome contain a TP covalently linked that, together with specific DNA sequences, constitute the replication origins.
[ "32", "33", "34" ]
144
9,842
0
false
Both 5′ ends of the linear genome contain a TP covalently linked that, together with specific DNA sequences, constitute the replication origins.
[]
Both 5′ ends of the linear genome contain a TP covalently linked that, together with specific DNA sequences, constitute the replication origins.
true
true
true
true
true
1,568
0
DISCUSSION
1
32
[ "b32", "b33", "b34" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
The replicative eukaryotic-type [family B, (34)]
[ "32", "33", "34" ]
48
9,843
0
false
The replicative eukaryotic-type
[ "family B, (34)" ]
The replicative eukaryotic-type
true
true
false
true
false
1,568
0
DISCUSSION
1
32
[ "b32", "b33", "b34" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
DNA polymerase catalyses both, the initial formation of the covalent complex between a free TP molecule and the 5′ terminal nucleotide, and its further elongation coupled to strand displacement.
[ "32", "33", "34" ]
194
9,844
0
false
DNA polymerase catalyses both, the initial formation of the covalent complex between a free TP molecule and the 5′ terminal nucleotide, and its further elongation coupled to strand displacement.
[]
DNA polymerase catalyses both, the initial formation of the covalent complex between a free TP molecule and the 5′ terminal nucleotide, and its further elongation coupled to strand displacement.
true
true
true
true
true
1,568
0
DISCUSSION
1
32
[ "b32", "b33", "b34" ]
17,071,961
NA|pmid-1883199|NA|pmid-3127204
Such coupling can be accounted for by the polymerase itself, as in the case of bacteriophage φ29, or by the assistance of unwinding proteins as it occurs in adenovirus.
[ "32", "33", "34" ]
168
9,845
0
false
Such coupling can be accounted for by the polymerase itself, as in the case of bacteriophage φ29, or by the assistance of unwinding proteins as it occurs in adenovirus.
[]
Such coupling can be accounted for by the polymerase itself, as in the case of bacteriophage φ29, or by the assistance of unwinding proteins as it occurs in adenovirus.
true
true
true
true
true
1,568
1
DISCUSSION
1
6
[ "b6", "b35" ]
17,071,961
NA|pmid-8969297|pmid-11006291
Here, we have carried out a biochemical characterization of the main properties of the DNA polymerases encoded by bacteriophages GA-1 and Nf, whose linear genome is also replicated via a protein-priming mechanism (6,35).
[ "6", "35" ]
220
9,846
0
false
Here, we have carried out a biochemical characterization of the main properties of the DNA polymerases encoded by bacteriophages GA-1 and Nf, whose linear genome is also replicated via a protein-priming mechanism.
[ "6,35" ]
Here, we have carried out a biochemical characterization of the main properties of the DNA polymerases encoded by bacteriophages GA-1 and Nf, whose linear genome is also replicated via a protein-priming mechanism.
true
true
true
true
true
1,569
2
DISCUSSION
1
11
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
Based on the high degree of identity between φ29, Nf and GA-1 DNA polymerases, the protein structure homology-modelling server Swiss-Model (36,37) has provided a model for GA-1 and Nf DNA polymerases, obtained by using the recently solved crystallographic structure of φ29 DNA polymerase as template (11).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
305
9,847
1
false
Based on the high degree of identity between φ29, Nf and GA-1 DNA polymerases, the protein structure homology-modelling server Swiss-Model has provided a model for GA-1 and Nf DNA polymerases, obtained by using the recently solved crystallographic structure of φ29 DNA polymerase as template.
[ "36,37", "11" ]
Based on the high degree of identity between φ29, Nf and GA-1 DNA polymerases, the protein structure homology-modelling server Swiss-Model has provided a model for GA-1 and Nf DNA polymerases, obtained by using the recently solved crystallographic structure of φ29 DNA polymerase as template.
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The predicted structures exhibit two well-structured independent domains (see Figure 8A for GA-1 DNA polymerase model).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
119
9,848
0
false
The predicted structures exhibit two well-structured independent domains (see Figure 8A for GA-1 DNA polymerase model).
[]
The predicted structures exhibit two well-structured independent domains (see Figure 8A for GA-1 DNA polymerase model).
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The N-terminal exonuclease domain [that is structurally conserved in the A, B and C families of DNA polymerases (38)] of both Nf and GA-1 DNA polymerases has the three universally conserved motifs Exo I, Exo II and Exo III containing the four carboxylic residues involved in binding the two metal ions responsible for th...
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
466
9,849
0
false
The N-terminal exonuclease domain of both Nf and GA-1 DNA polymerases has the three universally conserved motifs Exo I, Exo II and Exo III containing the four carboxylic residues involved in binding the two metal ions responsible for the 3′–5′ exonuclease activity, as well as other residues described as primer-terminus...
[ "that is structurally conserved in the A, B and C families of DNA polymerases (38)", "38–40", "24,29,41–43" ]
The N-terminal exonuclease domain of both Nf and GA-1 DNA polymerases has the three universally conserved motifs Exo I, Exo II and Exo III containing the four carboxylic residues involved in binding the two metal ions responsible for the 3′–5′ exonuclease activity, as well as other residues described as primer-terminus...
true
true
true
true
true
1,570
2
DISCUSSION
1
44
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
This domain also presents the Kx2h motif that contains a Lys residue which plays an auxiliary role in the exonucleolytic catalysis in family B DNA polymerases (44), and the (S/T)Lx2h motif, whose residues have been involved in making contacts with DNA and TP (29,42,45,46).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
273
9,850
1
false
This domain also presents the Kx2h motif that contains a Lys residue which plays an auxiliary role in the exonucleolytic catalysis in family B DNA polymerases, and the (S/T)Lx2h motif, whose residues have been involved in making contacts with DNA and TP.
[ "44", "29,42,45,46" ]
This domain also presents the Kx2h motif that contains a Lys residue which plays an auxiliary role in the exonucleolytic catalysis in family B DNA polymerases, and the (S/T)Lx2h motif, whose residues have been involved in making contacts with DNA and TP.
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The C-terminal polymerization domain shows the universal palm, fingers and thumb subdomains structured as a partially open right hand and forming a U-shaped groove predicted to bind the duplex DNA, like in other DNA polymerases cocrystallized with this substrate (47–51).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
271
9,851
0
false
The C-terminal polymerization domain shows the universal palm, fingers and thumb subdomains structured as a partially open right hand and forming a U-shaped groove predicted to bind the duplex DNA, like in other DNA polymerases cocrystallized with this substrate.
[ "47–51" ]
The C-terminal polymerization domain shows the universal palm, fingers and thumb subdomains structured as a partially open right hand and forming a U-shaped groove predicted to bind the duplex DNA, like in other DNA polymerases cocrystallized with this substrate.
true
true
true
true
true
1,570
2
DISCUSSION
1
52
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
Primer-terminus will lie on the palm subdomain as it includes the conserved motifs Dx2SLYP (motif A) and YxDTDS (motif C) containing the three catalytic carboxylates responsible for the polymerization catalysis (48,51–56), the KxY motif including DNA ligands at the polymerase site (52), and the YxGG/A and Tx2G/AR motif...
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
399
9,852
1
false
Primer-terminus will lie on the palm subdomain as it includes the conserved motifs Dx2SLYP (motif A) and YxDTDS (motif C) containing the three catalytic carboxylates responsible for the polymerization catalysis, the KxY motif including DNA ligands at the polymerase site, and the YxGG/A and Tx2G/AR motifs whose residues...
[ "48,51–56", "52", "52,57,58" ]
Primer-terminus will lie on the palm subdomain as it includes the conserved motifs Dx2SLYP (motif A) and YxDTDS (motif C) containing the three catalytic carboxylates responsible for the polymerization catalysis, the KxY motif including DNA ligands at the polymerase site, and the YxGG/A and Tx2G/AR motifs whose residues...
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The fingers subdomain includes motifs Pre-B and Kx3NSxYG (motif B) responsible for interacting with the incoming nucleotide and the template strand (52,59–61).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
159
9,853
0
false
The fingers subdomain includes motifs Pre-B and Kx3NSxYG (motif B) responsible for interacting with the incoming nucleotide and the template strand.
[ "52,59–61" ]
The fingers subdomain includes motifs Pre-B and Kx3NSxYG (motif B) responsible for interacting with the incoming nucleotide and the template strand.
true
true
true
true
true
1,570
2
DISCUSSION
1
62
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
The thumb subdomain contains a Leu residue involved in stabilizing the primer-terminus at the exonuclease site, in addition to other positively charged residues implicated in steadying primer-terminus at the polymerization site as well as in coordinating both the exonuclease and polymerization activities (62).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
311
9,854
1
false
The thumb subdomain contains a Leu residue involved in stabilizing the primer-terminus at the exonuclease site, in addition to other positively charged residues implicated in steadying primer-terminus at the polymerization site as well as in coordinating both the exonuclease and polymerization activities.
[ "62" ]
The thumb subdomain contains a Leu residue involved in stabilizing the primer-terminus at the exonuclease site, in addition to other positively charged residues implicated in steadying primer-terminus at the polymerization site as well as in coordinating both the exonuclease and polymerization activities.
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
In addition, as the rest of protein-priming DNA polymerases, those of Nf and GA-1 also contain two specific insertions into the sequence of the polymerase domain called terminal protein regions 1 and 2 (TPR1 and TPR2) (12,13,63).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
229
9,855
0
false
In addition, as the rest of protein-priming DNA polymerases, those of Nf and GA-1 also contain two specific insertions into the sequence of the polymerase domain called terminal protein regions 1 and 2 (TPR1 and TPR2).
[ "12,13,63" ]
In addition, as the rest of protein-priming DNA polymerases, those of Nf and GA-1 also contain two specific insertions into the sequence of the polymerase domain called terminal protein regions 1 and 2 (TPR1 and TPR2).
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
TPR1 is located between motif A and fingers subdomain and contains residues involved in making contacts with both dsDNA and TP (13,63).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
135
9,856
0
false
TPR1 is located between motif A and fingers subdomain and contains residues involved in making contacts with both dsDNA and TP.
[ "13,63" ]
TPR1 is located between motif A and fingers subdomain and contains residues involved in making contacts with both dsDNA and TP.
true
true
true
true
true
1,570
2
DISCUSSION
1
36
[ "b36", "b37", "b11", "b38", "b38", "b40", "b24", "b29", "b41", "b43", "b44", "b29", "b42", "b45", "b46", "b47", "b51", "b48", "b51", "b56", "b52", "b52", "b57", "b58", "b52", "b59", "b61", "b62", "b12", "b13", "b63", "b13", "b63", "b11", "b14", "...
17,071,961
NA|pmid-16476976|pmid-8367287|pmid-1409668|NA|pmid-9504803|pmid-12824332|pmid-15546620|pmid-2790959|pmid-2790959|pmid-1989886|pmid-8605889|pmid-9786901|pmid-11071805|pmid-11884636|pmid-9231901|pmid-9786901|pmid-9642062|pmid-12473453|pmid-15033354|pmid-8469987|pmid-9440698|pmid-9440688|pmid-9440698|pmid-9440683|pmid-862...
TPR2 immediately follows the fingers subdomain, and together with the palm, fingers and thumb subdomains forms a tunnel that will embrace the DNA and TP substrates, providing the required stability to account for processive TP-DNA replication (11,14,15).
[ "36", "37", "11", "38", "38", "40", "24", "29", "41", "43", "44", "29", "42", "45", "46", "47", "51", "48", "51", "56", "52", "52", "57", "58", "52", "59", "61", "62", "12", "13", "63", "13", "63", "11", "14", "15" ]
254
9,857
0
false
TPR2 immediately follows the fingers subdomain, and together with the palm, fingers and thumb subdomains forms a tunnel that will embrace the DNA and TP substrates, providing the required stability to account for processive TP-DNA replication.
[ "11,14,15" ]
TPR2 immediately follows the fingers subdomain, and together with the palm, fingers and thumb subdomains forms a tunnel that will embrace the DNA and TP substrates, providing the required stability to account for processive TP-DNA replication.
true
true
true
true
true
1,570
3
DISCUSSION
1
64
[ "b64", "b65" ]
17,071,961
pmid-2498321|pmid-4336040|pmid-2838173
Most replicative DNA-dependent DNA polymerases possess an associated 3′–5′ exonuclease activity that enhances base substitution fidelity from a few fold to more than two orders of magnitude (64,65).
[ "64", "65" ]
198
9,858
0
false
Most replicative DNA-dependent DNA polymerases possess an associated 3′–5′ exonuclease activity that enhances base substitution fidelity from a few fold to more than two orders of magnitude.
[ "64,65" ]
Most replicative DNA-dependent DNA polymerases possess an associated 3′–5′ exonuclease activity that enhances base substitution fidelity from a few fold to more than two orders of magnitude.
true
true
true
true
true
1,571
4
DISCUSSION
1
66
[ "b66", "b69" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
Efficient editing of polymerization errors requires the primer-terminus to be properly placed at the catalytic site by virtue of DNA ligand residues that form a cleft designed to place exclusively ssDNA (frayed terminus) (66–69).
[ "66", "69" ]
229
9,859
0
false
Efficient editing of polymerization errors requires the primer-terminus to be properly placed at the catalytic site by virtue of DNA ligand residues that form a cleft designed to place exclusively ssDNA (frayed terminus).
[ "66–69" ]
Efficient editing of polymerization errors requires the primer-terminus to be properly placed at the catalytic site by virtue of DNA ligand residues that form a cleft designed to place exclusively ssDNA (frayed terminus).
true
true
true
true
true
1,572
4
DISCUSSION
1
66
[ "b66", "b69" ]
17,071,961
pmid-15546620|pmid-2118623|pmid-11090274|pmid-16511564|pmid-15546620|pmid-15845765|pmid-2541768|pmid-9215631
Whereas Nf DNA polymerase was able to degrade efficiently the ssDNA substrates, the 3′–5′ exonuclease activity of GA-1 DNA polymerase could be only detected by using pNP-TMP, a substrate used to dissociate the catalytic efficiency in hydrolysing the phosphodiester bond from DNA binding.
[ "66", "69" ]
287
9,860
0
false
Whereas Nf DNA polymerase was able to degrade efficiently the ssDNA substrates, the 3′–5′ exonuclease activity of GA-1 DNA polymerase could be only detected by using pNP-TMP, a substrate used to dissociate the catalytic efficiency in hydrolysing the phosphodiester bond from DNA binding.
[]
Whereas Nf DNA polymerase was able to degrade efficiently the ssDNA substrates, the 3′–5′ exonuclease activity of GA-1 DNA polymerase could be only detected by using pNP-TMP, a substrate used to dissociate the catalytic efficiency in hydrolysing the phosphodiester bond from DNA binding.
true
true
true
true
true
1,572
5
DISCUSSION
0
null
null
17,071,961
NA|pmid-10799555|pmid-8969297|pmid-11381102
The preference for excision of a mismatched primer/template molecule with respect to a matched one displayed by GA-1 and Nf DNA polymerases, together with the dynamic equilibrium between the polymerization and exonuclease activities (Pol/Exo assay) show that both are coupled and act coordinately to remove the misinsert...
null
335
9,861
0
false
null
null
The preference for excision of a mismatched primer/template molecule with respect to a matched one displayed by GA-1 and Nf DNA polymerases, together with the dynamic equilibrium between the polymerization and exonuclease activities (Pol/Exo assay) show that both are coupled and act coordinately to remove the misinsert...
true
true
true
true
true
1,573
6
DISCUSSION
1
1
[ "b1", "b70", "b10", "b71", "b72", "b73", "b74", "b75" ]
17,071,961
NA|NA|pmid-2498321|pmid-3081736|pmid-1655759|pmid-7918621|pmid-9135160|pmid-9108156
The results presented in this paper clearly indicate that Nf and GA-1 DNA polymerases can account for their genome replication without the assistance of unwinding and processivity factors, in contrast to most replicative DNA polymerases which require their physical association to processivity factors and DNA unwinding ...
[ "1", "70", "10", "71", "72", "73", "74", "75" ]
336
9,862
0
false
The results presented in this paper clearly indicate that Nf and GA-1 DNA polymerases can account for their genome replication without the assistance of unwinding and processivity factors, in contrast to most replicative DNA polymerases which require their physical association to processivity factors and DNA unwinding ...
[ "1,70" ]
The results presented in this paper clearly indicate that Nf and GA-1 DNA polymerases can account for their genome replication without the assistance of unwinding and processivity factors, in contrast to most replicative DNA polymerases which require their physical association to processivity factors and DNA unwinding ...
true
true
true
true
true
1,574
6
DISCUSSION
1
10
[ "b1", "b70", "b10", "b71", "b72", "b73", "b74", "b75" ]
17,071,961
NA|NA|pmid-2498321|pmid-3081736|pmid-1655759|pmid-7918621|pmid-9135160|pmid-9108156
Strand displacement capacity has also been shown for other protein-primed DNA polymerases as those of bacteriophages φ29 (10), Cp-1 (71) and PRD1 (72,73).
[ "1", "70", "10", "71", "72", "73", "74", "75" ]
154
9,863
1
false
Strand displacement capacity has also been shown for other protein-primed DNA polymerases as those of bacteriophages φ29, Cp-1 and PRD1.
[ "10", "71", "72,73" ]
Strand displacement capacity has also been shown for other protein-primed DNA polymerases as those of bacteriophages φ29, Cp-1 and PRD1.
true
true
true
true
true
1,574
6
DISCUSSION
1
1
[ "b1", "b70", "b10", "b71", "b72", "b73", "b74", "b75" ]
17,071,961
NA|NA|pmid-2498321|pmid-3081736|pmid-1655759|pmid-7918621|pmid-9135160|pmid-9108156
On the contrary, adenovirus DNA polymerase, although processive, cannot couple polymerization to strand displacement, requiring the DNA unwinding activity of the adenovirus DBP to perform strand displacement (74,75).
[ "1", "70", "10", "71", "72", "73", "74", "75" ]
216
9,864
0
false
On the contrary, adenovirus DNA polymerase, although processive, cannot couple polymerization to strand displacement, requiring the DNA unwinding activity of the adenovirus DBP to perform strand displacement.
[ "74,75" ]
On the contrary, adenovirus DNA polymerase, although processive, cannot couple polymerization to strand displacement, requiring the DNA unwinding activity of the adenovirus DBP to perform strand displacement.
true
true
true
true
true
1,574
7
DISCUSSION
1
76
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
Whereas it was possible to obtain GA-1 DNA replication by using exclusively the GA-1 TP and DNA polymerase, Nf DNA polymerase, although provided with competent strand displacement and processivity features, required the presence of Nf DBP for an effective in vitro replication of Nf TP-DNA.
[ "76", "77", "74", "77", "78", "77" ]
290
9,865
0
false
Whereas it was possible to obtain GA-1 DNA replication by using exclusively the GA-1 TP and DNA polymerase, Nf DNA polymerase, although provided with competent strand displacement and processivity features, required the presence of Nf DBP for an effective in vitro replication of Nf TP-DNA.
[]
Whereas it was possible to obtain GA-1 DNA replication by using exclusively the GA-1 TP and DNA polymerase, Nf DNA polymerase, although provided with competent strand displacement and processivity features, required the presence of Nf DBP for an effective in vitro replication of Nf TP-DNA.
true
true
true
true
true
1,575
7
DISCUSSION
1
76
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
Results presented here show that Nf DBP strongly stimulates the formation of the TP-dAMP initiation complex by decreasing the Km for dATP and facilitates the transition from initiation to elongation, as it occurs in φ29 (76).
[ "76", "77", "74", "77", "78", "77" ]
225
9,866
1
false
Results presented here show that Nf DBP strongly stimulates the formation of the TP-dAMP initiation complex by decreasing the Km for dATP and facilitates the transition from initiation to elongation, as it occurs in φ29.
[ "76" ]
Results presented here show that Nf DBP strongly stimulates the formation of the TP-dAMP initiation complex by decreasing the Km for dATP and facilitates the transition from initiation to elongation, as it occurs in φ29.
true
true
true
true
true
1,575
7
DISCUSSION
1
76
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
These results point to either a specific and direct contact between DBP and DNA polymerase that promotes conformational changes at the polymerization active site or to an effect of DBP in conferring the optimal template structure to direct initiating nucleotide insertion.
[ "76", "77", "74", "77", "78", "77" ]
272
9,867
0
false
These results point to either a specific and direct contact between DBP and DNA polymerase that promotes conformational changes at the polymerization active site or to an effect of DBP in conferring the optimal template structure to direct initiating nucleotide insertion.
[]
These results point to either a specific and direct contact between DBP and DNA polymerase that promotes conformational changes at the polymerization active site or to an effect of DBP in conferring the optimal template structure to direct initiating nucleotide insertion.
true
true
true
true
true
1,575
7
DISCUSSION
1
77
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
A similar role has been proposed for adenovirus DBP, a DNA unwinding protein (77).
[ "76", "77", "74", "77", "78", "77" ]
82
9,868
1
false
A similar role has been proposed for adenovirus DBP, a DNA unwinding protein.
[ "77" ]
A similar role has been proposed for adenovirus DBP, a DNA unwinding protein.
true
true
true
true
true
1,575
7
DISCUSSION
1
74
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
As in the case of φ29 and Nf DBP, this protein stimulates the rate of initiation also by decreasing the Km for the initiating nucleotide (74).
[ "76", "77", "74", "77", "78", "77" ]
142
9,869
1
false
As in the case of φ29 and Nf DBP, this protein stimulates the rate of initiation also by decreasing the Km for the initiating nucleotide.
[ "74" ]
As in the case of φ29 and Nf DBP, this protein stimulates the rate of initiation also by decreasing the Km for the initiating nucleotide.
true
true
true
true
true
1,575
7
DISCUSSION
1
76
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
The fact that an adenovirus DBP mutant defective in unwinding can still stimulate initiation precludes the unwinding role as the one responsible for such an activation (77,78).
[ "76", "77", "74", "77", "78", "77" ]
176
9,870
0
false
The fact that an adenovirus DBP mutant defective in unwinding can still stimulate initiation precludes the unwinding role as the one responsible for such an activation.
[ "77,78" ]
The fact that an adenovirus DBP mutant defective in unwinding can still stimulate initiation precludes the unwinding role as the one responsible for such an activation.
true
true
true
true
true
1,575
7
DISCUSSION
1
77
[ "b76", "b77", "b74", "b77", "b78", "b77" ]
17,071,961
pmid-3088545|pmid-12747551|pmid-9135160|pmid-12747551|pmid-12502807|pmid-12747551
In this case, contacts between DBP and pTP/DNA polymerase complex have been reported (77).
[ "76", "77", "74", "77", "78", "77" ]
90
9,871
1
false
In this case, contacts between DBP and pTP/DNA polymerase complex have been reported.
[ "77" ]
In this case, contacts between DBP and pTP/DNA polymerase complex have been reported.
true
true
true
true
true
1,575
8
DISCUSSION
0
null
null
17,071,961
null
The effect of Nf DBP in promoting elongation of the initiation products could be due to a decrease of the Km also for the incorporation of the dNMPs during the transition stage from initiation to elongation, to a different type of contact with the DNA polymerase that helps transition to elongation, or both.
null
308
9,872
0
false
null
null
The effect of Nf DBP in promoting elongation of the initiation products could be due to a decrease of the Km also for the incorporation of the dNMPs during the transition stage from initiation to elongation, to a different type of contact with the DNA polymerase that helps transition to elongation, or both.
true
true
true
true
true
1,576
8
DISCUSSION
0
null
null
17,071,961
null
The similarity in replication rates when comparing M13 DNA replication, performed in the absence of DBP (2400 nt/min), with Nf TP-DNA replication in the presence of DBP (2260 nt/min), suggests that the DBP stimulatory role is restricted to the first phases of Nf TP-DNA replication.
null
282
9,873
0
false
null
null
The similarity in replication rates when comparing M13 DNA replication, performed in the absence of DBP (2400 nt/min), with Nf TP-DNA replication in the presence of DBP (2260 nt/min), suggests that the DBP stimulatory role is restricted to the first phases of Nf TP-DNA replication.
true
true
true
true
true
1,576
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
The ability displayed by GA-1 DNA polymerase to hydrolyse the pNP-TMP substrate, together with its high efficiency in carrying out protein-primed initiation and elongation, allowed us to rule out a global misfolding as the cause of its hindered capacity to use ssDNA as substrate of its 3′–5′ exonuclease activity, as we...
[ "11" ]
374
9,874
0
false
The ability displayed by GA-1 DNA polymerase to hydrolyse the pNP-TMP substrate, together with its high efficiency in carrying out protein-primed initiation and elongation, allowed us to rule out a global misfolding as the cause of its hindered capacity to use ssDNA as substrate of its 3′–5′ exonuclease activity, as we...
[]
The ability displayed by GA-1 DNA polymerase to hydrolyse the pNP-TMP substrate, together with its high efficiency in carrying out protein-primed initiation and elongation, allowed us to rule out a global misfolding as the cause of its hindered capacity to use ssDNA as substrate of its 3′–5′ exonuclease activity, as we...
true
true
true
true
true
1,577
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
These results could indicate that GA-1 DNA polymerase has developed an extraordinary selectivity to use exclusively its natural primer, the TP, a rather unusual behaviour not shared by the rest of reported replicative protein-primed DNA polymerases that can use both types of primers, TP and DNA.
[ "11" ]
296
9,875
0
false
These results could indicate that GA-1 DNA polymerase has developed an extraordinary selectivity to use exclusively its natural primer, the TP, a rather unusual behaviour not shared by the rest of reported replicative protein-primed DNA polymerases that can use both types of primers, TP and DNA.
[]
These results could indicate that GA-1 DNA polymerase has developed an extraordinary selectivity to use exclusively its natural primer, the TP, a rather unusual behaviour not shared by the rest of reported replicative protein-primed DNA polymerases that can use both types of primers, TP and DNA.
true
true
true
true
true
1,577
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
The polymerization domain could be occluded somehow in the absence of TP, preventing the binding of GA-1 DNA polymerase to DNA substrates other than TP-DNA, restricting the use of the polymerase for TP-DNA replication.
[ "11" ]
218
9,876
0
false
The polymerization domain could be occluded somehow in the absence of TP, preventing the binding of GA-1 DNA polymerase to DNA substrates other than TP-DNA, restricting the use of the polymerase for TP-DNA replication.
[]
The polymerization domain could be occluded somehow in the absence of TP, preventing the binding of GA-1 DNA polymerase to DNA substrates other than TP-DNA, restricting the use of the polymerase for TP-DNA replication.
true
true
true
true
true
1,577
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
This fact would also explain why GA-1 DNA polymerase is highly impaired in the use of ssDNA as substrate of the exonuclease activity, taking into account that the cleft that binds the primer strand in the editing mode emanates from the polymerization active site [see Figure 8A and (11)].
[ "11" ]
288
9,877
0
false
This fact would also explain why GA-1 DNA polymerase is highly impaired in the use of ssDNA as substrate of the exonuclease activity, taking into account that the cleft that binds the primer strand in the editing mode emanates from the polymerization active site.
[ "see Figure 8A and (11)" ]
This fact would also explain why GA-1 DNA polymerase is highly impaired in the use of ssDNA as substrate of the exonuclease activity, taking into account that the cleft that binds the primer strand in the editing mode emanates from the polymerization active site.
true
true
true
true
true
1,577
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
Substrates such as the pNP-TMP can be exonucleolyticaly degraded since its small size would allow it to diffuse into the exonuclease site.
[ "11" ]
138
9,878
0
false
Substrates such as the pNP-TMP can be exonucleolyticaly degraded since its small size would allow it to diffuse into the exonuclease site.
[]
Substrates such as the pNP-TMP can be exonucleolyticaly degraded since its small size would allow it to diffuse into the exonuclease site.
true
true
true
true
true
1,577
9
DISCUSSION
1
11
[ "b11" ]
17,071,961
pmid-15546620
If this hypothesis were correct, the sequestration of the DNA polymerase by DNAs other than the viral TP-DNA would be impeded, optimizing the usage of the DNA polymerase for viral replication.
[ "11" ]
192
9,879
0
false
If this hypothesis were correct, the sequestration of the DNA polymerase by DNAs other than the viral TP-DNA would be impeded, optimizing the usage of the DNA polymerase for viral replication.
[]
If this hypothesis were correct, the sequestration of the DNA polymerase by DNAs other than the viral TP-DNA would be impeded, optimizing the usage of the DNA polymerase for viral replication.
true
true
true
true
true
1,577
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
The high degree of both sequence identity and similarity (54% and 67.5%, respectively) shared by GA-1 and φ29 DNA polymerases makes difficult to find out structural differences between the modelled GA-1 DNA polymerase structure and the crystallized φ29 DNA polymerase that could be responsible for the substrate specific...
[ "11", "14" ]
338
9,880
0
false
The high degree of both sequence identity and similarity (54% and 67.5%, respectively) shared by GA-1 and φ29 DNA polymerases makes difficult to find out structural differences between the modelled GA-1 DNA polymerase structure and the crystallized φ29 DNA polymerase that could be responsible for the substrate specific...
[]
The high degree of both sequence identity and similarity (54% and 67.5%, respectively) shared by GA-1 and φ29 DNA polymerases makes difficult to find out structural differences between the modelled GA-1 DNA polymerase structure and the crystallized φ29 DNA polymerase that could be responsible for the substrate specific...
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
The major difference is found at the β-turn-β structure of the TPR1 insertion.
[ "11", "14" ]
78
9,881
0
false
The major difference is found at the β-turn-β structure of the TPR1 insertion.
[]
The major difference is found at the β-turn-β structure of the TPR1 insertion.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
Homology modelled φ29 DNA polymerase/DNA complex allows to predict a direct contact between the loop formed by the TPR1 β-turn-β and the DNA substrate through its major groove (11) (see also Figure 8B).
[ "11", "14" ]
202
9,882
1
false
Homology modelled φ29 DNA polymerase/DNA complex allows to predict a direct contact between the loop formed by the TPR1 β-turn-β and the DNA substrate through its major groove (see also Figure 8B).
[ "11" ]
Homology modelled φ29 DNA polymerase/DNA complex allows to predict a direct contact between the loop formed by the TPR1 β-turn-β and the DNA substrate through its major groove (see also Figure 8B).
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
Overlapping of GA-1 and φ29 DNA polymerase structures shows differences in this region of the enzyme because of one position displacement of the GA-1 sequence Arg309–Phe310 with respect to the corresponding one in φ29 DNA polymerase (see Figure 8B).
[ "11", "14" ]
249
9,883
0
false
Overlapping of GA-1 and φ29 DNA polymerase structures shows differences in this region of the enzyme because of one position displacement of the GA-1 sequence Arg309–Phe310 with respect to the corresponding one in φ29 DNA polymerase (see Figure 8B).
[]
Overlapping of GA-1 and φ29 DNA polymerase structures shows differences in this region of the enzyme because of one position displacement of the GA-1 sequence Arg309–Phe310 with respect to the corresponding one in φ29 DNA polymerase (see Figure 8B).
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
This could imply that the large side chains of these two residues in GA-1 DNA polymerase were facing towards the deepest part of the DNA major groove sterically hindering an initial DNA binding, in contrast to the outer orientation showed by the corresponding residues of φ29 DNA polymerase.
[ "11", "14" ]
291
9,884
0
false
This could imply that the large side chains of these two residues in GA-1 DNA polymerase were facing towards the deepest part of the DNA major groove sterically hindering an initial DNA binding, in contrast to the outer orientation showed by the corresponding residues of φ29 DNA polymerase.
[]
This could imply that the large side chains of these two residues in GA-1 DNA polymerase were facing towards the deepest part of the DNA major groove sterically hindering an initial DNA binding, in contrast to the outer orientation showed by the corresponding residues of φ29 DNA polymerase.
true
true
true
true
true
1,578
10
DISCUSSION
1
14
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
Structural comparison of φ29 apo polymerase and DNA polymerase/TP heterodimer structures shows that significant differences in the DNA polymerase structure occur only in the loop between residues 304 and 314 in the TPR1 subdomain (14).
[ "11", "14" ]
235
9,885
1
false
Structural comparison of φ29 apo polymerase and DNA polymerase/TP heterodimer structures shows that significant differences in the DNA polymerase structure occur only in the loop between residues 304 and 314 in the TPR1 subdomain.
[ "14" ]
Structural comparison of φ29 apo polymerase and DNA polymerase/TP heterodimer structures shows that significant differences in the DNA polymerase structure occur only in the loop between residues 304 and 314 in the TPR1 subdomain.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
This region has to curve out to allow TP access to the active site of the polymerase, the TP priming domain occupying the DNA binding cleft.
[ "11", "14" ]
140
9,886
0
false
This region has to curve out to allow TP access to the active site of the polymerase, the TP priming domain occupying the DNA binding cleft.
[]
This region has to curve out to allow TP access to the active site of the polymerase, the TP priming domain occupying the DNA binding cleft.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
Similar conformational changes are predicted to occur in GA-1 DNA polymerase TPR1 loop.
[ "11", "14" ]
87
9,887
0
false
Similar conformational changes are predicted to occur in GA-1 DNA polymerase TPR1 loop.
[]
Similar conformational changes are predicted to occur in GA-1 DNA polymerase TPR1 loop.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
As the TP priming domain is elongated, the growing DNA must displace it.
[ "11", "14" ]
72
9,888
0
false
As the TP priming domain is elongated, the growing DNA must displace it.
[]
As the TP priming domain is elongated, the growing DNA must displace it.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
After the incorporation of ∼6 nt, total dissociation of the heterodimer will take place and the TPR1 loop will adopt the orientation showed in the apoenzyme, fitting into the DNA major groove to confer binding stability.
[ "11", "14" ]
220
9,889
0
false
After the incorporation of ∼6 nt, total dissociation of the heterodimer will take place and the TPR1 loop will adopt the orientation showed in the apoenzyme, fitting into the DNA major groove to confer binding stability.
[]
After the incorporation of ∼6 nt, total dissociation of the heterodimer will take place and the TPR1 loop will adopt the orientation showed in the apoenzyme, fitting into the DNA major groove to confer binding stability.
true
true
true
true
true
1,578
10
DISCUSSION
1
11
[ "b11", "b14" ]
17,071,961
pmid-15546620|pmid-16511564
The main binding difference is that in this latter case, the DNA would be already placed into the polymerase active site before the TPR1 loop adopts its final straight conformation.
[ "11", "14" ]
181
9,890
0
false
The main binding difference is that in this latter case, the DNA would be already placed into the polymerase active site before the TPR1 loop adopts its final straight conformation.
[]
The main binding difference is that in this latter case, the DNA would be already placed into the polymerase active site before the TPR1 loop adopts its final straight conformation.
true
true
true
true
true
1,578
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
Various mechanisms of human chromosome replication are still unclear, including whether the molecular structure and biological function of genes are correlated with replication timing on chromosomes.
[ "1", "2", "3", "4", "5", "6" ]
199
9,891
0
false
Various mechanisms of human chromosome replication are still unclear, including whether the molecular structure and biological function of genes are correlated with replication timing on chromosomes.
[]
Various mechanisms of human chromosome replication are still unclear, including whether the molecular structure and biological function of genes are correlated with replication timing on chromosomes.
true
true
true
true
true
1,579
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
A better understanding of the replication process of human chromosomes may be achieved by obtaining a detailed knowledge of their time of replication, and many recent studies have addressed replication timing of human genome based on such a strategy (1,2).
[ "1", "2", "3", "4", "5", "6" ]
256
9,892
0
false
A better understanding of the replication process of human chromosomes may be achieved by obtaining a detailed knowledge of their time of replication, and many recent studies have addressed replication timing of human genome based on such a strategy.
[ "1,2" ]
A better understanding of the replication process of human chromosomes may be achieved by obtaining a detailed knowledge of their time of replication, and many recent studies have addressed replication timing of human genome based on such a strategy.
true
true
true
true
true
1,579
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
Recently, DNA tiling microarrays have been used to assay patterns of DNA replication at different stages of S phase on human chromosomes 21 and 22 (3).
[ "1", "2", "3", "4", "5", "6" ]
151
9,893
1
false
Recently, DNA tiling microarrays have been used to assay patterns of DNA replication at different stages of S phase on human chromosomes 21 and 22.
[ "3" ]
Recently, DNA tiling microarrays have been used to assay patterns of DNA replication at different stages of S phase on human chromosomes 21 and 22.
true
true
true
true
true
1,579
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
However, statistical analysis on tiling array data introduces new challenges beyond the standard analysis approaches to the widely used RNA expression profiling microarrays due to noisy and heterogeneous errors in tiling array probes compared to gene expression arrays.
[ "1", "2", "3", "4", "5", "6" ]
269
9,894
0
false
However, statistical analysis on tiling array data introduces new challenges beyond the standard analysis approaches to the widely used RNA expression profiling microarrays due to noisy and heterogeneous errors in tiling array probes compared to gene expression arrays.
[]
However, statistical analysis on tiling array data introduces new challenges beyond the standard analysis approaches to the widely used RNA expression profiling microarrays due to noisy and heterogeneous errors in tiling array probes compared to gene expression arrays.
true
true
true
true
true
1,579
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
This is likely due to the minimal probe selection process, which results in a wide range of probe sensitivities and specificities on the arrays.
[ "1", "2", "3", "4", "5", "6" ]
144
9,895
0
false
This is likely due to the minimal probe selection process, which results in a wide range of probe sensitivities and specificities on the arrays.
[]
This is likely due to the minimal probe selection process, which results in a wide range of probe sensitivities and specificities on the arrays.
true
true
true
true
true
1,579
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
Furthermore, experiments that use tiling arrays are typically performed with a limited number of replicates—three in the above-mentioned replication study.
[ "1", "2", "3", "4", "5", "6" ]
155
9,896
0
false
Furthermore, experiments that use tiling arrays are typically performed with a limited number of replicates—three in the above-mentioned replication study.
[]
Furthermore, experiments that use tiling arrays are typically performed with a limited number of replicates—three in the above-mentioned replication study.
true
true
true
true
true
1,579
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
Consequently, many classical statistical methods that rely on a relatively large sample size and homogeneous variance for their maximal performance are severely underpowered and biased when applied to this kind of data.
[ "1", "2", "3", "4", "5", "6" ]
219
9,897
0
false
Consequently, many classical statistical methods that rely on a relatively large sample size and homogeneous variance for their maximal performance are severely underpowered and biased when applied to this kind of data.
[]
Consequently, many classical statistical methods that rely on a relatively large sample size and homogeneous variance for their maximal performance are severely underpowered and biased when applied to this kind of data.
true
true
true
true
true
1,579
0
INTRODUCTION
1
4
[ "B1", "B2", "B3", "B4", "B5", "B6" ]
17,430,969
pmid-15611667|pmid-15591350|pmid-15845769|NA|pmid-14993201|pmid-16046496|pmid-14555628
Indeed, recent studies introduced several approaches to tiling data analysis, including hidden Markov models (4), G-TRANS (5) and empirical Bayes model (TileMap) (6); however, their statistical inference is based on individual error estimates that may not be accurate for an extremely large number of tiling array probes...
[ "1", "2", "3", "4", "5", "6" ]
355
9,898
1
false
Indeed, recent studies introduced several approaches to tiling data analysis, including hidden Markov models, G-TRANS and empirical Bayes model (TileMap) ; however, their statistical inference is based on individual error estimates that may not be accurate for an extremely large number of tiling array probes with a sma...
[ "4", "5", "6" ]
Indeed, recent studies introduced several approaches to tiling data analysis, including hidden Markov models, G-TRANS and empirical Bayes model (TileMap) ; however, their statistical inference is based on individual error estimates that may not be accurate for an extremely large number of tiling array probes with a sma...
true
true
true
true
true
1,579
1
INTRODUCTION
1
3
[ "B3", "B7" ]
17,430,969
pmid-15845769|pmid-14555628|pmid-15611667|pmid-15591350
Based on a non-parametric test on sliding windows of tiling array probes, Jeon et al.
[ "3", "7" ]
85
9,899
0
false
Based on a non-parametric test on sliding windows of tiling array probes, Jeon et al.
[]
Based on a non-parametric test on sliding windows of tiling array probes, Jeon et al.
true
true
true
true
true
1,580