Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
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INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6", "B7", "B8", "B9", "B6" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Degradation of TDG is critical for S-phase progression and cell proliferation, implicating that this UDG interferes negatively with vital processes of DNA replication.
[ "1", "2", "3–6", "7", "8", "9", "6" ]
167
9,700
0
false
Degradation of TDG is critical for S-phase progression and cell proliferation, implicating that this UDG interferes negatively with vital processes of DNA replication.
[]
Degradation of TDG is critical for S-phase progression and cell proliferation, implicating that this UDG interferes negatively with vital processes of DNA replication.
true
true
true
true
true
1,542
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6", "B7", "B8", "B9", "B6" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Strikingly, TDG levels decline just when UNG2 expression comes up and vice versa, suggesting that uracil repair is handled by distinct pathways throughout the cell cycle that are coordinated by the ubiquitin–proteasome system.
[ "1", "2", "3–6", "7", "8", "9", "6" ]
226
9,701
0
false
Strikingly, TDG levels decline just when UNG2 expression comes up and vice versa, suggesting that uracil repair is handled by distinct pathways throughout the cell cycle that are coordinated by the ubiquitin–proteasome system.
[]
Strikingly, TDG levels decline just when UNG2 expression comes up and vice versa, suggesting that uracil repair is handled by distinct pathways throughout the cell cycle that are coordinated by the ubiquitin–proteasome system.
true
true
true
true
true
1,542
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Our data establish that two prominent members of the UDG family, TDG and UNG2, underlie strict anticyclic cell cycle regulation.
[ "9", "9" ]
128
9,702
0
false
Our data establish that two prominent members of the UDG family, TDG and UNG2, underlie strict anticyclic cell cycle regulation.
[]
Our data establish that two prominent members of the UDG family, TDG and UNG2, underlie strict anticyclic cell cycle regulation.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
While TDG is highly expressed throughout the G2-M and G1 phases its levels rapidly decline at the G1–S transition just when UNG2 starts to rise above background.
[ "9", "9" ]
161
9,703
0
false
While TDG is highly expressed throughout the G2-M and G1 phases its levels rapidly decline at the G1–S transition just when UNG2 starts to rise above background.
[]
While TDG is highly expressed throughout the G2-M and G1 phases its levels rapidly decline at the G1–S transition just when UNG2 starts to rise above background.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
The UNG2 protein then peaks at the beginning of S-phase and gradually declines towards termination of DNA replication (see also reference 9), when TDG expression resumes.
[ "9", "9" ]
170
9,704
0
false
The UNG2 protein then peaks at the beginning of S-phase and gradually declines towards termination of DNA replication, when TDG expression resumes.
[ "see also reference 9" ]
The UNG2 protein then peaks at the beginning of S-phase and gradually declines towards termination of DNA replication, when TDG expression resumes.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
This implicates that the two biochemically redundant UDGs control non-redundant, cell cycle stage-specific pathways for uracil repair; while UNG2 is active during DNA replication, TDG functions in non-replicating DNA, notably, when U arises mainly through deamination of cytosine.
[ "9", "9" ]
280
9,705
0
false
This implicates that the two biochemically redundant UDGs control non-redundant, cell cycle stage-specific pathways for uracil repair; while UNG2 is active during DNA replication, TDG functions in non-replicating DNA, notably, when U arises mainly through deamination of cytosine.
[]
This implicates that the two biochemically redundant UDGs control non-redundant, cell cycle stage-specific pathways for uracil repair; while UNG2 is active during DNA replication, TDG functions in non-replicating DNA, notably, when U arises mainly through deamination of cytosine.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Strikingly, although the pattern of cell cycle regulation of the two UDGs is diametrically opposed, the underlying mechanism appears to be the same.
[ "9", "9" ]
148
9,706
0
false
Strikingly, although the pattern of cell cycle regulation of the two UDGs is diametrically opposed, the underlying mechanism appears to be the same.
[]
Strikingly, although the pattern of cell cycle regulation of the two UDGs is diametrically opposed, the underlying mechanism appears to be the same.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
As shown here for TDG and reported previously for UNG2 (9), both are subject to cell cycle controlled ubiquitylation and proteasome degradation.
[ "9", "9" ]
144
9,707
1
false
As shown here for TDG and reported previously for UNG2, both are subject to cell cycle controlled ubiquitylation and proteasome degradation.
[ "9" ]
As shown here for TDG and reported previously for UNG2, both are subject to cell cycle controlled ubiquitylation and proteasome degradation.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Thus, the ubiquitin–proteasome system appears to be at the heart of the coordination of redundant BER pathways, which would be an as yet unrecognized function.
[ "9", "9" ]
159
9,708
0
false
Thus, the ubiquitin–proteasome system appears to be at the heart of the coordination of redundant BER pathways, which would be an as yet unrecognized function.
[]
Thus, the ubiquitin–proteasome system appears to be at the heart of the coordination of redundant BER pathways, which would be an as yet unrecognized function.
true
true
true
true
true
1,543
0
DISCUSSION
1
9
[ "B9", "B9" ]
17,526,518
pmid-12483510|pmid-15568983|pmid-7819187|pmid-10074426|pmid-10499592|pmid-11554300|pmid-9016624|pmid-10393198|pmid-15084312|pmid-11554300|pmid-15084312|pmid-15084312
Whether this interesting concept of coordination is a feature restricted to TDG and UNG2 only, or whether it applies more generally to DNA repair remains to be resolved.
[ "9", "9" ]
169
9,709
0
false
Whether this interesting concept of coordination is a feature restricted to TDG and UNG2 only, or whether it applies more generally to DNA repair remains to be resolved.
[]
Whether this interesting concept of coordination is a feature restricted to TDG and UNG2 only, or whether it applies more generally to DNA repair remains to be resolved.
true
true
true
true
true
1,543
1
DISCUSSION
0
null
null
17,526,518
null
We wanted to get some insight into why TDG needs to be eliminated before S-phase from ectopically expressing the glycosylase to levels saturating its degradation.
null
162
9,710
0
false
null
null
We wanted to get some insight into why TDG needs to be eliminated before S-phase from ectopically expressing the glycosylase to levels saturating its degradation.
true
true
true
true
true
1,544
1
DISCUSSION
0
null
null
17,526,518
null
TDG expression at >30-fold the endogenous level could readily be obtained by transient transfection, and such amounts were indeed saturating in the sense that low amounts of the protein remained detectable in S-phase arrested cell populations.
null
243
9,711
0
false
null
null
TDG expression at >30-fold the endogenous level could readily be obtained by transient transfection, and such amounts were indeed saturating in the sense that low amounts of the protein remained detectable in S-phase arrested cell populations.
true
true
true
true
true
1,544
1
DISCUSSION
0
null
null
17,526,518
null
Yet, attempts to maintain high expression in culture failed; upon selection of stable clones, TDG expression declined to levels <5-fold that were compatible with complete degradation of the protein in S-phase.
null
209
9,712
0
false
null
null
Yet, attempts to maintain high expression in culture failed; upon selection of stable clones, TDG expression declined to levels <5-fold that were compatible with complete degradation of the protein in S-phase.
true
true
true
true
true
1,544
1
DISCUSSION
0
null
null
17,526,518
null
Thus, the presence of TDG in S-phase seems incompatible with cell cycle progression and proliferation, and this is in line with the observation that 293T cells transiently expressing high levels of wild-type TDG accumulate in S-phase.
null
234
9,713
0
false
null
null
Thus, the presence of TDG in S-phase seems incompatible with cell cycle progression and proliferation, and this is in line with the observation that 293T cells transiently expressing high levels of wild-type TDG accumulate in S-phase.
true
true
true
true
true
1,544
2
DISCUSSION
1
1
[ "B1", "B19", "B10", "B20", "B1", "B8", "B21", "B22" ]
17,526,518
pmid-12483510|pmid-12711670|pmid-11889051|pmid-9867812|pmid-12483510|pmid-10393198|pmid-15479784|pmid-10912000
Interference with S-phase progression might occur at the level of U excision (1).
[ "1", "19", "10", "20", "1", "8", "21", "22" ]
81
9,714
1
false
Interference with S-phase progression might occur at the level of U excision.
[ "1" ]
Interference with S-phase progression might occur at the level of U excision.
true
true
true
true
true
1,545
2
DISCUSSION
1
1
[ "B1", "B19", "B10", "B20", "B1", "B8", "B21", "B22" ]
17,526,518
pmid-12483510|pmid-12711670|pmid-11889051|pmid-9867812|pmid-12483510|pmid-10393198|pmid-15479784|pmid-10912000
If misincorporated, U must be eliminated from newly synthesized DNA in a way that is coordinated with the replication process.
[ "1", "19", "10", "20", "1", "8", "21", "22" ]
126
9,715
0
false
If misincorporated, U must be eliminated from newly synthesized DNA in a way that is coordinated with the replication process.
[]
If misincorporated, U must be eliminated from newly synthesized DNA in a way that is coordinated with the replication process.
true
true
true
true
true
1,545
2
DISCUSSION
1
19
[ "B1", "B19", "B10", "B20", "B1", "B8", "B21", "B22" ]
17,526,518
pmid-12483510|pmid-12711670|pmid-11889051|pmid-9867812|pmid-12483510|pmid-10393198|pmid-15479784|pmid-10912000
Given its enzymatic properties, TDG would be totally unsuited for this task; by processing A•U only inefficiently (19) and binding to AP sites with high affinity (10,20), it would perturb the replication process.
[ "1", "19", "10", "20", "1", "8", "21", "22" ]
212
9,716
1
false
Given its enzymatic properties, TDG would be totally unsuited for this task; by processing A•U only inefficiently and binding to AP sites with high affinity, it would perturb the replication process.
[ "19", "10,20" ]
Given its enzymatic properties, TDG would be totally unsuited for this task; by processing A•U only inefficiently and binding to AP sites with high affinity, it would perturb the replication process.
true
true
true
true
true
1,545
2
DISCUSSION
1
1
[ "B1", "B19", "B10", "B20", "B1", "B8", "B21", "B22" ]
17,526,518
pmid-12483510|pmid-12711670|pmid-11889051|pmid-9867812|pmid-12483510|pmid-10393198|pmid-15479784|pmid-10912000
By contrast, UNG2 would be the glycosylase of choice here; it processes U•A with a comparably high rate, and it associates with replication factors at the replication fork.
[ "1", "19", "10", "20", "1", "8", "21", "22" ]
172
9,717
0
false
By contrast, UNG2 would be the glycosylase of choice here; it processes U•A with a comparably high rate, and it associates with replication factors at the replication fork.
[]
By contrast, UNG2 would be the glycosylase of choice here; it processes U•A with a comparably high rate, and it associates with replication factors at the replication fork.
true
true
true
true
true
1,545
2
DISCUSSION
1
1
[ "B1", "B19", "B10", "B20", "B1", "B8", "B21", "B22" ]
17,526,518
pmid-12483510|pmid-12711670|pmid-11889051|pmid-9867812|pmid-12483510|pmid-10393198|pmid-15479784|pmid-10912000
Consistently, UNG was shown to keep genomic uracil levels low (1,8,21,22).
[ "1", "19", "10", "20", "1", "8", "21", "22" ]
74
9,718
0
false
Consistently, UNG was shown to keep genomic uracil levels low.
[ "1,8,21,22" ]
Consistently, UNG was shown to keep genomic uracil levels low.
true
true
true
true
true
1,545
3
DISCUSSION
1
19
[ "B19", "B12", "B20", "B10", "B23" ]
17,526,518
pmid-12711670|pmid-10938281|pmid-9867812|pmid-11889051|pmid-15823533
Considering the rather broad substrate spectrum of TDG (19), however, its presence in S-phase might cause other forms of interference.
[ "19", "12", "20", "10", "23" ]
134
9,719
1
false
Considering the rather broad substrate spectrum of TDG, however, its presence in S-phase might cause other forms of interference.
[ "19" ]
Considering the rather broad substrate spectrum of TDG, however, its presence in S-phase might cause other forms of interference.
true
true
true
true
true
1,546
3
DISCUSSION
1
19
[ "B19", "B12", "B20", "B10", "B23" ]
17,526,518
pmid-12711670|pmid-10938281|pmid-9867812|pmid-11889051|pmid-15823533
TDG could induce the formation of DNA double-strand breaks either directly, if it removed substrate bases close to each other in opposite DNA strands, or indirectly, through the generation of replication blocking lesions such as AP sites or single-strand breaks.
[ "19", "12", "20", "10", "23" ]
262
9,720
0
false
TDG could induce the formation of DNA double-strand breaks either directly, if it removed substrate bases close to each other in opposite DNA strands, or indirectly, through the generation of replication blocking lesions such as AP sites or single-strand breaks.
[]
TDG could induce the formation of DNA double-strand breaks either directly, if it removed substrate bases close to each other in opposite DNA strands, or indirectly, through the generation of replication blocking lesions such as AP sites or single-strand breaks.
true
true
true
true
true
1,546
3
DISCUSSION
1
19
[ "B19", "B12", "B20", "B10", "B23" ]
17,526,518
pmid-12711670|pmid-10938281|pmid-9867812|pmid-11889051|pmid-15823533
The latter would be aided by the inability of TDG to dissociate freely from AP sites (12,20).
[ "19", "12", "20", "10", "23" ]
93
9,721
0
false
The latter would be aided by the inability of TDG to dissociate freely from AP sites.
[ "12,20" ]
The latter would be aided by the inability of TDG to dissociate freely from AP sites.
true
true
true
true
true
1,546
3
DISCUSSION
1
19
[ "B19", "B12", "B20", "B10", "B23" ]
17,526,518
pmid-12711670|pmid-10938281|pmid-9867812|pmid-11889051|pmid-15823533
In vitro, AP-site release is facilitated by a SUMOylation-induced conformational change in TDG, a rate-limiting step that appears useful for a temporary protection of the labile intermediate in the repair process (10,23).
[ "19", "12", "20", "10", "23" ]
221
9,722
0
false
In vitro, AP-site release is facilitated by a SUMOylation-induced conformational change in TDG, a rate-limiting step that appears useful for a temporary protection of the labile intermediate in the repair process.
[ "10,23" ]
In vitro, AP-site release is facilitated by a SUMOylation-induced conformational change in TDG, a rate-limiting step that appears useful for a temporary protection of the labile intermediate in the repair process.
true
true
true
true
true
1,546
3
DISCUSSION
1
19
[ "B19", "B12", "B20", "B10", "B23" ]
17,526,518
pmid-12711670|pmid-10938281|pmid-9867812|pmid-11889051|pmid-15823533
The protective nature of this dissociation delay, however, may turn into a disadvantage in the context of DNA replication; it might generate situations where TDG is bound to AP sites in front of an approaching replication fork where it acts as a road block, causing fork stalling and eventually collapse.
[ "19", "12", "20", "10", "23" ]
304
9,723
0
false
The protective nature of this dissociation delay, however, may turn into a disadvantage in the context of DNA replication; it might generate situations where TDG is bound to AP sites in front of an approaching replication fork where it acts as a road block, causing fork stalling and eventually collapse.
[]
The protective nature of this dissociation delay, however, may turn into a disadvantage in the context of DNA replication; it might generate situations where TDG is bound to AP sites in front of an approaching replication fork where it acts as a road block, causing fork stalling and eventually collapse.
true
true
true
true
true
1,546
4
DISCUSSION
0
null
null
17,526,518
null
A special case of mutagenic interference during S-phase may relate to TDG's ability to remove T from G•T mismatches.
null
116
9,724
0
false
null
null
A special case of mutagenic interference during S-phase may relate to TDG's ability to remove T from G•T mismatches.
true
true
true
true
true
1,547
4
DISCUSSION
0
null
null
17,526,518
null
While this feature provides an excellent means to counter mutagenesis by deamination of 5-meC, it may represent a disadvantage during DNA replication, where G•T mispairs arise predominantly by DNA polymerase errors.
null
215
9,725
0
false
null
null
While this feature provides an excellent means to counter mutagenesis by deamination of 5-meC, it may represent a disadvantage during DNA replication, where G•T mispairs arise predominantly by DNA polymerase errors.
true
true
true
true
true
1,547
4
DISCUSSION
0
null
null
17,526,518
null
The inability of TDG to discriminate between parental and newly synthesized DNA strands would fix C to T transition mutations in cases where the T is in the parental strand.
null
173
9,726
0
false
null
null
The inability of TDG to discriminate between parental and newly synthesized DNA strands would fix C to T transition mutations in cases where the T is in the parental strand.
true
true
true
true
true
1,547
4
DISCUSSION
0
null
null
17,526,518
null
In addition, TDG induced postreplicative G•T repair in the parental DNA strand, particularly in the parental lagging strand, could destabilize the replication fork and thereby impede the replication process.
null
207
9,727
0
false
null
null
In addition, TDG induced postreplicative G•T repair in the parental DNA strand, particularly in the parental lagging strand, could destabilize the replication fork and thereby impede the replication process.
true
true
true
true
true
1,547
4
DISCUSSION
0
null
null
17,526,518
null
Thus, G•T correction during DNA synthesis should be left to the postreplicative mismatch repair system, which is designed to correct the error in the newly synthesized DNA strand.
null
179
9,728
0
false
null
null
Thus, G•T correction during DNA synthesis should be left to the postreplicative mismatch repair system, which is designed to correct the error in the newly synthesized DNA strand.
true
true
true
true
true
1,547
0
INTRODUCTION
1
1
[ "B1", "B2", "B3 B4 B5 B6 B7 B8 B9 B10", "B11 B12 B13 B14 B15", "B3", "B5", "B16" ]
17,660,189
NA|pmid-15053630|NA|pmid-9888851|pmid-10028965|pmid-10698742|pmid-12785930|pmid-14525424|pmid-14746451|pmid-16585526|pmid-8751447|pmid-9426189|pmid-9072805|pmid-11456512|pmid-14624600|NA|pmid-10028965|NA
The knowledge of the distribution of excess electron sites for DNA single strands is attracting increasing attention.
[ "1", "2", "3–10", "11–15", "3", "5", "16" ]
117
9,729
0
false
The knowledge of the distribution of excess electron sites for DNA single strands is attracting increasing attention.
[]
The knowledge of the distribution of excess electron sites for DNA single strands is attracting increasing attention.
true
true
true
true
true
1,548
0
INTRODUCTION
1
3–10
[ "B1", "B2", "B3 B4 B5 B6 B7 B8 B9 B10", "B11 B12 B13 B14 B15", "B3", "B5", "B16" ]
17,660,189
NA|pmid-15053630|NA|pmid-9888851|pmid-10028965|pmid-10698742|pmid-12785930|pmid-14525424|pmid-14746451|pmid-16585526|pmid-8751447|pmid-9426189|pmid-9072805|pmid-11456512|pmid-14624600|NA|pmid-10028965|NA
The formation of anions in DNA fragments has been found to be related to important biochemical processes such as DNA damage and repair (3–10), charge transfer along DNA (11–15), and the initiation of reactions leading to mutation (3,5,16).
[ "1", "2", "3–10", "11–15", "3", "5", "16" ]
239
9,730
1
false
The formation of anions in DNA fragments has been found to be related to important biochemical processes such as DNA damage and repair, charge transfer along DNA, and the initiation of reactions leading to mutation.
[ "3–10", "11–15", "3,5,16" ]
The formation of anions in DNA fragments has been found to be related to important biochemical processes such as DNA damage and repair, charge transfer along DNA, and the initiation of reactions leading to mutation.
true
true
true
true
true
1,548
1
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
Experimentally based investigations suggest that the nucleobases have small electron affinities (EAs), ∼0.1 eV for thymine (T), cytosine (C) and uracil (U) (17).
[ "17", "18", "19", "20–22", "23", "1" ]
161
9,731
1
false
Experimentally based investigations suggest that the nucleobases have small electron affinities (EAs), ∼0.1 eV for thymine (T), cytosine (C) and uracil (U).
[ "17" ]
Experimentally based investigations suggest that the nucleobases have small electron affinities (EAs), ∼0.1 eV for thymine (T), cytosine (C) and uracil (U).
true
true
true
true
true
1,549
1
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
Negative EA values have been determined for adenine (A) and cytosine in gas-phase experiments (18,19).
[ "17", "18", "19", "20–22", "23", "1" ]
102
9,732
0
false
Negative EA values have been determined for adenine (A) and cytosine in gas-phase experiments.
[ "18,19" ]
Negative EA values have been determined for adenine (A) and cytosine in gas-phase experiments.
true
true
true
true
true
1,549
1
INTRODUCTION
1
20–22
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
The identification of the existence of two types of anions (dipole bound and covalent) (20–22) partly explains the differences among the different experimental EA values (23).
[ "17", "18", "19", "20–22", "23", "1" ]
175
9,733
1
false
The identification of the existence of two types of anions (dipole bound and covalent) partly explains the differences among the different experimental EA values.
[ "20–22", "23" ]
The identification of the existence of two types of anions (dipole bound and covalent) partly explains the differences among the different experimental EA values.
true
true
true
true
true
1,549
1
INTRODUCTION
1
1
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
Recent experiments on the electron-capturing efficiencies of short DNA oligomers provide the only estimate of the relative order of the vertical attachment energies (VAEs) for DNA single strands (1).
[ "17", "18", "19", "20–22", "23", "1" ]
199
9,734
1
false
Recent experiments on the electron-capturing efficiencies of short DNA oligomers provide the only estimate of the relative order of the vertical attachment energies (VAEs) for DNA single strands.
[ "1" ]
Recent experiments on the electron-capturing efficiencies of short DNA oligomers provide the only estimate of the relative order of the vertical attachment energies (VAEs) for DNA single strands.
true
true
true
true
true
1,549
1
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
However, the direct experimental determination of the EAs of nucleosides and nucleotides has proven difficult.
[ "17", "18", "19", "20–22", "23", "1" ]
110
9,735
0
false
However, the direct experimental determination of the EAs of nucleosides and nucleotides has proven difficult.
[]
However, the direct experimental determination of the EAs of nucleosides and nucleotides has proven difficult.
true
true
true
true
true
1,549
1
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B20 B21 B22", "B23", "B1" ]
17,660,189
NA|NA|NA|NA|NA|NA|NA|NA
Large DNA fragments, such as nucleotides, are non-volatile and the requirement for the vaporization of the species without thermal degradation makes it difficult to carry out reliable experimental studies in the gas phase.
[ "17", "18", "19", "20–22", "23", "1" ]
222
9,736
0
false
Large DNA fragments, such as nucleotides, are non-volatile and the requirement for the vaporization of the species without thermal degradation makes it difficult to carry out reliable experimental studies in the gas phase.
[]
Large DNA fragments, such as nucleotides, are non-volatile and the requirement for the vaporization of the species without thermal degradation makes it difficult to carry out reliable experimental studies in the gas phase.
true
true
true
true
true
1,549
2
INTRODUCTION
1
24
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
Theoretical investigations at various levels of sophistication have complemented the experimental studies.
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
106
9,737
0
false
Theoretical investigations at various levels of sophistication have complemented the experimental studies.
[]
Theoretical investigations at various levels of sophistication have complemented the experimental studies.
true
true
true
true
true
1,550
2
INTRODUCTION
1
26–28
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
While second-order Møller–Plesset perturbation theory (MP2) underestimates the adiabatic electron affinities (AEAs) for the five bases (24,25), density functional theory (DFT) approaches yield experimentally consistent AEA values for the individual bases (26–28).
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
263
9,738
1
false
While second-order Møller–Plesset perturbation theory underestimates the adiabatic electron affinities (AEAs) for the five bases, density functional theory (DFT) approaches yield experimentally consistent AEA values for the individual bases.
[ "MP2", "24,25", "26–28" ]
While second-order Møller–Plesset perturbation theory underestimates the adiabatic electron affinities (AEAs) for the five bases, density functional theory (DFT) approaches yield experimentally consistent AEA values for the individual bases.
true
true
true
true
true
1,550
2
INTRODUCTION
1
24
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
Theoretical studies of excess charge in DNA have been extended to the prediction of the EAs of subunits such as nucleosides and nucleotides.
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
140
9,739
0
false
Theoretical studies of excess charge in DNA have been extended to the prediction of the EAs of subunits such as nucleosides and nucleotides.
[]
Theoretical studies of excess charge in DNA have been extended to the prediction of the EAs of subunits such as nucleosides and nucleotides.
true
true
true
true
true
1,550
2
INTRODUCTION
1
24
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
Semi-empirical methods have been applied to evaluate the EAs of nucleosides and nucleotides.
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
92
9,740
0
false
Semi-empirical methods have been applied to evaluate the EAs of nucleosides and nucleotides.
[]
Semi-empirical methods have been applied to evaluate the EAs of nucleosides and nucleotides.
true
true
true
true
true
1,550
2
INTRODUCTION
1
31
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
With the reliably calibrated B3LYP/DZP++ approach (31), meaningful predictions of the EAs of the 2′-deoxyribonucleosides have been completed (2).
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
145
9,741
1
false
With the reliably calibrated B3LYP/DZP++ approach, meaningful predictions of the EAs of the 2′-deoxyribonucleosides have been completed.
[ "31", "2" ]
With the reliably calibrated B3LYP/DZP++ approach, meaningful predictions of the EAs of the 2′-deoxyribonucleosides have been completed.
true
true
true
true
true
1,550
2
INTRODUCTION
1
24
[ "B24", "B25", "B26 B27 B28", "B29", "B30", "B31", "B2", "B10", "B32 B33 B34 B35" ]
17,660,189
NA|NA|pmid-11457153|pmid-12862488|pmid-11890827|pmid-12537022|NA|pmid-11782134|pmid-15053630|pmid-16585526|pmid-16433542|pmid-16848454|pmid-16915601|pmid-15656644
Recently, the EAs of the pyrimidine nucleotides (3′-dCMP, 3′-dTMP, 5′-dCMP, 5′-dTMP) have also been predicted at the B3LYP/DZP++ level of theory (10,32–35).
[ "24", "25", "26–28", "29", "30", "31", "2", "10", "32–35" ]
156
9,742
0
false
Recently, the EAs of the pyrimidine nucleotides (3′-dCMP, 3′-dTMP, 5′-dCMP, 5′-dTMP) have also been predicted at the B3LYP/DZP++ level of theory.
[ "10,32–35" ]
Recently, the EAs of the pyrimidine nucleotides (3′-dCMP, 3′-dTMP, 5′-dCMP, 5′-dTMP) have also been predicted at the B3LYP/DZP++ level of theory.
true
true
true
true
true
1,550
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
To understand the effects of excess electrons on single-strand DNA, the backbone of DNA should be realistically simulated in the model study.
[ "10", "32", "33", "1", "2", "26" ]
141
9,743
0
false
To understand the effects of excess electrons on single-strand DNA, the backbone of DNA should be realistically simulated in the model study.
[]
To understand the effects of excess electrons on single-strand DNA, the backbone of DNA should be realistically simulated in the model study.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Previous studies reveal that the phosphate group at either the 3′ or 5′ position increases the electron acquisition ability of the pyrimidines (10,32,33).
[ "10", "32", "33", "1", "2", "26" ]
154
9,744
0
false
Previous studies reveal that the phosphate group at either the 3′ or 5′ position increases the electron acquisition ability of the pyrimidines.
[ "10,32,33" ]
Previous studies reveal that the phosphate group at either the 3′ or 5′ position increases the electron acquisition ability of the pyrimidines.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Thus, properly modeled systems representing single-strand DNA should include the phosphate group at both the 3′ and 5′ positions of the nucleotides.
[ "10", "32", "33", "1", "2", "26" ]
148
9,745
0
false
Thus, properly modeled systems representing single-strand DNA should include the phosphate group at both the 3′ and 5′ positions of the nucleotides.
[]
Thus, properly modeled systems representing single-strand DNA should include the phosphate group at both the 3′ and 5′ positions of the nucleotides.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Moreover, the knowledge of the distribution of the excess electron sites and the availability of reliable EAs for the purine nucleotides are of equal importance.
[ "10", "32", "33", "1", "2", "26" ]
161
9,746
0
false
Moreover, the knowledge of the distribution of the excess electron sites and the availability of reliable EAs for the purine nucleotides are of equal importance.
[]
Moreover, the knowledge of the distribution of the excess electron sites and the availability of reliable EAs for the purine nucleotides are of equal importance.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
The vertical attachment of electrons to guanine-rich DNA single strands appears to predominate over entrapment by the cytosine-rich strands, as reported in the important 2005 experiment by Ray et al.
[ "10", "32", "33", "1", "2", "26" ]
199
9,747
0
false
The vertical attachment of electrons to guanine-rich DNA single strands appears to predominate over entrapment by the cytosine-rich strands, as reported in the important 2005 experiment by Ray et al.
[]
The vertical attachment of electrons to guanine-rich DNA single strands appears to predominate over entrapment by the cytosine-rich strands, as reported in the important 2005 experiment by Ray et al.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Although previous studies of the pyrimidine nucleosides and nucleotides suggest that the excess electron is mainly located on the bases in the electron-attached radical anions, the small AEA values and the large dipole moments of the purine bases (2,26) suggest that the situation for the purine nucleotides might be dif...
[ "10", "32", "33", "1", "2", "26" ]
327
9,748
0
false
Although previous studies of the pyrimidine nucleosides and nucleotides suggest that the excess electron is mainly located on the bases in the electron-attached radical anions, the small AEA values and the large dipole moments of the purine bases suggest that the situation for the purine nucleotides might be different.
[ "2,26" ]
Although previous studies of the pyrimidine nucleosides and nucleotides suggest that the excess electron is mainly located on the bases in the electron-attached radical anions, the small AEA values and the large dipole moments of the purine bases suggest that the situation for the purine nucleotides might be different.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Here, we report a theoretical investigation of electron attachment to reasonable models of DNA single strands.
[ "10", "32", "33", "1", "2", "26" ]
110
9,749
0
false
Here, we report a theoretical investigation of electron attachment to reasonable models of DNA single strands.
[]
Here, we report a theoretical investigation of electron attachment to reasonable models of DNA single strands.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
The 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP) systems in their protonated forms have been selected as models (see Scheme 1).
[ "10", "32", "33", "1", "2", "26" ]
283
9,750
0
false
The 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP) systems in their protonated forms have been selected as models.
[ "see Scheme 1" ]
The 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP) systems in their protonated forms have been selected as models.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
For a better description of the influence of the 3′–5′ phosphodiester linkage in DNA, the -OPO3H moiety at the 5′ position was terminated with a methyl group.
[ "10", "32", "33", "1", "2", "26" ]
158
9,751
0
false
For a better description of the influence of the 3′–5′ phosphodiester linkage in DNA, the -OPO3H moiety at the 5′ position was terminated with a methyl group.
[]
For a better description of the influence of the 3′–5′ phosphodiester linkage in DNA, the -OPO3H moiety at the 5′ position was terminated with a methyl group.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
These systems represent the most complete descriptions to date of the minimal DNA subunits and are expected to provide reliable information concerning electron attachment to single-strand DNA.
[ "10", "32", "33", "1", "2", "26" ]
192
9,752
0
false
These systems represent the most complete descriptions to date of the minimal DNA subunits and are expected to provide reliable information concerning electron attachment to single-strand DNA.
[]
These systems represent the most complete descriptions to date of the minimal DNA subunits and are expected to provide reliable information concerning electron attachment to single-strand DNA.
true
true
true
true
true
1,551
3
INTRODUCTION
1
10
[ "B10", "B32", "B33", "B1", "B2", "B26" ]
17,660,189
pmid-16585526|pmid-16433542|pmid-16848454|NA|pmid-15053630|pmid-11457153
Scheme 1.Models of the DNA single strands: 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP).
[ "10", "32", "33", "1", "2", "26" ]
244
9,753
0
false
Scheme 1.Models of the DNA single strands: 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP).
[]
Scheme 1.Models of the DNA single strands: 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP).
true
true
true
true
true
1,551
4
INTRODUCTION
0
null
null
17,660,189
null
Models of the DNA single strands: 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP).
null
235
9,754
0
false
null
null
Models of the DNA single strands: 2′-deoxyguanosine-3′,5′-diphosphate (3′,5′-dGDP), 2′-deoxyadenosine-3′,5′-diphosphate (3′,5′-dADP), 2′-deoxycytidine-3′,5′-diphosphate (3′,5′-dCDP) and 2′-deoxythymidine-3′,5′-diphosphate (3′,5′-dTDP).
true
true
true
true
true
1,552
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,090,600
pmid-15677316|pmid-10811210|NA
The tertiary structure prediction of a protein using amino acid sequence information alone is one of the fundamental unsolved problems in computational biology/molecular biophysics (1).
[ "1", "2", "3" ]
185
9,755
1
false
The tertiary structure prediction of a protein using amino acid sequence information alone is one of the fundamental unsolved problems in computational biology/molecular biophysics.
[ "1" ]
The tertiary structure prediction of a protein using amino acid sequence information alone is one of the fundamental unsolved problems in computational biology/molecular biophysics.
true
true
true
true
true
1,553
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,090,600
pmid-15677316|pmid-10811210|NA
The folding of protein molecules with a large number of degrees of freedom spontaneously into a unique three-dimensional (3-D) structure is of scientific interest intrinsically and due to its application in structure based drug design endeavors.
[ "1", "2", "3" ]
245
9,756
0
false
The folding of protein molecules with a large number of degrees of freedom spontaneously into a unique three-dimensional structure is of scientific interest intrinsically and due to its application in structure based drug design endeavors.
[ "3-D" ]
The folding of protein molecules with a large number of degrees of freedom spontaneously into a unique three-dimensional structure is of scientific interest intrinsically and due to its application in structure based drug design endeavors.
true
true
true
true
true
1,553
0
INTRODUCTION
1
2
[ "b1", "b2", "b3" ]
17,090,600
pmid-15677316|pmid-10811210|NA
The cost and time factors involved in experimental techniques urge for an early in silico solution to protein folding problem (2).
[ "1", "2", "3" ]
130
9,757
1
false
The cost and time factors involved in experimental techniques urge for an early in silico solution to protein folding problem.
[ "2" ]
The cost and time factors involved in experimental techniques urge for an early in silico solution to protein folding problem.
true
true
true
true
true
1,553
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,090,600
pmid-15677316|pmid-10811210|NA
The ultimate goal is to use computer algorithms to identify amino acid sequences that not only adopt particular 3-D structures but also perform specific functions i.e.
[ "1", "2", "3" ]
167
9,758
0
false
The ultimate goal is to use computer algorithms to identify amino acid sequences that not only adopt particular 3-D structures but also perform specific functions i.e.
[]
The ultimate goal is to use computer algorithms to identify amino acid sequences that not only adopt particular 3-D structures but also perform specific functions i.e.
true
true
true
true
true
1,553
0
INTRODUCTION
1
3
[ "b1", "b2", "b3" ]
17,090,600
pmid-15677316|pmid-10811210|NA
to propose designer proteins (3).
[ "1", "2", "3" ]
33
9,759
1
false
to propose designer proteins.
[ "3" ]
to propose designer proteins.
false
true
true
true
false
1,553
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
Contemporary approaches for protein structure prediction can be broadly classified under two categories viz.
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
108
9,760
0
false
Contemporary approaches for protein structure prediction can be broadly classified under two categories viz.
[]
Contemporary approaches for protein structure prediction can be broadly classified under two categories viz.
true
true
true
true
true
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
(i) comparative modeling, which includes homology modeling and threading (4–7) and (ii) de novo folding (8–12).
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
111
9,761
0
false
(i) comparative modeling, which includes homology modeling and threading and (ii) de novo folding.
[ "4–7", "8–12" ]
(i) comparative modeling, which includes homology modeling and threading and (ii) de novo folding.
false
false
true
true
false
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
The first category of methods utilizes the structures of already solved proteins as templates (either locally or globally, at the sequence level or at the sub-structure level).
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
176
9,762
0
false
The first category of methods utilizes the structures of already solved proteins as templates (either locally or globally, at the sequence level or at the sub-structure level).
[]
The first category of methods utilizes the structures of already solved proteins as templates (either locally or globally, at the sequence level or at the sub-structure level).
true
true
true
true
true
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
With large amounts of genome and proteome data accumulating via sequencing projects, comparative modeling has become the method of choice to characterize sequences where related representatives of a family exist in structural databases (13–18).
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
244
9,763
0
false
With large amounts of genome and proteome data accumulating via sequencing projects, comparative modeling has become the method of choice to characterize sequences where related representatives of a family exist in structural databases.
[ "13–18" ]
With large amounts of genome and proteome data accumulating via sequencing projects, comparative modeling has become the method of choice to characterize sequences where related representatives of a family exist in structural databases.
true
true
true
true
true
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
There are several web servers based on comparative modeling approaches such as Swiss Model (4), CPHmodels (19), FAMS (20) and ModWeb (21).
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
138
9,764
1
false
There are several web servers based on comparative modeling approaches such as Swiss Model, CPHmodels, FAMS and ModWeb.
[ "4", "19", "20", "21" ]
There are several web servers based on comparative modeling approaches such as Swiss Model, CPHmodels, FAMS and ModWeb.
true
true
true
true
true
1,554
1
INTRODUCTION
1
22
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
The assessors for comparative modeling at CASP6 (Critical Assessment of protein Structure Prediction methods) have noted small improvements in model quality despite increase in the available structures but marginal improvement in alignment accuracy when compared to CASP5 (22).
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
277
9,765
1
false
The assessors for comparative modeling at CASP6 (Critical Assessment of protein Structure Prediction methods) have noted small improvements in model quality despite increase in the available structures but marginal improvement in alignment accuracy when compared to CASP5.
[ "22" ]
The assessors for comparative modeling at CASP6 (Critical Assessment of protein Structure Prediction methods) have noted small improvements in model quality despite increase in the available structures but marginal improvement in alignment accuracy when compared to CASP5.
true
true
true
true
true
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
A natural limit for these approaches is the quantity of information available in the structural databases.
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
106
9,766
0
false
A natural limit for these approaches is the quantity of information available in the structural databases.
[]
A natural limit for these approaches is the quantity of information available in the structural databases.
true
true
true
true
true
1,554
1
INTRODUCTION
1
4
[ "b4", "b7", "b8", "b12", "b13", "b18", "b4", "b19", "b20", "b21", "b22" ]
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
This highlights the importance of de novo techniques for protein folding.
[ "4", "7", "8", "12", "13", "18", "4", "19", "20", "21", "22" ]
73
9,767
0
false
This highlights the importance of de novo techniques for protein folding.
[]
This highlights the importance of de novo techniques for protein folding.
true
true
true
true
true
1,554
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Significant progress has been made in recent years towards physics-based computation of protein structure, from a knowledge of the amino acid sequence.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
151
9,768
0
false
Significant progress has been made in recent years towards physics-based computation of protein structure, from a knowledge of the amino acid sequence.
[]
Significant progress has been made in recent years towards physics-based computation of protein structure, from a knowledge of the amino acid sequence.
true
true
true
true
true
1,555
2
INTRODUCTION
1
26
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
This approach, commonly referred to as an ab initio method (23–25) is based on the thermodynamic hypothesis formulated by Anfinsen (1973), according to which the native structure of a protein corresponds to the global minimum of its free energy under given conditions (26).
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
273
9,769
1
false
This approach, commonly referred to as an ab initio method is based on the thermodynamic hypothesis formulated by Anfinsen (1973), according to which the native structure of a protein corresponds to the global minimum of its free energy under given conditions.
[ "23–25", "26" ]
This approach, commonly referred to as an ab initio method is based on the thermodynamic hypothesis formulated by Anfinsen (1973), according to which the native structure of a protein corresponds to the global minimum of its free energy under given conditions.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Protein structure prediction using ab initio method is accomplished by a search for a conformation corresponding to the global-minimum of an appropriate potential energy function without the use of secondary structure prediction, homology modeling, threading etc.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
263
9,770
0
false
Protein structure prediction using ab initio method is accomplished by a search for a conformation corresponding to the global-minimum of an appropriate potential energy function without the use of secondary structure prediction, homology modeling, threading etc.
[]
Protein structure prediction using ab initio method is accomplished by a search for a conformation corresponding to the global-minimum of an appropriate potential energy function without the use of secondary structure prediction, homology modeling, threading etc.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
In contrast, methods characterized as de novo use the ab initio strategies partly as well as database information directly or indirectly.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
137
9,771
0
false
In contrast, methods characterized as de novo use the ab initio strategies partly as well as database information directly or indirectly.
[]
In contrast, methods characterized as de novo use the ab initio strategies partly as well as database information directly or indirectly.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Table 1 summarizes different known web servers/groups for protein structure prediction and the function(s) therein.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
115
9,772
0
false
Table 1 summarizes different known web servers/groups for protein structure prediction and the function(s) therein.
[]
Table 1 summarizes different known web servers/groups for protein structure prediction and the function(s) therein.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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 tertiary structure prediction of protein starting from its sequence has been successfully demonstrated on protein sequences <85 residues in length by Baker's group (28,29) using a fragment assembly methodology.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
214
9,773
0
false
The tertiary structure prediction of protein starting from its sequence has been successfully demonstrated on protein sequences <85 residues in length by Baker's group using a fragment assembly methodology.
[ "28,29" ]
The tertiary structure prediction of protein starting from its sequence has been successfully demonstrated on protein sequences <85 residues in length by Baker's group using a fragment assembly methodology.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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 ProtInfo web server by Samudrala et al.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
43
9,774
0
false
The ProtInfo web server by Samudrala et al.
[]
The ProtInfo web server by Samudrala et al.
true
true
true
true
true
1,555
2
INTRODUCTION
1
30
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
(30) predicts protein tertiary structure for sequences <100 amino acids using de novo methodology, where by structures are generated using simulated annealing search phase which minimizes a target scoring function.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
214
9,775
1
false
predicts protein tertiary structure for sequences <100 amino acids using de novo methodology, where by structures are generated using simulated annealing search phase which minimizes a target scoring function.
[ "30" ]
predicts protein tertiary structure for sequences <100 amino acids using de novo methodology, where by structures are generated using simulated annealing search phase which minimizes a target scoring function.
false
true
true
true
false
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Scratch web server by Baldi et al.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
34
9,776
0
false
Scratch web server by Baldi et al.
[]
Scratch web server by Baldi et al.
true
true
true
true
true
1,555
2
INTRODUCTION
1
31
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
(31) predicts the protein tertiary structure as well as structural features starting from the sequence information alone.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
121
9,777
1
false
predicts the protein tertiary structure as well as structural features starting from the sequence information alone.
[ "31" ]
predicts the protein tertiary structure as well as structural features starting from the sequence information alone.
false
true
true
true
false
1,555
2
INTRODUCTION
1
32
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Astro-fold (32) an ab initio structure prediction framework by Klepeis and Floudas employs local interactions and hydrophobicity for the identification of helices and beta-sheets respectively followed by global optimization, stochastic optimization and torsion angle dynamics.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
276
9,778
1
false
Astro-fold an ab initio structure prediction framework by Klepeis and Floudas employs local interactions and hydrophobicity for the identification of helices and beta-sheets respectively followed by global optimization, stochastic optimization and torsion angle dynamics.
[ "32" ]
Astro-fold an ab initio structure prediction framework by Klepeis and Floudas employs local interactions and hydrophobicity for the identification of helices and beta-sheets respectively followed by global optimization, stochastic optimization and torsion angle dynamics.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
De novo structure prediction by simfold energy function with the multi-canonical ensemble fragment assembly has been developed by Fujitsuka et al.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
146
9,779
0
false
De novo structure prediction by simfold energy function with the multi-canonical ensemble fragment assembly has been developed by Fujitsuka et al.
[]
De novo structure prediction by simfold energy function with the multi-canonical ensemble fragment assembly has been developed by Fujitsuka et al.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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 function has been tested on 38 proteins along with the fragment assembly simulations and predicts structures within 6.5 Å RMSD (root mean square deviation) of the native in 12 of the cases.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
193
9,780
0
false
The function has been tested on 38 proteins along with the fragment assembly simulations and predicts structures within 6.5 Å RMSD (root mean square deviation) of the native in 12 of the cases.
[]
The function has been tested on 38 proteins along with the fragment assembly simulations and predicts structures within 6.5 Å RMSD (root mean square deviation) of the native in 12 of the cases.
true
true
true
true
true
1,555
2
INTRODUCTION
1
23
[ "b23", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32", "b33" ]
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
Arriving at structures between 3 and 6 Å RMSD of the native expeditiously using ab initio or de novo methodologies remains a formidable challenge.
[ "23", "25", "26", "27", "28", "29", "30", "31", "32", "33" ]
146
9,781
0
false
Arriving at structures between 3 and 6 Å RMSD of the native expeditiously using ab initio or de novo methodologies remains a formidable challenge.
[]
Arriving at structures between 3 and 6 Å RMSD of the native expeditiously using ab initio or de novo methodologies remains a formidable challenge.
true
true
true
true
true
1,555
3
INTRODUCTION
0
null
null
17,090,600
null
We have developed a computationally viable de novo strategy for tertiary structure prediction, processing and evaluation.
null
121
9,782
0
false
null
null
We have developed a computationally viable de novo strategy for tertiary structure prediction, processing and evaluation.
true
true
true
true
true
1,556
3
INTRODUCTION
0
null
null
17,090,600
null
The web server christened Bhageerath takes as input the amino acid sequence and secondary structure information for a query protein and returns 10 candidate structures for the native.
null
183
9,783
0
false
null
null
The web server christened Bhageerath takes as input the amino acid sequence and secondary structure information for a query protein and returns 10 candidate structures for the native.
true
true
true
true
true
1,556
3
INTRODUCTION
0
null
null
17,090,600
null
In this article, we report the validation and testing of the protein structure prediction web suite Bhageerath with application to 50 small globular proteins.
null
158
9,784
0
false
null
null
In this article, we report the validation and testing of the protein structure prediction web suite Bhageerath with application to 50 small globular proteins.
true
true
true
true
true
1,556
3
INTRODUCTION
0
null
null
17,090,600
null
The programs are written in standard C++, with a total of more than ∼8000 lines of code and are easily portable on any POSIX (UNIX, LINUX, IRIX and AIX) compliant system.
null
170
9,785
0
false
null
null
The programs are written in standard C++, with a total of more than ∼8000 lines of code and are easily portable on any POSIX (UNIX, LINUX, IRIX and AIX) compliant system.
true
true
true
true
true
1,556
0
DISCUSSION
0
null
null
17,090,600
pmid-15677316|pmid-10811210|NA
We describe here an energy based computational web server Bhageerath, for an automated candidate tertiary structure prediction.
null
127
9,786
0
false
null
null
We describe here an energy based computational web server Bhageerath, for an automated candidate tertiary structure prediction.
true
true
true
true
true
1,557
0
DISCUSSION
0
null
null
17,090,600
pmid-15677316|pmid-10811210|NA
The web server permits predictive folding with moderate computational resources.
null
80
9,787
0
false
null
null
The web server permits predictive folding with moderate computational resources.
true
true
true
true
true
1,557
0
DISCUSSION
0
null
null
17,090,600
pmid-15677316|pmid-10811210|NA
The validation of the computational protocol on 50 globular proteins has shown that the web server selects one or more candidate structures within an RMSD of 3–6 Å with respect to the native in the 10 lowest energy structures.
null
226
9,788
0
false
null
null
The validation of the computational protocol on 50 globular proteins has shown that the web server selects one or more candidate structures within an RMSD of 3–6 Å with respect to the native in the 10 lowest energy structures.
true
true
true
true
true
1,557
0
DISCUSSION
0
null
null
17,090,600
pmid-15677316|pmid-10811210|NA
The results presented are for proteins having 2–3 secondary elements with α, β and α/β structures and are obtained solely from the amino acid sequence and secondary structure information (without the aid of multiple sequence alignment, or fold recognition).
null
257
9,789
0
false
null
null
The results presented are for proteins having 2–3 secondary elements with α, β and α/β structures and are obtained solely from the amino acid sequence and secondary structure information (without the aid of multiple sequence alignment, or fold recognition).
true
true
true
true
true
1,557
0
DISCUSSION
0
null
null
17,090,600
pmid-15677316|pmid-10811210|NA
The results provide a benchmark as to the level of model accuracy one can expect from this web server.
null
102
9,790
0
false
null
null
The results provide a benchmark as to the level of model accuracy one can expect from this web server.
true
true
true
true
true
1,557
1
DISCUSSION
0
null
null
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
All of the eight modules are currently being executed on a cluster with 32 dedicated UltraSparc III 900 MHz processors.
null
119
9,791
0
false
null
null
All of the eight modules are currently being executed on a cluster with 32 dedicated UltraSparc III 900 MHz processors.
true
true
true
true
true
1,558
1
DISCUSSION
0
null
null
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
In contrast to typical short return times (ranging from 1 to 10 min) for receiving results from comparative modeling servers, the expected prediction time with Bhageerath web server for two helix systems is 4–5 min while for three helix systems it is ∼2–3
null
255
9,792
0
false
null
null
In contrast to typical short return times (ranging from 1 to 10 min) for receiving results from comparative modeling servers, the expected prediction time with Bhageerath web server for two helix systems is 4–5 min while for three helix systems it is ∼2–3
true
true
false
true
false
1,558
1
DISCUSSION
0
null
null
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
h. However, this depends on the length of the sequence, number of secondary structure elements and the number of structures accepted after the biophysical filters for processing the energetics of each trial structure at the atomic level.
null
237
9,793
0
false
null
null
h. However, this depends on the length of the sequence, number of secondary structure elements and the number of structures accepted after the biophysical filters for processing the energetics of each trial structure at the atomic level.
false
true
true
true
false
1,558
1
DISCUSSION
0
null
null
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
It is currently able to process ∼4–5
null
36
9,794
0
false
null
null
It is currently able to process ∼4–5
true
true
false
true
false
1,558
1
DISCUSSION
0
null
null
17,090,600
pmid-9504803|pmid-11151004|pmid-7643405|pmid-11237627|pmid-8800466|pmid-14579324|pmid-9504803|NA|pmid-11021542|pmid-8254673|pmid-16187345
normally sized jobs per day on 32 processors.
null
45
9,795
0
false
null
null
normally sized jobs per day on 32 processors.
false
true
true
true
false
1,558
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 current version of the web server elicits secondary structure information from the user.
[ "43", "47", "35" ]
92
9,796
0
false
The current version of the web server elicits secondary structure information from the user.
[]
The current version of the web server elicits secondary structure information from the user.
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 new sequences where secondary structure information is not available, web based secondary structure prediction tools can be employed.
[ "43", "47", "35" ]
137
9,797
0
false
For new sequences where secondary structure information is not available, web based secondary structure prediction tools can be employed.
[]
For new sequences where secondary structure information is not available, web based secondary structure prediction tools can be employed.
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
We have characterized the results obtained from five different freely available secondary structure prediction servers (43–47) available on the web for the 50 test proteins.
[ "43", "47", "35" ]
173
9,798
0
false
We have characterized the results obtained from five different freely available secondary structure prediction servers available on the web for the 50 test proteins.
[ "43–47" ]
We have characterized the results obtained from five different freely available secondary structure prediction servers available on the web for the 50 test proteins.
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 predictions are provided in the supplementary information (Supplementary Table S9).
[ "43", "47", "35" ]
87
9,799
0
false
The predictions are provided in the supplementary information (Supplementary Table S9).
[]
The predictions are provided in the supplementary information (Supplementary Table S9).
true
true
true
true
true
1,559