Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
The essence of the KO system is that it is a pathway based definition of orthologous genes.
[ "10" ]
91
10,600
0
false
The essence of the KO system is that it is a pathway based definition of orthologous genes.
[]
The essence of the KO system is that it is a pathway based definition of orthologous genes.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
The KO entry represents an ortholog group that is linked to a box (gene product) in the KEGG pathway diagram.
[ "10" ]
109
10,601
0
false
The KO entry represents an ortholog group that is linked to a box (gene product) in the KEGG pathway diagram.
[]
The KO entry represents an ortholog group that is linked to a box (gene product) in the KEGG pathway diagram.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
Thus, once the KO identifiers, or the K numbers, are assigned to genes in the genome, which is manually verified in KEGG, organism-specific pathways can be computationally generated.
[ "10" ]
182
10,602
0
false
Thus, once the KO identifiers, or the K numbers, are assigned to genes in the genome, which is manually verified in KEGG, organism-specific pathways can be computationally generated.
[]
Thus, once the KO identifiers, or the K numbers, are assigned to genes in the genome, which is manually verified in KEGG, organism-specific pathways can be computationally generated.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
The KO system has since been expanded to include the BRITE functional hierarchies, such as hierarchical classifications of protein families.
[ "10" ]
140
10,603
0
false
The KO system has since been expanded to include the BRITE functional hierarchies, such as hierarchical classifications of protein families.
[]
The KO system has since been expanded to include the BRITE functional hierarchies, such as hierarchical classifications of protein families.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
A set of K numbers in the genome can be mapped, i.e.
[ "10" ]
52
10,604
0
false
A set of K numbers in the genome can be mapped, i.e.
[]
A set of K numbers in the genome can be mapped, i.e.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
to specific classes of receptors, which may then be linked to specific classes of ligands in the chemical category of the BRITE database (see Figure 1).
[ "10" ]
152
10,605
0
false
to specific classes of receptors, which may then be linked to specific classes of ligands in the chemical category of the BRITE database (see Figure 1).
[]
to specific classes of receptors, which may then be linked to specific classes of ligands in the chemical category of the BRITE database.
false
true
true
true
false
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
In essence, the KEGG database provides a reference knowledge base for linking genomes to the biological systems, and now to the environments as well (10).
[ "10" ]
154
10,606
1
false
In essence, the KEGG database provides a reference knowledge base for linking genomes to the biological systems, and now to the environments as well.
[ "10" ]
In essence, the KEGG database provides a reference knowledge base for linking genomes to the biological systems, and now to the environments as well.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
Here, we report a web-based server called KAAS (KEGG Automatic Annotation Server) to automate the processes of the K number assignment and the subsequent pathway mapping and BRITE mapping.
[ "10" ]
188
10,607
0
false
Here, we report a web-based server called KAAS (KEGG Automatic Annotation Server) to automate the processes of the K number assignment and the subsequent pathway mapping and BRITE mapping.
[]
Here, we report a web-based server called KAAS (KEGG Automatic Annotation Server) to automate the processes of the K number assignment and the subsequent pathway mapping and BRITE mapping.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
Figure 1.An example of the genome annotation with the KO identifiers or the K numbers by the KAAS service, which is integrated into the KEGG resource.
[ "10" ]
150
10,608
0
false
Figure 1.An example of the genome annotation with the KO identifiers or the K numbers by the KAAS service, which is integrated into the KEGG resource.
[]
Figure 1.An example of the genome annotation with the KO identifiers or the K numbers by the KAAS service, which is integrated into the KEGG resource.
true
true
true
true
true
1,688
2
INTRODUCTION
1
10
[ "B10" ]
17,526,522
pmid-16381885
Once the KAAS assigns K numbers to query genes, the mapping to KEGG pathways and BRITE hierchies is generated using the existing framework of the KEGG system.
[ "10" ]
158
10,609
0
false
Once the KAAS assigns K numbers to query genes, the mapping to KEGG pathways and BRITE hierchies is generated using the existing framework of the KEGG system.
[]
Once the KAAS assigns K numbers to query genes, the mapping to KEGG pathways and BRITE hierchies is generated using the existing framework of the KEGG system.
true
true
true
true
true
1,688
3
INTRODUCTION
0
null
null
17,526,522
null
An example of the genome annotation with the KO identifiers or the K numbers by the KAAS service, which is integrated into the KEGG resource.
null
141
10,610
0
false
null
null
An example of the genome annotation with the KO identifiers or the K numbers by the KAAS service, which is integrated into the KEGG resource.
true
true
true
true
true
1,689
3
INTRODUCTION
0
null
null
17,526,522
null
Once the KAAS assigns K numbers to query genes, the mapping to KEGG pathways and BRITE hierchies is generated using the existing framework of the KEGG system.
null
158
10,611
0
false
null
null
Once the KAAS assigns K numbers to query genes, the mapping to KEGG pathways and BRITE hierchies is generated using the existing framework of the KEGG system.
true
true
true
true
true
1,689
0
INTRODUCTION
1
1
[ "b1", "b2", "b4" ]
17,158,166
pmid-870828|pmid-16809333|pmid-16794078
Virus genome analysis has a long history.
[ "1", "2", "4" ]
41
10,612
0
false
Virus genome analysis has a long history.
[]
Virus genome analysis has a long history.
true
true
true
true
true
1,690
0
INTRODUCTION
1
1
[ "b1", "b2", "b4" ]
17,158,166
pmid-870828|pmid-16809333|pmid-16794078
In 1977, Frederick Sanger successfully sequenced the entire genome of Phage φphiv;X174 (1).
[ "1", "2", "4" ]
91
10,613
1
false
In 1977, Frederick Sanger successfully sequenced the entire genome of Phage φphiv;X174.
[ "1" ]
In 1977, Frederick Sanger successfully sequenced the entire genome of Phage φphiv;X174.
true
true
true
true
true
1,690
0
INTRODUCTION
1
1
[ "b1", "b2", "b4" ]
17,158,166
pmid-870828|pmid-16809333|pmid-16794078
Since that time, a huge number of virus genomes have been sequenced.
[ "1", "2", "4" ]
68
10,614
0
false
Since that time, a huge number of virus genomes have been sequenced.
[]
Since that time, a huge number of virus genomes have been sequenced.
true
true
true
true
true
1,690
0
INTRODUCTION
1
1
[ "b1", "b2", "b4" ]
17,158,166
pmid-870828|pmid-16809333|pmid-16794078
Virus genome sequences provide researchers with important information needed to analyze virus evolution, pathogenicity and diversity (2–4).
[ "1", "2", "4" ]
139
10,615
0
false
Virus genome sequences provide researchers with important information needed to analyze virus evolution, pathogenicity and diversity.
[ "2–4" ]
Virus genome sequences provide researchers with important information needed to analyze virus evolution, pathogenicity and diversity.
true
true
true
true
true
1,690
1
INTRODUCTION
0
null
null
17,158,166
null
The International Nucleotide Sequence Database Collaboration (INSDC) makes a substantial amount of genomic data available in a public database.
null
143
10,616
0
false
null
null
The International Nucleotide Sequence Database Collaboration (INSDC) makes a substantial amount of genomic data available in a public database.
true
true
true
true
true
1,691
1
INTRODUCTION
0
null
null
17,158,166
null
However, these genomic data are stored in the same database as general gene registrations and are not distinguished.
null
116
10,617
0
false
null
null
However, these genomic data are stored in the same database as general gene registrations and are not distinguished.
true
true
true
true
true
1,691
1
INTRODUCTION
0
null
null
17,158,166
null
In some cases, the specific prefix of the accession number (AE, AL, AP, BS, BX, CP, CR, CT, CU and CY) refers to a registration from a genome project ().
null
153
10,618
0
false
null
null
In some cases, the specific prefix of the accession number (AE, AL, AP, BS, BX, CP, CR, CT, CU and CY) refers to a registration from a genome project ().
true
true
true
true
true
1,691
1
INTRODUCTION
0
null
null
17,158,166
null
However, for many genome data, the prefix is the same as that of general gene registrations, making it difficult to extract genomic data.
null
137
10,619
0
false
null
null
However, for many genome data, the prefix is the same as that of general gene registrations, making it difficult to extract genomic data.
true
true
true
true
true
1,691
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9" ]
17,158,166
pmid-16381892|pmid-15702954|pmid-11125070|pmid-14681415|pmid-11752256
There are several virus genome databases such as DPVweb (5), HCVDB (6), VIDA (7) and VirGen (8).
[ "5", "6", "7", "8", "9" ]
96
10,620
1
false
There are several virus genome databases such as DPVweb, HCVDB, VIDA and VirGen.
[ "5", "6", "7", "8" ]
There are several virus genome databases such as DPVweb, HCVDB, VIDA and VirGen.
true
true
true
true
true
1,692
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9" ]
17,158,166
pmid-16381892|pmid-15702954|pmid-11125070|pmid-14681415|pmid-11752256
However, most of these are limited to specific groups of viruses.
[ "5", "6", "7", "8", "9" ]
65
10,621
0
false
However, most of these are limited to specific groups of viruses.
[]
However, most of these are limited to specific groups of viruses.
true
true
true
true
true
1,692
2
INTRODUCTION
1
5
[ "b5", "b6", "b7", "b8", "b9" ]
17,158,166
pmid-16381892|pmid-15702954|pmid-11125070|pmid-14681415|pmid-11752256
Thus, to fill the need for a comprehensive virus genome database, weconstructed Genome Information Broker for Viruses (GIB-V), which includes all groups of viruses and is updated regularly with the release of our DNA Data Bank of Japan (DDBJ) data.
[ "5", "6", "7", "8", "9" ]
248
10,622
0
false
Thus, to fill the need for a comprehensive virus genome database, weconstructed Genome Information Broker for Viruses (GIB-V), which includes all groups of viruses and is updated regularly with the release of our DNA Data Bank of Japan (DDBJ) data.
[]
Thus, to fill the need for a comprehensive virus genome database, weconstructed Genome Information Broker for Viruses (GIB-V), which includes all groups of viruses and is updated regularly with the release of our DNA Data Bank of Japan (DDBJ) data.
true
true
true
true
true
1,692
2
INTRODUCTION
1
9
[ "b5", "b6", "b7", "b8", "b9" ]
17,158,166
pmid-16381892|pmid-15702954|pmid-11125070|pmid-14681415|pmid-11752256
GIB-V was created with the use of the Genome Information Browser (GIB) (9), an online microbial genome analysis system that we have developed.
[ "5", "6", "7", "8", "9" ]
142
10,623
1
false
GIB-V was created with the use of the Genome Information Browser (GIB), an online microbial genome analysis system that we have developed.
[ "9" ]
GIB-V was created with the use of the Genome Information Browser (GIB), an online microbial genome analysis system that we have developed.
true
true
true
true
true
1,692
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,945,960
pmid-9392700|pmid-1325733
More than 300 million people worldwide are estimated to be chronically infected by hepatitis B virus (HBV) (1) and
[ "1", "2" ]
114
10,624
1
false
More than 300 million people worldwide are estimated to be chronically infected by hepatitis B virus (HBV) and
[ "1" ]
More than 300 million people worldwide are estimated to be chronically infected by hepatitis B virus (HBV) and
true
true
false
true
false
1,693
0
INTRODUCTION
1
2
[ "b1", "b2" ]
16,945,960
pmid-9392700|pmid-1325733
chronic HBV infection carriers have a great risk to develop severe liver diseases, including cirrhosis and liver cancer, resulting in a million deaths annually (2).
[ "1", "2" ]
164
10,625
1
false
chronic HBV infection carriers have a great risk to develop severe liver diseases, including cirrhosis and liver cancer, resulting in a million deaths annually.
[ "2" ]
chronic HBV infection carriers have a great risk to develop severe liver diseases, including cirrhosis and liver cancer, resulting in a million deaths annually.
false
true
true
true
false
1,693
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,945,960
pmid-9392700|pmid-1325733
No treatment for the efficient elimination of HBV in infected patients exists as yet.
[ "1", "2" ]
85
10,626
0
false
No treatment for the efficient elimination of HBV in infected patients exists as yet.
[]
No treatment for the efficient elimination of HBV in infected patients exists as yet.
true
true
true
true
true
1,693
0
INTRODUCTION
1
1
[ "b1", "b2" ]
16,945,960
pmid-9392700|pmid-1325733
Therefore more knowledge about HBV replication is needed to enable the design of more efficient antiviral drugs.
[ "1", "2" ]
112
10,627
0
false
Therefore more knowledge about HBV replication is needed to enable the design of more efficient antiviral drugs.
[]
Therefore more knowledge about HBV replication is needed to enable the design of more efficient antiviral drugs.
true
true
true
true
true
1,693
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
HBV is a member of the Hepadnaviridae family, consisting of hepatotropic DNA viruses which also includes related animal viruses such as duck HBV (DHBV) and heron hepatitis virus.
[ "3", "5", "6", "8", "9", "12" ]
178
10,628
0
false
HBV is a member of the Hepadnaviridae family, consisting of hepatotropic DNA viruses which also includes related animal viruses such as duck HBV (DHBV) and heron hepatitis virus.
[]
HBV is a member of the Hepadnaviridae family, consisting of hepatotropic DNA viruses which also includes related animal viruses such as duck HBV (DHBV) and heron hepatitis virus.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
HBV has a small (3.2 kb), relaxed circular, partially double-stranded DNA genome and replicates this DNA genome through an RNA intermediate, the pregenomic RNA (pgRNA), by reverse transcription [for reviews see (3–5)].
[ "3", "5", "6", "8", "9", "12" ]
218
10,629
0
false
HBV has a small, relaxed circular, partially double-stranded DNA genome and replicates this DNA genome through an RNA intermediate, the pregenomic RNA (pgRNA), by reverse transcription.
[ "3.2 kb", "for reviews see (3–5)" ]
HBV has a small, relaxed circular, partially double-stranded DNA genome and replicates this DNA genome through an RNA intermediate, the pregenomic RNA (pgRNA), by reverse transcription.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
The RNA pregenome also serves as the mRNA for the capsid (or core) protein and the P protein.
[ "3", "5", "6", "8", "9", "12" ]
93
10,630
0
false
The RNA pregenome also serves as the mRNA for the capsid (or core) protein and the P protein.
[]
The RNA pregenome also serves as the mRNA for the capsid (or core) protein and the P protein.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
The P protein contains the evolutionarily conserved RT domain, a middle spacer region, a C-terminal RNase H (RH) domain and a unique terminal protein (TP) domain at its N-terminus, which acts as a protein primer for reverse transcription.
[ "3", "5", "6", "8", "9", "12" ]
238
10,631
0
false
The P protein contains the evolutionarily conserved RT domain, a middle spacer region, a C-terminal RNase H (RH) domain and a unique terminal protein (TP) domain at its N-terminus, which acts as a protein primer for reverse transcription.
[]
The P protein contains the evolutionarily conserved RT domain, a middle spacer region, a C-terminal RNase H (RH) domain and a unique terminal protein (TP) domain at its N-terminus, which acts as a protein primer for reverse transcription.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
Replication is initiated by the binding of P to epsilon (ɛ) (Figure 1), a 60 nt bulged stem–loop at the 5′ end of the pgRNA (6–8).
[ "3", "5", "6", "8", "9", "12" ]
130
10,632
0
false
Replication is initiated by the binding of P to epsilon (ɛ) (Figure 1), a 60 nt bulged stem–loop at the 5′ end of the pgRNA.
[ "6–8" ]
Replication is initiated by the binding of P to epsilon (ɛ) (Figure 1), a 60 nt bulged stem–loop at the 5′ end of the pgRNA.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
This binding event triggers encapsidation of the P–ɛ complex by capsid proteins, resulting in a priming competent, encapsidated complex.
[ "3", "5", "6", "8", "9", "12" ]
136
10,633
0
false
This binding event triggers encapsidation of the P–ɛ complex by capsid proteins, resulting in a priming competent, encapsidated complex.
[]
This binding event triggers encapsidation of the P–ɛ complex by capsid proteins, resulting in a priming competent, encapsidated complex.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
The product of the priming reaction is a 4 nt DNA, synthesized off a template in the primer bulge in ɛ, whose 5′ end is covalently attached to a tyrosine residue in the TP domain.
[ "3", "5", "6", "8", "9", "12" ]
179
10,634
0
false
The product of the priming reaction is a 4 nt DNA, synthesized off a template in the primer bulge in ɛ, whose 5′ end is covalently attached to a tyrosine residue in the TP domain.
[]
The product of the priming reaction is a 4 nt DNA, synthesized off a template in the primer bulge in ɛ, whose 5′ end is covalently attached to a tyrosine residue in the TP domain.
true
true
true
true
true
1,694
1
INTRODUCTION
1
3
[ "b3", "b5", "b6", "b8", "b9", "b12" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
This complex subsequently translocates to a 3′-proximal RNA element in the pregenome where full-length (−)-DNA synthesis is primed by the 4 nt DNA oligonucleotide (9–12).
[ "3", "5", "6", "8", "9", "12" ]
170
10,635
0
false
This complex subsequently translocates to a 3′-proximal RNA element in the pregenome where full-length (−)-DNA synthesis is primed by the 4 nt DNA oligonucleotide.
[ "9–12" ]
This complex subsequently translocates to a 3′-proximal RNA element in the pregenome where full-length (−)-DNA synthesis is primed by the 4 nt DNA oligonucleotide.
true
true
true
true
true
1,694
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Detailed biochemical studies of the P–ɛ interaction have been made possible in recent years by the development of DHBV cell-free reconstitution systems consisting of P, ɛ and cellular chaperones (13–17).
[ "13", "17", "18", "12", "16", "19" ]
203
10,636
0
false
Detailed biochemical studies of the P–ɛ interaction have been made possible in recent years by the development of DHBV cell-free reconstitution systems consisting of P, ɛ and cellular chaperones.
[ "13–17" ]
Detailed biochemical studies of the P–ɛ interaction have been made possible in recent years by the development of DHBV cell-free reconstitution systems consisting of P, ɛ and cellular chaperones.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
The system shows both P–ɛ binding and priming.
[ "13", "17", "18", "12", "16", "19" ]
46
10,637
0
false
The system shows both P–ɛ binding and priming.
[]
The system shows both P–ɛ binding and priming.
true
true
true
true
true
1,695
2
INTRODUCTION
1
18
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Using truncated P protein constructs in these in vitro systems it was demonstrated that P–ɛ interaction requires sequences from both RT and TP protein domains (18).
[ "13", "17", "18", "12", "16", "19" ]
164
10,638
1
false
Using truncated P protein constructs in these in vitro systems it was demonstrated that P–ɛ interaction requires sequences from both RT and TP protein domains.
[ "18" ]
Using truncated P protein constructs in these in vitro systems it was demonstrated that P–ɛ interaction requires sequences from both RT and TP protein domains.
true
true
true
true
true
1,695
2
INTRODUCTION
1
12
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
On the RNA side, the loop at the apical stem–loop of DHBV-ɛ is found to be essential for binding and primer synthesis (12).
[ "13", "17", "18", "12", "16", "19" ]
123
10,639
1
false
On the RNA side, the loop at the apical stem–loop of DHBV-ɛ is found to be essential for binding and primer synthesis.
[ "12" ]
On the RNA side, the loop at the apical stem–loop of DHBV-ɛ is found to be essential for binding and primer synthesis.
true
true
true
true
true
1,695
2
INTRODUCTION
1
16
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Recent SELEX experiments in such a system further defined the structure and sequence elements in the apical stem–loop of DHBV crucial for binding and/or priming (16).
[ "13", "17", "18", "12", "16", "19" ]
166
10,640
1
false
Recent SELEX experiments in such a system further defined the structure and sequence elements in the apical stem–loop of DHBV crucial for binding and/or priming.
[ "16" ]
Recent SELEX experiments in such a system further defined the structure and sequence elements in the apical stem–loop of DHBV crucial for binding and/or priming.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
For instance, the middle of the stem underlying the loop should be weakly or not base paired at all.
[ "13", "17", "18", "12", "16", "19" ]
100
10,641
0
false
For instance, the middle of the stem underlying the loop should be weakly or not base paired at all.
[]
For instance, the middle of the stem underlying the loop should be weakly or not base paired at all.
true
true
true
true
true
1,695
2
INTRODUCTION
1
19
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Most recently, a cell-free and chaperone dependent in vitro reconstitution system was developed also for human HBV (19).
[ "13", "17", "18", "12", "16", "19" ]
120
10,642
1
false
Most recently, a cell-free and chaperone dependent in vitro reconstitution system was developed also for human HBV.
[ "19" ]
Most recently, a cell-free and chaperone dependent in vitro reconstitution system was developed also for human HBV.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
It shows P–ɛ binding but, in contrast to the DHBV system, not priming.
[ "13", "17", "18", "12", "16", "19" ]
70
10,643
0
false
It shows P–ɛ binding but, in contrast to the DHBV system, not priming.
[]
It shows P–ɛ binding but, in contrast to the DHBV system, not priming.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Similar to DHBV, in human HBV sequences from both the RT and TP domains are required for binding of P to ɛ.
[ "13", "17", "18", "12", "16", "19" ]
107
10,644
0
false
Similar to DHBV, in human HBV sequences from both the RT and TP domains are required for binding of P to ɛ.
[]
Similar to DHBV, in human HBV sequences from both the RT and TP domains are required for binding of P to ɛ.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Surprisingly, and in contrast to DHBV P–ɛ where the ɛ-apical loop is essential, in human HBV it is not needed for binding.
[ "13", "17", "18", "12", "16", "19" ]
122
10,645
0
false
Surprisingly, and in contrast to DHBV P–ɛ where the ɛ-apical loop is essential, in human HBV it is not needed for binding.
[]
Surprisingly, and in contrast to DHBV P–ɛ where the ɛ-apical loop is essential, in human HBV it is not needed for binding.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
The ɛ-apical loop is, however, required for encapsidation.
[ "13", "17", "18", "12", "16", "19" ]
58
10,646
0
false
The ɛ-apical loop is, however, required for encapsidation.
[]
The ɛ-apical loop is, however, required for encapsidation.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Moreover, the structural features, requirement for base pairing in the stem part of the apical stem–loop, differ from those in DHBV.
[ "13", "17", "18", "12", "16", "19" ]
132
10,647
0
false
Moreover, the structural features, requirement for base pairing in the stem part of the apical stem–loop, differ from those in DHBV.
[]
Moreover, the structural features, requirement for base pairing in the stem part of the apical stem–loop, differ from those in DHBV.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
In human HBV, the upper part of the stem of the apical stem–loop needs to be base paired and the bulged out U is essential for binding.
[ "13", "17", "18", "12", "16", "19" ]
135
10,648
0
false
In human HBV, the upper part of the stem of the apical stem–loop needs to be base paired and the bulged out U is essential for binding.
[]
In human HBV, the upper part of the stem of the apical stem–loop needs to be base paired and the bulged out U is essential for binding.
true
true
true
true
true
1,695
2
INTRODUCTION
1
13
[ "b13", "b17", "b18", "b12", "b16", "b19" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Although the structural basis and sequence requirements for P–ɛ binding and priming are emerging, a full understanding of the molecular basis for the specific interactions between P and ɛ awaits high-resolution structural studies.
[ "13", "17", "18", "12", "16", "19" ]
230
10,649
0
false
Although the structural basis and sequence requirements for P–ɛ binding and priming are emerging, a full understanding of the molecular basis for the specific interactions between P and ɛ awaits high-resolution structural studies.
[]
Although the structural basis and sequence requirements for P–ɛ binding and priming are emerging, a full understanding of the molecular basis for the specific interactions between P and ɛ awaits high-resolution structural studies.
true
true
true
true
true
1,695
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
Some high-resolution data have already been obtained on the human HBV ɛ apical stem–loop from NMR studies (20).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
111
10,650
1
false
Some high-resolution data have already been obtained on the human HBV ɛ apical stem–loop from NMR studies.
[ "20" ]
Some high-resolution data have already been obtained on the human HBV ɛ apical stem–loop from NMR studies.
true
true
true
true
true
1,696
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
We note in passing that the residues in the ɛ apical stem–loop are either totally conserved or show rare non-disruptive mutations (20).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
135
10,651
1
false
We note in passing that the residues in the ɛ apical stem–loop are either totally conserved or show rare non-disruptive mutations.
[ "20" ]
We note in passing that the residues in the ɛ apical stem–loop are either totally conserved or show rare non-disruptive mutations.
true
true
true
true
true
1,696
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
The tip of ɛ contains a CUGUGC sequence, for which secondary structure predictions have predicted a hexaloop structure (21–23).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
127
10,652
0
false
The tip of ɛ contains a CUGUGC sequence, for which secondary structure predictions have predicted a hexaloop structure.
[ "21–23" ]
The tip of ɛ contains a CUGUGC sequence, for which secondary structure predictions have predicted a hexaloop structure.
true
true
true
true
true
1,696
3
INTRODUCTION
1
24
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
However, enzymatic probing studies have suggested a base pair between the first and fifth residue of this hexaloop (24).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
120
10,653
1
false
However, enzymatic probing studies have suggested a base pair between the first and fifth residue of this hexaloop.
[ "24" ]
However, enzymatic probing studies have suggested a base pair between the first and fifth residue of this hexaloop.
true
true
true
true
true
1,696
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
Our previous NMR studies confirmed the presence of this base pair indicating that the loop forms a pseudo-triloop motif (20).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
125
10,654
1
false
Our previous NMR studies confirmed the presence of this base pair indicating that the loop forms a pseudo-triloop motif.
[ "20" ]
Our previous NMR studies confirmed the presence of this base pair indicating that the loop forms a pseudo-triloop motif.
true
true
true
true
true
1,696
3
INTRODUCTION
1
25
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
The pseudo-triloop is a recently proposed structural motif that consists of a hexaloop with transloop base pairing between residues 1 and 5 and a bulged out residue 6 (25).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
172
10,655
1
false
The pseudo-triloop is a recently proposed structural motif that consists of a hexaloop with transloop base pairing between residues 1 and 5 and a bulged out residue 6.
[ "25" ]
The pseudo-triloop is a recently proposed structural motif that consists of a hexaloop with transloop base pairing between residues 1 and 5 and a bulged out residue 6.
true
true
true
true
true
1,696
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
Hairpin loops with the potential to form pseudo-triloops are found in many RNA sequences, e.g.
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
94
10,656
0
false
Hairpin loops with the potential to form pseudo-triloops are found in many RNA sequences, e.g.
[]
Hairpin loops with the potential to form pseudo-triloops are found in many RNA sequences, e.g.
true
true
true
true
true
1,696
3
INTRODUCTION
1
31
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
the brome mosaic virus (25,26), the iron responsive element (IRE) (27,28), domain IIId of the internal ribosomal entry site (IRES) of the hepatitis C virus (29,30), the 5′ terminal hairpin of R-U5 of simian foamy virus (31) and HIV-1 TAR (32).
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
243
10,657
1
false
the brome mosaic virus, the iron responsive element (IRE), domain IIId of the internal ribosomal entry site (IRES) of the hepatitis C virus, the 5′ terminal hairpin of R-U5 of simian foamy virus and HIV-1 TAR.
[ "25,26", "27,28", "29,30", "31", "32" ]
the brome mosaic virus, the iron responsive element (IRE), domain IIId of the internal ribosomal entry site (IRES) of the hepatitis C virus, the 5′ terminal hairpin of R-U5 of simian foamy virus and HIV-1 TAR.
false
true
true
true
false
1,696
3
INTRODUCTION
1
20
[ "b20", "b20", "b21", "b23", "b24", "b20", "b25", "b25", "b26", "b27", "b28", "b29", "b30", "b31", "b32" ]
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
The common appearance of the pseudo-triloop motif in different RNA sequences suggests that it might be an important protein binding motif.
[ "20", "20", "21", "23", "24", "20", "25", "25", "26", "27", "28", "29", "30", "31", "32" ]
138
10,658
0
false
The common appearance of the pseudo-triloop motif in different RNA sequences suggests that it might be an important protein binding motif.
[]
The common appearance of the pseudo-triloop motif in different RNA sequences suggests that it might be an important protein binding motif.
true
true
true
true
true
1,696
4
INTRODUCTION
1
33
[ "b33", "b38" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
Here we present the high-resolution 3D structure of the human HBV ɛ apical stem–loop, i.e.
[ "33", "38" ]
90
10,659
0
false
Here we present the high-resolution 3D structure of the human HBV ɛ apical stem–loop, i.e.
[]
Here we present the high-resolution 3D structure of the human HBV ɛ apical stem–loop, i.e.
true
true
true
true
true
1,697
4
INTRODUCTION
1
33
[ "b33", "b38" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
of the 27 nt fragment which includes the pseudo-triloop and the conserved U bulge in the underlying stem (Figure 1b).
[ "33", "38" ]
117
10,660
0
false
of the 27 nt fragment which includes the pseudo-triloop and the conserved U bulge in the underlying stem (Figure 1b).
[]
of the 27 nt fragment which includes the pseudo-triloop and the conserved U bulge in the underlying stem (Figure 1b).
false
true
true
true
false
1,697
4
INTRODUCTION
1
33
[ "b33", "b38" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
Thanks to selective 2H/13C/15N-uridine-labelling, NMR spectral resolution could be increased and spectral overlap reduced (33–38), so that a set of highly reliable structural restraints for the structure derivation based on NOE, RDC and 1H chemical shift NMR data could be derived.
[ "33", "38" ]
281
10,661
0
false
Thanks to selective 2H/13C/15N-uridine-labelling, NMR spectral resolution could be increased and spectral overlap reduced, so that a set of highly reliable structural restraints for the structure derivation based on NOE, RDC and 1H chemical shift NMR data could be derived.
[ "33–38" ]
Thanks to selective 2H/13C/15N-uridine-labelling, NMR spectral resolution could be increased and spectral overlap reduced, so that a set of highly reliable structural restraints for the structure derivation based on NOE, RDC and 1H chemical shift NMR data could be derived.
true
true
true
true
true
1,697
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
Here we present the high-resolution 3D solution structure of the apical stem–loop of epsilon, the binding site of the viral reverse transcriptase in HBV.
null
153
10,662
0
false
null
null
Here we present the high-resolution 3D solution structure of the apical stem–loop of epsilon, the binding site of the viral reverse transcriptase in HBV.
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
Chemical shift analysis showed that both helical regions are mainly A-type, and thus the structure determination has two main objectives, to determine the structure of the pseudo-triloop (PTL) motif at the tip of the apical stem–loop and the global structure of the whole molecule induced by the U23 interruption.
null
313
10,663
0
false
null
null
Chemical shift analysis showed that both helical regions are mainly A-type, and thus the structure determination has two main objectives, to determine the structure of the pseudo-triloop (PTL) motif at the tip of the apical stem–loop and the global structure of the whole molecule induced by the U23 interruption.
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
As a consequence, we divided our structure calculation into two separate parts.
null
79
10,664
0
false
null
null
As a consequence, we divided our structure calculation into two separate parts.
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
For determination of the PTL conformation, only the top 8 nt were included in the calculations (calculation A).
null
111
10,665
0
false
null
null
For determination of the PTL conformation, only the top 8 nt were included in the calculations (calculation A).
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
This enabled us to make a thorough sampling of conformational space.
null
68
10,666
0
false
null
null
This enabled us to make a thorough sampling of conformational space.
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
The dissection of the molecule for computational purposes also facilitated the analysis as we could evaluate the PTL conformations without considering whether the global geometry was optimal or not.
null
198
10,667
0
false
null
null
The dissection of the molecule for computational purposes also facilitated the analysis as we could evaluate the PTL conformations without considering whether the global geometry was optimal or not.
true
true
true
true
true
1,698
0
DISCUSSION
0
null
null
16,945,960
pmid-9392700|pmid-1325733
Thus, fewer trial structures had to be calculated.
null
50
10,668
0
false
null
null
Thus, fewer trial structures had to be calculated.
true
true
true
true
true
1,698
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
For the global structure, a protocol was designed to determine the geometry relying mainly on the RDC data.
[ "47", "47", "44" ]
107
10,669
0
false
For the global structure, a protocol was designed to determine the geometry relying mainly on the RDC data.
[]
For the global structure, a protocol was designed to determine the geometry relying mainly on the RDC data.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
Here, we exploited the modular build of the apical stem–loop RNA and used semi rigid-body dynamics to reorient the two helical regions relative to each other (step B2) (47).
[ "47", "47", "44" ]
173
10,670
1
false
Here, we exploited the modular build of the apical stem–loop RNA and used semi rigid-body dynamics to reorient the two helical regions relative to each other (step B2).
[ "47" ]
Here, we exploited the modular build of the apical stem–loop RNA and used semi rigid-body dynamics to reorient the two helical regions relative to each other (step B2).
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
During this step, the five independent parameters of the alignment tensor were optimized simultaneously with the stem orientation.
[ "47", "47", "44" ]
130
10,671
0
false
During this step, the five independent parameters of the alignment tensor were optimized simultaneously with the stem orientation.
[]
During this step, the five independent parameters of the alignment tensor were optimized simultaneously with the stem orientation.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
This approach takes away the need for time consuming grid searches to determine the alignment tensor and hence increases computational efficiency.
[ "47", "47", "44" ]
146
10,672
0
false
This approach takes away the need for time consuming grid searches to determine the alignment tensor and hence increases computational efficiency.
[]
This approach takes away the need for time consuming grid searches to determine the alignment tensor and hence increases computational efficiency.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
However, we noticed that the two stem regions had to be kept rigid as otherwise the alignment tensor had a tendency to ‘blow up’.
[ "47", "47", "44" ]
129
10,673
0
false
However, we noticed that the two stem regions had to be kept rigid as otherwise the alignment tensor had a tendency to ‘blow up’.
[]
However, we noticed that the two stem regions had to be kept rigid as otherwise the alignment tensor had a tendency to ‘blow up’.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
In the initial structure, determined by NOE restraints (Step B1), the local geometry is only optimized with respect to the NOE restraints and not for the RDC restraints.
[ "47", "47", "44" ]
169
10,674
0
false
In the initial structure, determined by NOE restraints (Step B1), the local geometry is only optimized with respect to the NOE restraints and not for the RDC restraints.
[]
In the initial structure, determined by NOE restraints (Step B1), the local geometry is only optimized with respect to the NOE restraints and not for the RDC restraints.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
Hence, initially there is a tendency to underestimate the axial component of the alignment tensor.
[ "47", "47", "44" ]
98
10,675
0
false
Hence, initially there is a tendency to underestimate the axial component of the alignment tensor.
[]
Hence, initially there is a tendency to underestimate the axial component of the alignment tensor.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
If both the geometry of the molecule and the alignment tensor are optimized simultaneously, computations incorrectly satisfy the experimental RDCs by increasing the components of the alignment tensor excessively (resulting in the alignment tensor ‘blowing up’).
[ "47", "47", "44" ]
261
10,676
0
false
If both the geometry of the molecule and the alignment tensor are optimized simultaneously, computations incorrectly satisfy the experimental RDCs by increasing the components of the alignment tensor excessively (resulting in the alignment tensor ‘blowing up’).
[]
If both the geometry of the molecule and the alignment tensor are optimized simultaneously, computations incorrectly satisfy the experimental RDCs by increasing the components of the alignment tensor excessively (resulting in the alignment tensor ‘blowing up’).
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
The rigid-body dynamics step ensures that this does not happen.
[ "47", "47", "44" ]
63
10,677
0
false
The rigid-body dynamics step ensures that this does not happen.
[]
The rigid-body dynamics step ensures that this does not happen.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
After realigning the two stem regions of the molecule, the local geometry is reoptimized in the final step (B3).
[ "47", "47", "44" ]
112
10,678
0
false
After realigning the two stem regions of the molecule, the local geometry is reoptimized in the final step (B3).
[]
After realigning the two stem regions of the molecule, the local geometry is reoptimized in the final step (B3).
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
Using this protocol, the RDCs are mainly used for determining the global structure of the molecule while the NOEs determine the local structure.
[ "47", "47", "44" ]
144
10,679
0
false
Using this protocol, the RDCs are mainly used for determining the global structure of the molecule while the NOEs determine the local structure.
[]
Using this protocol, the RDCs are mainly used for determining the global structure of the molecule while the NOEs determine the local structure.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
The outline of our strategy resembles the local-to-global structure determination approach presented by McCallum and Pardi (47).
[ "47", "47", "44" ]
128
10,680
1
false
The outline of our strategy resembles the local-to-global structure determination approach presented by McCallum and Pardi.
[ "47" ]
The outline of our strategy resembles the local-to-global structure determination approach presented by McCallum and Pardi.
true
true
true
true
true
1,699
1
DISCUSSION
1
44
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
Wijmenga and co-workers (44) have shown recently that for nucleic acids aligned with Pf1 phages, the rhombicity of the molecular alignment tensor can be predicted accurately from the shape of the molecule.
[ "47", "47", "44" ]
205
10,681
1
false
Wijmenga and co-workers have shown recently that for nucleic acids aligned with Pf1 phages, the rhombicity of the molecular alignment tensor can be predicted accurately from the shape of the molecule.
[ "44" ]
Wijmenga and co-workers have shown recently that for nucleic acids aligned with Pf1 phages, the rhombicity of the molecular alignment tensor can be predicted accurately from the shape of the molecule.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
We utilized this in the final selection of molecules by demanding that the rhombicities of the alignment tensor calculated by PALES and by the gyration tensor method should agree.
[ "47", "47", "44" ]
179
10,682
0
false
We utilized this in the final selection of molecules by demanding that the rhombicities of the alignment tensor calculated by PALES and by the gyration tensor method should agree.
[]
We utilized this in the final selection of molecules by demanding that the rhombicities of the alignment tensor calculated by PALES and by the gyration tensor method should agree.
true
true
true
true
true
1,699
1
DISCUSSION
1
47
[ "b47", "b47", "b44" ]
16,945,960
pmid-10516465|NA|pmid-3039907|pmid-8627750|pmid-7692081|pmid-9774643|pmid-12589752|pmid-12589752|pmid-16718586
In this way, structures which have a rhombicity, and hence alignment tensor, inconsistent with their overall structure are removed from the set.
[ "47", "47", "44" ]
144
10,683
0
false
In this way, structures which have a rhombicity, and hence alignment tensor, inconsistent with their overall structure are removed from the set.
[]
In this way, structures which have a rhombicity, and hence alignment tensor, inconsistent with their overall structure are removed from the set.
true
true
true
true
true
1,699
2
DISCUSSION
1
48
[ "b48" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Our methodology streamlines the structure determination by the subdivision of the problem into two separate and simpler problems.
[ "48" ]
129
10,684
0
false
Our methodology streamlines the structure determination by the subdivision of the problem into two separate and simpler problems.
[]
Our methodology streamlines the structure determination by the subdivision of the problem into two separate and simpler problems.
true
true
true
true
true
1,700
2
DISCUSSION
1
48
[ "b48" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
This strategy is only applicable if the molecule under study has a suitably modular build as the apical stem–loop of epsilon.
[ "48" ]
125
10,685
0
false
This strategy is only applicable if the molecule under study has a suitably modular build as the apical stem–loop of epsilon.
[]
This strategy is only applicable if the molecule under study has a suitably modular build as the apical stem–loop of epsilon.
true
true
true
true
true
1,700
2
DISCUSSION
1
48
[ "b48" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
For the global structure determination, we circumvent the problem of determining the components of the alignment tensor by grid searching.
[ "48" ]
138
10,686
0
false
For the global structure determination, we circumvent the problem of determining the components of the alignment tensor by grid searching.
[]
For the global structure determination, we circumvent the problem of determining the components of the alignment tensor by grid searching.
true
true
true
true
true
1,700
2
DISCUSSION
1
48
[ "b48" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
This strategy is less time consuming and if only fairly few RDCs are measured should be less prone to errors than a grid search which would overestimate the rhombicity and underestimate the axial component of the alignment tensor if the RDC space is sampled anisotropically (a common problem for elongated helical molecu...
[ "48" ]
330
10,687
1
false
This strategy is less time consuming and if only fairly few RDCs are measured should be less prone to errors than a grid search which would overestimate the rhombicity and underestimate the axial component of the alignment tensor if the RDC space is sampled anisotropically (a common problem for elongated helical molecu...
[ "48" ]
This strategy is less time consuming and if only fairly few RDCs are measured should be less prone to errors than a grid search which would overestimate the rhombicity and underestimate the axial component of the alignment tensor if the RDC space is sampled anisotropically (a common problem for elongated helical molecu...
true
true
true
true
true
1,700
2
DISCUSSION
1
48
[ "b48" ]
16,945,960
pmid-11090140|pmid-15542664|pmid-8806527|pmid-9774643|pmid-15314208|pmid-16474122|pmid-11295749
Importantly, both strategies are applicable to a wide range of RNA molecules appropriate for structural studies using NMR spectroscopy.
[ "48" ]
135
10,688
0
false
Importantly, both strategies are applicable to a wide range of RNA molecules appropriate for structural studies using NMR spectroscopy.
[]
Importantly, both strategies are applicable to a wide range of RNA molecules appropriate for structural studies using NMR spectroscopy.
true
true
true
true
true
1,700
3
DISCUSSION
0
null
null
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
The PTL at the tip of the apical stem–loop does not have a rigid and well-defined structure.
null
92
10,689
0
false
null
null
The PTL at the tip of the apical stem–loop does not have a rigid and well-defined structure.
true
true
true
true
true
1,701
3
DISCUSSION
0
null
null
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
The refinement with classical NOE and torsion angle restraints resulted in conformations of the triloop, where the two first residues, U12 and G13, alternate between the major and minor groove sides, showing all four possible permutations of minor–major groove conformations of U12 and G13.
null
290
10,690
0
false
null
null
The refinement with classical NOE and torsion angle restraints resulted in conformations of the triloop, where the two first residues, U12 and G13, alternate between the major and minor groove sides, showing all four possible permutations of minor–major groove conformations of U12 and G13.
true
true
true
true
true
1,701
3
DISCUSSION
0
null
null
16,945,960
pmid-12409471|pmid-12409471|pmid-7684464|pmid-8811080|pmid-7690471|pmid-12409471|pmid-10836792|pmid-10836792|pmid-11873757|pmid-7870579|NA|pmid-11073218|pmid-11101890|pmid-10936101|NA
However, only conformations with U12 and G13 in the major and minor groove, respectively, were found to fit also 1H chemical shifts.
null
132
10,691
0
false
null
null
However, only conformations with U12 and G13 in the major and minor groove, respectively, were found to fit also 1H chemical shifts.
true
true
true
true
true
1,701
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
Besides the lack of convergence based on NOE and torsion angle data, there are some additional indications of flexibility within the HBV PTL.
[ "49", "43" ]
141
10,692
0
false
Besides the lack of convergence based on NOE and torsion angle data, there are some additional indications of flexibility within the HBV PTL.
[]
Besides the lack of convergence based on NOE and torsion angle data, there are some additional indications of flexibility within the HBV PTL.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
First, inclusion of RDCs in the loop refinement (using the magnitude of the alignment tensor determined from the full 27 nt molecule) did not improve the convergence of the loop structures.
[ "49", "43" ]
189
10,693
0
false
First, inclusion of RDCs in the loop refinement (using the magnitude of the alignment tensor determined from the full 27 nt molecule) did not improve the convergence of the loop structures.
[]
First, inclusion of RDCs in the loop refinement (using the magnitude of the alignment tensor determined from the full 27 nt molecule) did not improve the convergence of the loop structures.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
Second, an inspection of the RDCs shows that compared to the stem RDCs, the loop RDCs appear small (Supplementary Figure S3), which could be the result of averaging of RDCs due to motion of the loop residues.
[ "49", "43" ]
208
10,694
0
false
Second, an inspection of the RDCs shows that compared to the stem RDCs, the loop RDCs appear small (Supplementary Figure S3), which could be the result of averaging of RDCs due to motion of the loop residues.
[]
Second, an inspection of the RDCs shows that compared to the stem RDCs, the loop RDCs appear small (Supplementary Figure S3), which could be the result of averaging of RDCs due to motion of the loop residues.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
The same phenomenon is observed for the bulge residues in Loop B RNA from the IRES in Enterovirus (49).
[ "49", "43" ]
103
10,695
1
false
The same phenomenon is observed for the bulge residues in Loop B RNA from the IRES in Enterovirus.
[ "49" ]
The same phenomenon is observed for the bulge residues in Loop B RNA from the IRES in Enterovirus.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
In addition, comparison of experimental and back-calculated 1H chemical shifts suggest the possible presence of flexibility.
[ "49", "43" ]
124
10,696
0
false
In addition, comparison of experimental and back-calculated 1H chemical shifts suggest the possible presence of flexibility.
[]
In addition, comparison of experimental and back-calculated 1H chemical shifts suggest the possible presence of flexibility.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
The loop conformations showing the best correspondence with the experimental 1H chemical shifts have an r.m.s.d.
[ "49", "43" ]
112
10,697
0
false
The loop conformations showing the best correspondence with the experimental 1H chemical shifts have an r.m.s.d.
[]
The loop conformations showing the best correspondence with the experimental 1H chemical shifts have an r.m.s.d.
true
true
true
true
true
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
in the range of ≈0.25–0.30 p.p.m.
[ "49", "43" ]
33
10,698
0
false
in the range of ≈0.25–0.30 p.p.m.
[]
in the range of ≈0.25–0.30 p.p.m.
false
true
true
true
false
1,702
4
DISCUSSION
1
49
[ "b49", "b43" ]
16,945,960
NA|pmid-15808230|pmid-15134450|pmid-11693565
(Supplementary Figure S2).
[ "49", "43" ]
26
10,699
0
false
(Supplementary Figure S2).
[]
(Supplementary Figure S2).
false
false
true
true
false
1,702