Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
The extent to which the detailed conformation of a melting bubble resembles that of a transient base pair flip-out is, however, presently unknown.
[ "14" ]
146
1,000
0
false
The extent to which the detailed conformation of a melting bubble resembles that of a transient base pair flip-out is, however, presently unknown.
[]
The extent to which the detailed conformation of a melting bubble resembles that of a transient base pair flip-out is, however, presently unknown.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
The well-known ability of a base pair mismatch to disrupt local base pairing as well as stacking, nonetheless, makes it a reasonable analog of the base pair flip-out.
[ "14" ]
166
1,001
0
false
The well-known ability of a base pair mismatch to disrupt local base pairing as well as stacking, nonetheless, makes it a reasonable analog of the base pair flip-out.
[]
The well-known ability of a base pair mismatch to disrupt local base pairing as well as stacking, nonetheless, makes it a reasonable analog of the base pair flip-out.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
Precisely how these bubbles change the conformation as well as the local stiffness of DNA remains an open question.
[ "14" ]
115
1,002
0
false
Precisely how these bubbles change the conformation as well as the local stiffness of DNA remains an open question.
[]
Precisely how these bubbles change the conformation as well as the local stiffness of DNA remains an open question.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
To quantify these effects, time-dependent fluorescence resonance energy transfer (FRET) experiments will be used to measure the distance, and its fluctuation amplitude, between donor and acceptor fluorophores appended to the two ends of a short DNA fragment.
[ "14" ]
258
1,003
0
false
To quantify these effects, time-dependent fluorescence resonance energy transfer (FRET) experiments will be used to measure the distance, and its fluctuation amplitude, between donor and acceptor fluorophores appended to the two ends of a short DNA fragment.
[]
To quantify these effects, time-dependent fluorescence resonance energy transfer (FRET) experiments will be used to measure the distance, and its fluctuation amplitude, between donor and acceptor fluorophores appended to the two ends of a short DNA fragment.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
Time dependent FRET measurements are preferable to single-molecule fluorescence experiments (14), for at least two reasons.
[ "14" ]
123
1,004
1
false
Time dependent FRET measurements are preferable to single-molecule fluorescence experiments, for at least two reasons.
[ "14" ]
Time dependent FRET measurements are preferable to single-molecule fluorescence experiments, for at least two reasons.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
First, they avoid inevitable complications in the analyte's conformation induced by its attachment to a surface.
[ "14" ]
112
1,005
0
false
First, they avoid inevitable complications in the analyte's conformation induced by its attachment to a surface.
[]
First, they avoid inevitable complications in the analyte's conformation induced by its attachment to a surface.
true
true
true
true
true
177
5
INTRODUCTION
1
14
[ "b14" ]
16,954,151
NA
Second, the higher signal to noise levels possible with FRET permit direct correlation between DNA local flexibility and its conformational state.
[ "14" ]
146
1,006
0
false
Second, the higher signal to noise levels possible with FRET permit direct correlation between DNA local flexibility and its conformational state.
[]
Second, the higher signal to noise levels possible with FRET permit direct correlation between DNA local flexibility and its conformational state.
true
true
true
true
true
177
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,000,640
pmid-11237011|pmid-15016989
Long interspersed elements (LINEs) and short interspersed elements (SINEs) are mobile genetic elements that transpose through an RNA intermediate.
[ "1", "2" ]
146
1,007
0
false
Long interspersed elements (LINEs) and short interspersed elements (SINEs) are mobile genetic elements that transpose through an RNA intermediate.
[]
Long interspersed elements (LINEs) and short interspersed elements (SINEs) are mobile genetic elements that transpose through an RNA intermediate.
true
true
true
true
true
178
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,000,640
pmid-11237011|pmid-15016989
LINEs and SINEs exist in many kinds of eukaryotic genomes where they constitute a significant portion of the host genomic DNA.
[ "1", "2" ]
126
1,008
0
false
LINEs and SINEs exist in many kinds of eukaryotic genomes where they constitute a significant portion of the host genomic DNA.
[]
LINEs and SINEs exist in many kinds of eukaryotic genomes where they constitute a significant portion of the host genomic DNA.
true
true
true
true
true
178
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,000,640
pmid-11237011|pmid-15016989
For example, the haploid human genome contains ∼850 000 LINE copies and 1 500 000
[ "1", "2" ]
81
1,009
0
false
For example, the haploid human genome contains ∼850 000 LINE copies and 1 500 000
[]
For example, the haploid human genome contains ∼850 000 LINE copies and 1 500 000
true
true
false
true
false
178
0
INTRODUCTION
1
1
[ "b1", "b2" ]
17,000,640
pmid-11237011|pmid-15016989
SINE copies, which cover ∼21 and ∼13% of the human genome, respectively (1).
[ "1", "2" ]
76
1,010
1
false
SINE copies, which cover ∼21 and ∼13% of the human genome, respectively.
[ "1" ]
SINE copies, which cover ∼21 and ∼13% of the human genome, respectively.
true
true
true
true
true
178
0
INTRODUCTION
1
2
[ "b1", "b2" ]
17,000,640
pmid-11237011|pmid-15016989
In addition, LINEs and SINEs are thought to have a large impact on the complexity and evolution of eukaryotic genomes (2).
[ "1", "2" ]
122
1,011
1
false
In addition, LINEs and SINEs are thought to have a large impact on the complexity and evolution of eukaryotic genomes.
[ "2" ]
In addition, LINEs and SINEs are thought to have a large impact on the complexity and evolution of eukaryotic genomes.
true
true
true
true
true
178
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
LINEs and SINEs are first transcribed into RNA, which is then reverse transcribed into complementary DNA that is subsequently integrated into a new location within the host genome.
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
180
1,012
0
false
LINEs and SINEs are first transcribed into RNA, which is then reverse transcribed into complementary DNA that is subsequently integrated into a new location within the host genome.
[]
LINEs and SINEs are first transcribed into RNA, which is then reverse transcribed into complementary DNA that is subsequently integrated into a new location within the host genome.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
This ‘copy-and-paste’ mechanism is called retrotransposition and the number of these elements expands by this process.
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
118
1,013
0
false
This ‘copy-and-paste’ mechanism is called retrotransposition and the number of these elements expands by this process.
[]
This ‘copy-and-paste’ mechanism is called retrotransposition and the number of these elements expands by this process.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
LINEs encode an endonuclease (EN) and a reverse transcriptase (RT), each of which is required for LINE retrotransposition (3–7).
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
128
1,014
0
false
LINEs encode an endonuclease (EN) and a reverse transcriptase (RT), each of which is required for LINE retrotransposition.
[ "3–7" ]
LINEs encode an endonuclease (EN) and a reverse transcriptase (RT), each of which is required for LINE retrotransposition.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
The LINE-encoded EN nicks a target site DNA, thereby generating a free 3′-OH group; the LINE-encoded RT then reverse transcribes its own RNA using the 3′-OH as a primer (8,9).
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
175
1,015
0
false
The LINE-encoded EN nicks a target site DNA, thereby generating a free 3′-OH group; the LINE-encoded RT then reverse transcribes its own RNA using the 3′-OH as a primer.
[ "8,9" ]
The LINE-encoded EN nicks a target site DNA, thereby generating a free 3′-OH group; the LINE-encoded RT then reverse transcribes its own RNA using the 3′-OH as a primer.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
This process by which a LINE element is integrated into a host genomic DNA is termed target-primed reverse transcription (TPRT).
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
128
1,016
0
false
This process by which a LINE element is integrated into a host genomic DNA is termed target-primed reverse transcription (TPRT).
[]
This process by which a LINE element is integrated into a host genomic DNA is termed target-primed reverse transcription (TPRT).
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
LINE-encoded proteins should distinguish their own RNA from host mRNAs so that the LINE RNA is selectively reverse transcribed.
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
127
1,017
0
false
LINE-encoded proteins should distinguish their own RNA from host mRNAs so that the LINE RNA is selectively reverse transcribed.
[]
LINE-encoded proteins should distinguish their own RNA from host mRNAs so that the LINE RNA is selectively reverse transcribed.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
Some LINE-encoded proteins recognize their respective LINE RNAs through a specific sequence in the 3′-terminal tail (10–12).
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
124
1,018
0
false
Some LINE-encoded proteins recognize their respective LINE RNAs through a specific sequence in the 3′-terminal tail.
[ "10–12" ]
Some LINE-encoded proteins recognize their respective LINE RNAs through a specific sequence in the 3′-terminal tail.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
However, the structural basis by which a LINE protein recognizes a respective LINE RNA has not been elucidated.
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
111
1,019
0
false
However, the structural basis by which a LINE protein recognizes a respective LINE RNA has not been elucidated.
[]
However, the structural basis by which a LINE protein recognizes a respective LINE RNA has not been elucidated.
true
true
true
true
true
179
1
INTRODUCTION
1
3
[ "b3", "b7", "b8", "b9", "b10", "b12", "b7", "b13", "b14" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
The mammalian LINE, L1, which recognizes its own RNA through a poly A tail without a specific sequence at the 3′ tail (7,13,14), is the only exception, although the mechanism by which the L1 RT distinguishes its own RNA from endogenous host mRNAs also has not been elucidated.
[ "3", "7", "8", "9", "10", "12", "7", "13", "14" ]
276
1,020
0
false
The mammalian LINE, L1, which recognizes its own RNA through a poly A tail without a specific sequence at the 3′ tail, is the only exception, although the mechanism by which the L1 RT distinguishes its own RNA from endogenous host mRNAs also has not been elucidated.
[ "7,13,14" ]
The mammalian LINE, L1, which recognizes its own RNA through a poly A tail without a specific sequence at the 3′ tail, is the only exception, although the mechanism by which the L1 RT distinguishes its own RNA from endogenous host mRNAs also has not been elucidated.
true
true
true
true
true
179
2
INTRODUCTION
1
11
[ "b11", "b15", "b17", "b18", "b19" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
SINEs differ from LINEs in that they do not encode any protein(s) required for their own retrotransposition.
[ "11", "15", "17", "18", "19" ]
108
1,021
0
false
SINEs differ from LINEs in that they do not encode any protein(s) required for their own retrotransposition.
[]
SINEs differ from LINEs in that they do not encode any protein(s) required for their own retrotransposition.
true
true
true
true
true
180
2
INTRODUCTION
1
11
[ "b11", "b15", "b17", "b18", "b19" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
However, many SINEs and LINEs share a common 3′ tail sequence and research has shown that these SINEs utilize this common 3′ tail sequence to exploit the enzymatic machinery of LINEs for retrotransposition (11,15–17).
[ "11", "15", "17", "18", "19" ]
217
1,022
0
false
However, many SINEs and LINEs share a common 3′ tail sequence and research has shown that these SINEs utilize this common 3′ tail sequence to exploit the enzymatic machinery of LINEs for retrotransposition.
[ "11,15–17" ]
However, many SINEs and LINEs share a common 3′ tail sequence and research has shown that these SINEs utilize this common 3′ tail sequence to exploit the enzymatic machinery of LINEs for retrotransposition.
true
true
true
true
true
180
2
INTRODUCTION
1
11
[ "b11", "b15", "b17", "b18", "b19" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
In addition, L1 can also mobilize the mammalian SINEs, Alu, B1 and B2, through the poly (A) tail (18,19).
[ "11", "15", "17", "18", "19" ]
105
1,023
0
false
In addition, L1 can also mobilize the mammalian SINEs, Alu, B1 and B2, through the poly (A) tail.
[ "18,19" ]
In addition, L1 can also mobilize the mammalian SINEs, Alu, B1 and B2, through the poly (A) tail.
true
true
true
true
true
180
2
INTRODUCTION
1
11
[ "b11", "b15", "b17", "b18", "b19" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
Thus, SINEs are, so to speak, non-autonomous transposable elements that parasitize LINEs.
[ "11", "15", "17", "18", "19" ]
89
1,024
0
false
Thus, SINEs are, so to speak, non-autonomous transposable elements that parasitize LINEs.
[]
Thus, SINEs are, so to speak, non-autonomous transposable elements that parasitize LINEs.
true
true
true
true
true
180
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
Previously, we isolated one LINE (UnaL2) and two SINEs (UnaSINE1 and UnaSINE2) from the eel genome (11,17).
[ "11", "17", "11", "17", "11", "11" ]
107
1,025
0
false
Previously, we isolated one LINE (UnaL2) and two SINEs (UnaSINE1 and UnaSINE2) from the eel genome.
[ "11,17" ]
Previously, we isolated one LINE (UnaL2) and two SINEs from the eel genome.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
These elements have a conserved 3′ tail of ∼60 bp, the terminus of which has a repeated sequence (Figure 1A and B).
[ "11", "17", "11", "17", "11", "11" ]
115
1,026
0
false
These elements have a conserved 3′ tail of ∼60 bp, the terminus of which has a repeated sequence (Figure 1A and B).
[]
These elements have a conserved 3′ tail of ∼60 bp, the terminus of which has a repeated sequence.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
Using a retrotransposition assay in HeLa cells, we showed that the 3′ conserved tail of UnaL2 is required for retrotransposition of UnaL2.
[ "11", "17", "11", "17", "11", "11" ]
138
1,027
0
false
Using a retrotransposition assay in HeLa cells, we showed that the 3′ conserved tail of UnaL2 is required for retrotransposition of UnaL2.
[]
Using a retrotransposition assay in HeLa cells, we showed that the 3′ conserved tail of UnaL2 is required for retrotransposition of UnaL2.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
In addition, an element that we introduced, which contained the 3′ tail of UnaL2, UnaSINE1 or UnaSINE2,could be mobilized efficiently by the UnaL2 retrotransposition machinery in trans (11,17).
[ "11", "17", "11", "17", "11", "11" ]
193
1,028
0
false
In addition, an element that we introduced, which contained the 3′ tail of UnaL2, UnaSINE1 or UnaSINE2,could be mobilized efficiently by the UnaL2 retrotransposition machinery in trans.
[ "11,17" ]
In addition, an element that we introduced, which contained the 3′ tail of UnaL2, UnaSINE1 or UnaSINE2,could be mobilized efficiently by the UnaL2 retrotransposition machinery in trans.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
These results indicated that the 3′ tail of these elements is the only cis element required for retrotransposition and that UnaSINEs are mobilized by UnaL2.
[ "11", "17", "11", "17", "11", "11" ]
156
1,029
0
false
These results indicated that the 3′ tail of these elements is the only cis element required for retrotransposition and that UnaSINEs are mobilized by UnaL2.
[]
These results indicated that the 3′ tail of these elements is the only cis element required for retrotransposition and that UnaSINEs are mobilized by UnaL2.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
These results suggest that the 3′ tails contain a unique sequence specifically recognized by the UnaL2 protein, UnaL2p.
[ "11", "17", "11", "17", "11", "11" ]
119
1,030
0
false
These results suggest that the 3′ tails contain a unique sequence specifically recognized by the UnaL2 protein, UnaL2p.
[]
These results suggest that the 3′ tails contain a unique sequence specifically recognized by the UnaL2 protein, UnaL2p.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
The conserved 3′ tail of UnaL2 RNA has two parts, namely the stem–loop region and the 3′-terminal ([UGUAA]n) repeat (usually n = 3), both of which are required—apparently in distinct ways—for UnaL2 retrotransposition (Figure 1C)
[ "11", "17", "11", "17", "11", "11" ]
228
1,031
0
false
The conserved 3′ tail of UnaL2 RNA has two parts, namely the stem–loop region and the 3′-terminal ([UGUAA]n) repeat (usually n = 3), both of which are required—apparently in distinct ways—for UnaL2 retrotransposition (Figure 1C)
[]
The conserved 3′ tail of UnaL2 RNA has two parts, namely the stem–loop region and the 3′-terminal ([UGUAA]n) repeat (usually n = 3), both of which are required—apparently in distinct ways—for UnaL2 retrotransposition
true
true
false
true
false
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
Reverse transcription of the UnaL2 RNA is initiated from the 3′-terminal repeat and proceeds upstream of UnaL2 RNA through the 3′ conserved region.
[ "11", "17", "11", "17", "11", "11" ]
147
1,032
0
false
Reverse transcription of the UnaL2 RNA is initiated from the 3′-terminal repeat and proceeds upstream of UnaL2 RNA through the 3′ conserved region.
[]
Reverse transcription of the UnaL2 RNA is initiated from the 3′-terminal repeat and proceeds upstream of UnaL2 RNA through the 3′ conserved region.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
A template slippage reaction, which is reminiscent of telomere elongation by telomerase, occurs when the reverse transcription of UnaL2 RNA is initiated from the 3′-terminal repeat (11).
[ "11", "17", "11", "17", "11", "11" ]
186
1,033
1
false
A template slippage reaction, which is reminiscent of telomere elongation by telomerase, occurs when the reverse transcription of UnaL2 RNA is initiated from the 3′-terminal repeat.
[ "11" ]
A template slippage reaction, which is reminiscent of telomere elongation by telomerase, occurs when the reverse transcription of UnaL2 RNA is initiated from the 3′-terminal repeat.
true
true
true
true
true
181
3
INTRODUCTION
1
11
[ "b11", "b17", "b11", "b17", "b11", "b11" ]
17,000,640
pmid-12419252|pmid-15548748|pmid-12419252|pmid-15548748|pmid-12419252|pmid-12419252
‘Repetition’ of the 3′-terminal repeat is probably prerequisite for template slippage, although the role of repetition in retrotransposition has not been elucidated.
[ "11", "17", "11", "17", "11", "11" ]
165
1,034
0
false
‘Repetition’ of the 3′-terminal repeat is probably prerequisite for template slippage, although the role of repetition in retrotransposition has not been elucidated.
[]
‘Repetition’ of the 3′-terminal repeat is probably prerequisite for template slippage, although the role of repetition in retrotransposition has not been elucidated.
false
false
true
true
false
181
4
INTRODUCTION
1
20
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
A part of UnaL2 RNA is predicted to form a stem–loop secondary structure in which the stem is divided into two parts by a putative internal loop (Figure 1C).
[ "20", "20", "11" ]
157
1,035
0
false
A part of UnaL2 RNA is predicted to form a stem–loop secondary structure in which the stem is divided into two parts by a putative internal loop (Figure 1C).
[]
A part of UnaL2 RNA is predicted to form a stem–loop secondary structure in which the stem is divided into two parts by a putative internal loop (Figure 1C).
true
true
true
true
true
182
4
INTRODUCTION
1
20
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
We previously determined the solution structure of the upper stem–loop region (LINE17 RNA) and confirmed that this region indeed forms a stem–loop (20).
[ "20", "20", "11" ]
152
1,036
1
false
We previously determined the solution structure of the upper stem–loop region (LINE17 RNA) and confirmed that this region indeed forms a stem–loop.
[ "20" ]
We previously determined the solution structure of the upper stem–loop region (LINE17 RNA) and confirmed that this region indeed forms a stem–loop.
true
true
true
true
true
182
4
INTRODUCTION
1
20
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
The GGAUA loop forms a specific structure in which the uridine is exposed to the solvent and the adenosines are stacked.
[ "20", "20", "11" ]
120
1,037
0
false
The GGAUA loop forms a specific structure in which the uridine is exposed to the solvent and the adenosines are stacked.
[]
The GGAUA loop forms a specific structure in which the uridine is exposed to the solvent and the adenosines are stacked.
true
true
true
true
true
182
4
INTRODUCTION
1
20
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
The second guanosine stacks on the first guanosine and a sharp turn in the phosphodiester backbone occurs between the second guanosine and the adenosine at position 3.
[ "20", "20", "11" ]
167
1,038
0
false
The second guanosine stacks on the first guanosine and a sharp turn in the phosphodiester backbone occurs between the second guanosine and the adenosine at position 3.
[]
The second guanosine stacks on the first guanosine and a sharp turn in the phosphodiester backbone occurs between the second guanosine and the adenosine at position 3.
true
true
true
true
true
182
4
INTRODUCTION
1
20
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
Mutational analysis suggested that the particular GGAUA loop structure is requisite for retrotransposition and that UnaL2p specifically recognizes the second guanosine during retrotransposition (20).
[ "20", "20", "11" ]
199
1,039
1
false
Mutational analysis suggested that the particular GGAUA loop structure is requisite for retrotransposition and that UnaL2p specifically recognizes the second guanosine during retrotransposition.
[ "20" ]
Mutational analysis suggested that the particular GGAUA loop structure is requisite for retrotransposition and that UnaL2p specifically recognizes the second guanosine during retrotransposition.
true
true
true
true
true
182
4
INTRODUCTION
1
11
[ "b20", "b20", "b11" ]
17,000,640
pmid-15273327|pmid-15273327|pmid-12419252
Although the significance of the stem and putative internal loop structures on retrotransposition has not been thoroughly examined, deletion of the entire putative internal loop abolishes UnaL2 retrotransposition, suggesting that this region is required for the retrotransposition reaction (11).
[ "20", "20", "11" ]
295
1,040
1
false
Although the significance of the stem and putative internal loop structures on retrotransposition has not been thoroughly examined, deletion of the entire putative internal loop abolishes UnaL2 retrotransposition, suggesting that this region is required for the retrotransposition reaction.
[ "11" ]
Although the significance of the stem and putative internal loop structures on retrotransposition has not been thoroughly examined, deletion of the entire putative internal loop abolishes UnaL2 retrotransposition, suggesting that this region is required for the retrotransposition reaction.
true
true
true
true
true
182
5
INTRODUCTION
0
null
null
17,000,640
null
In the present study, we used NMR techniques with residual dipolar coupling (RDC) restraints to determine the solution structure of a 36 nt RNA, denoted LINE36, that contains nearly the entire stem–loop of UnaL2 RNA including the putative internal loop (Figure 1D).
null
265
1,041
0
false
null
null
In the present study, we used NMR techniques with residual dipolar coupling (RDC) restraints to determine the solution structure of a 36 nt RNA, denoted LINE36, that contains nearly the entire stem–loop of UnaL2 RNA including the putative internal loop (Figure 1D).
true
true
true
true
true
183
5
INTRODUCTION
0
null
null
17,000,640
null
Our results revealed that the putative internal loop region has a compact conformation with a bulged cytidine and a U–U mismatch that separate the upper and lower stems.
null
169
1,042
0
false
null
null
Our results revealed that the putative internal loop region has a compact conformation with a bulged cytidine and a U–U mismatch that separate the upper and lower stems.
true
true
true
true
true
183
5
INTRODUCTION
0
null
null
17,000,640
null
Although the upper and lower stems are nearly coaxial and thus appear to be a single long stem, molecular dynamics simulation showed that the entire stem fluctuates anisotropically by utilizing the bulged cytidine and U–U mismatch region as a hinge.
null
249
1,043
0
false
null
null
Although the upper and lower stems are nearly coaxial and thus appear to be a single long stem, molecular dynamics simulation showed that the entire stem fluctuates anisotropically by utilizing the bulged cytidine and U–U mismatch region as a hinge.
true
true
true
true
true
183
5
INTRODUCTION
0
null
null
17,000,640
null
Mutational analysis indicated that the bulged cytidine and U–U mismatch are required for efficient retrotransposition.
null
118
1,044
0
false
null
null
Mutational analysis indicated that the bulged cytidine and U–U mismatch are required for efficient retrotransposition.
true
true
true
true
true
183
0
DISCUSSION
0
null
null
17,000,640
pmid-11237011|pmid-15016989
We determined the solution structure of the 3′ conserved region of UnaL2 RNA.
null
77
1,045
0
false
null
null
We determined the solution structure of the 3′ conserved region of UnaL2 RNA.
true
true
true
true
true
184
0
DISCUSSION
0
null
null
17,000,640
pmid-11237011|pmid-15016989
The hinge region forms a compact structure comprising base pairs U10–U28/G9–C29 and the bulged C8.
null
98
1,046
0
false
null
null
The hinge region forms a compact structure comprising base pairs U10–U28/G9–C29 and the bulged C8.
true
true
true
true
true
184
0
DISCUSSION
0
null
null
17,000,640
pmid-11237011|pmid-15016989
The two stems separated by the bulged cytidine look like a single long stem.
null
76
1,047
0
false
null
null
The two stems separated by the bulged cytidine look like a single long stem.
true
true
true
true
true
184
0
DISCUSSION
0
null
null
17,000,640
pmid-11237011|pmid-15016989
The bulged cytidine along with the U–U mismatch in the hinge region probably confers a high degree of flexibility on the entire stem, allowing it to fluctuate anisotropically.
null
175
1,048
0
false
null
null
The bulged cytidine along with the U–U mismatch in the hinge region probably confers a high degree of flexibility on the entire stem, allowing it to fluctuate anisotropically.
true
true
true
true
true
184
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
UnaL2 can mobilize UnaSINE1 and UnaSINE2 because the UnaL2 retrotranspositional machinery recognizes their conserved 3′ tails (11,17).
[ "11", "17", "17" ]
134
1,049
0
false
UnaL2 can mobilize UnaSINE1 and UnaSINE2 because the UnaL2 retrotranspositional machinery recognizes their conserved 3′ tails.
[ "11,17" ]
UnaL2 can mobilize UnaSINE1 and UnaSINE2 because the UnaL2 retrotranspositional machinery recognizes their conserved 3′ tails.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
Putative secondary structures for the 3′ tail RNA of UnaL2 and UnaSINEs are shown in Figure 7A.
[ "11", "17", "17" ]
95
1,050
0
false
Putative secondary structures for the 3′ tail RNA of UnaL2 and UnaSINEs are shown in Figure 7A.
[]
Putative secondary structures for the 3′ tail RNA of UnaL2 and UnaSINEs are shown in Figure 7A.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
The UnaSINE1 structure conserves the bulged nucleotide (A) and the U–U mismatch.
[ "11", "17", "17" ]
80
1,051
0
false
The UnaSINE1 structure conserves the bulged nucleotide (A) and the U–U mismatch.
[]
The UnaSINE1 structure conserves the bulged nucleotide (A) and the U–U mismatch.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
The UnaSINE2 structure, on the other hand, lacks the U–U mismatch but instead has a mismatch between two adenosines, once of which is at the same position (position 8) as the bulged nucleotide of UnaL2/UnaSINE1.
[ "11", "17", "17" ]
211
1,052
0
false
The UnaSINE2 structure, on the other hand, lacks the U–U mismatch but instead has a mismatch between two adenosines, once of which is at the same position (position 8) as the bulged nucleotide of UnaL2/UnaSINE1.
[]
The UnaSINE2 structure, on the other hand, lacks the U–U mismatch but instead has a mismatch between two adenosines, once of which is at the same position (position 8) as the bulged nucleotide of UnaL2/UnaSINE1.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
These adenosines probably impart flexibility to the stem—as in the hinge region of UnaL2—and we speculate that this flexibility is requisite for retrotransposition.
[ "11", "17", "17" ]
164
1,053
0
false
These adenosines probably impart flexibility to the stem—as in the hinge region of UnaL2—and we speculate that this flexibility is requisite for retrotransposition.
[]
These adenosines probably impart flexibility to the stem—as in the hinge region of UnaL2—and we speculate that this flexibility is requisite for retrotransposition.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
To test this point, we predicted secondary structures for the 3′ tail RNA of zebrafish LINEs (and SINE) of the L2 clade (including UnaL2) that have a conserved 3′ tail as UnaL2 by using program Mfold and the sequence alignment with LINE36 (11, 17.
[ "11", "17", "17" ]
247
1,054
0
false
To test this point, we predicted secondary structures for the 3′ tail RNA of zebrafish LINEs (and SINE) of the L2 clade (including UnaL2) that have a conserved 3′ tail as UnaL2 by using program Mfold and the sequence alignment with LINE36 (11, 17.
[]
To test this point, we predicted secondary structures for the 3′ tail RNA of zebrafish LINEs (and SINE) of the L2 clade (including UnaL2) that have a conserved 3′ tail as UnaL2 by using program Mfold and the sequence alignment with LINE36 (11, 17.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
44, 45) (Figure 7B).
[ "11", "17", "17" ]
20
1,055
0
false
44, 45) (Figure 7B).
[]
44, 45) (Figure 7B).
false
false
true
true
false
185
1
DISCUSSION
1
17
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
These elements have similar stem structures, although the loop sequences are highly variable (17).
[ "11", "17", "17" ]
98
1,056
1
false
These elements have similar stem structures, although the loop sequences are highly variable.
[ "17" ]
These elements have similar stem structures, although the loop sequences are highly variable.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
All of these zebrafish elements except for ZfL2-2, which is a zebrafish homolog of UnaL2, have an A–A mismatch-like conformation in the stem.
[ "11", "17", "17" ]
141
1,057
0
false
All of these zebrafish elements except for ZfL2-2, which is a zebrafish homolog of UnaL2, have an A–A mismatch-like conformation in the stem.
[]
All of these zebrafish elements except for ZfL2-2, which is a zebrafish homolog of UnaL2, have an A–A mismatch-like conformation in the stem.
true
true
true
true
true
185
1
DISCUSSION
1
11
[ "b11", "b17", "b17" ]
17,000,640
pmid-2844414|pmid-8945518|pmid-7679954|pmid-12411507|pmid-7540721|pmid-15340053|pmid-8945518|pmid-10742098|pmid-11158327|pmid-12419252|pmid-15548748|pmid-15548748
The conservation of this A–A mismatch structure indicates that conformational flexibility in the stem is important for retrotransposition of LINEs/SINEs of the L2 clade.
[ "11", "17", "17" ]
169
1,058
0
false
The conservation of this A–A mismatch structure indicates that conformational flexibility in the stem is important for retrotransposition of LINEs/SINEs of the L2 clade.
[]
The conservation of this A–A mismatch structure indicates that conformational flexibility in the stem is important for retrotransposition of LINEs/SINEs of the L2 clade.
true
true
true
true
true
185
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
The iron responsive element (IRE), an RNA, contains a stem–loop structure that includes a bulged cytidine, as determined by NMR (46).
[ "46", "46", "11", "20", "11" ]
133
1,059
1
false
The iron responsive element (IRE), an RNA, contains a stem–loop structure that includes a bulged cytidine, as determined by NMR.
[ "46" ]
The iron responsive element (IRE), an RNA, contains a stem–loop structure that includes a bulged cytidine, as determined by NMR.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
It has been proposed that the loop structure of IRE RNA makes direct contact with the iron regulatory proteins and that the bulged cytidine functions to orient the hairpin for optimal protein binding (46).
[ "46", "46", "11", "20", "11" ]
205
1,060
1
false
It has been proposed that the loop structure of IRE RNA makes direct contact with the iron regulatory proteins and that the bulged cytidine functions to orient the hairpin for optimal protein binding.
[ "46" ]
It has been proposed that the loop structure of IRE RNA makes direct contact with the iron regulatory proteins and that the bulged cytidine functions to orient the hairpin for optimal protein binding.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
Analogously, the bulged cytidine of UnaL2 RNA might allow the stem to bend to achieve optimal binding of UnaL2p to the loop.
[ "46", "46", "11", "20", "11" ]
124
1,061
0
false
Analogously, the bulged cytidine of UnaL2 RNA might allow the stem to bend to achieve optimal binding of UnaL2p to the loop.
[]
Analogously, the bulged cytidine of UnaL2 RNA might allow the stem to bend to achieve optimal binding of UnaL2p to the loop.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
However, we propose that the function of the bulged cytidine differs between UnaL2 and the IRE, because the stem–loop of UnaL2 has functional aspects other than protein binding (see below).
[ "46", "46", "11", "20", "11" ]
189
1,062
0
false
However, we propose that the function of the bulged cytidine differs between UnaL2 and the IRE, because the stem–loop of UnaL2 has functional aspects other than protein binding (see below).
[]
However, we propose that the function of the bulged cytidine differs between UnaL2 and the IRE, because the stem–loop of UnaL2 has functional aspects other than protein binding (see below).
true
true
true
true
true
186
2
DISCUSSION
1
11
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
The conserved 3′ tail of UnaL2 RNA is thought to have two different roles in retrotransposition (11).
[ "46", "46", "11", "20", "11" ]
101
1,063
1
false
The conserved 3′ tail of UnaL2 RNA is thought to have two different roles in retrotransposition.
[ "11" ]
The conserved 3′ tail of UnaL2 RNA is thought to have two different roles in retrotransposition.
true
true
true
true
true
186
2
DISCUSSION
1
20
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
First, the conserved 3′ tail loop structure probably acts as a cis element that is recognized by UnaL2p to form a UnaL2 RNA–protein (RNP) complex (20).
[ "46", "46", "11", "20", "11" ]
151
1,064
1
false
First, the conserved 3′ tail loop structure probably acts as a cis element that is recognized by UnaL2p to form a UnaL2 RNA–protein (RNP) complex.
[ "20" ]
First, the conserved 3′ tail loop structure probably acts as a cis element that is recognized by UnaL2p to form a UnaL2 RNA–protein (RNP) complex.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
Second, a repeated sequence in the conserved 3′ end of the RNA acts as a template to initiate reverse transcription.
[ "46", "46", "11", "20", "11" ]
116
1,065
0
false
Second, a repeated sequence in the conserved 3′ end of the RNA acts as a template to initiate reverse transcription.
[]
Second, a repeated sequence in the conserved 3′ end of the RNA acts as a template to initiate reverse transcription.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
When the 3′ stem–loop RNA is reverse transcribed, UnaL2p dissociates from the loop RNA and the stem becomes unstructured to facilitate reverse transcription.
[ "46", "46", "11", "20", "11" ]
157
1,066
0
false
When the 3′ stem–loop RNA is reverse transcribed, UnaL2p dissociates from the loop RNA and the stem becomes unstructured to facilitate reverse transcription.
[]
When the 3′ stem–loop RNA is reverse transcribed, UnaL2p dissociates from the loop RNA and the stem becomes unstructured to facilitate reverse transcription.
true
true
true
true
true
186
2
DISCUSSION
1
11
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
Previously we found that a slippage reaction occurs during reverse transcription of UnaL2 RNA and we proposed that template slippage is required for dissociation of UnaL2p from the loop RNA (11).
[ "46", "46", "11", "20", "11" ]
195
1,067
1
false
Previously we found that a slippage reaction occurs during reverse transcription of UnaL2 RNA and we proposed that template slippage is required for dissociation of UnaL2p from the loop RNA.
[ "11" ]
Previously we found that a slippage reaction occurs during reverse transcription of UnaL2 RNA and we proposed that template slippage is required for dissociation of UnaL2p from the loop RNA.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
UnaL2p repetitively reverse transcribes the UGUAA repeat region during the template slippage reaction and such repetition at the same position should involve repeated conformational changes in the UnaL2 RNP.
[ "46", "46", "11", "20", "11" ]
207
1,068
0
false
UnaL2p repetitively reverse transcribes the UGUAA repeat region during the template slippage reaction and such repetition at the same position should involve repeated conformational changes in the UnaL2 RNP.
[]
UnaL2p repetitively reverse transcribes the UGUAA repeat region during the template slippage reaction and such repetition at the same position should involve repeated conformational changes in the UnaL2 RNP.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
Flexibility of the stem RNA at the hinge imparts spatial plasticity relative to the loop RNA (binding region) and the UGUAA repeat (reverse transcription initiation region) and this plasticity probably facilitates the conformational change in the UnaL2 RNP for template slippage.
[ "46", "46", "11", "20", "11" ]
279
1,069
0
false
Flexibility of the stem RNA at the hinge imparts spatial plasticity relative to the loop RNA (binding region) and the UGUAA repeat (reverse transcription initiation region) and this plasticity probably facilitates the conformational change in the UnaL2 RNP for template slippage.
[]
Flexibility of the stem RNA at the hinge imparts spatial plasticity relative to the loop RNA (binding region) and the UGUAA repeat (reverse transcription initiation region) and this plasticity probably facilitates the conformational change in the UnaL2 RNP for template slippage.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
On the other hand, the bulged nucleotide and the U–U mismatch in the hinge and the A–A mismatch conformation may promote the transition of the stem RNA from double-stranded to single-stranded by a means of making the stem unstable.
[ "46", "46", "11", "20", "11" ]
231
1,070
0
false
On the other hand, the bulged nucleotide and the U–U mismatch in the hinge and the A–A mismatch conformation may promote the transition of the stem RNA from double-stranded to single-stranded by a means of making the stem unstable.
[]
On the other hand, the bulged nucleotide and the U–U mismatch in the hinge and the A–A mismatch conformation may promote the transition of the stem RNA from double-stranded to single-stranded by a means of making the stem unstable.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
There is a bulged nucleotide in the upper stem of many zebrafish LINEs (Figure 7B).
[ "46", "46", "11", "20", "11" ]
83
1,071
0
false
There is a bulged nucleotide in the upper stem of many zebrafish LINEs (Figure 7B).
[]
There is a bulged nucleotide in the upper stem of many zebrafish LINEs (Figure 7B).
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
These bulges probably also facilitate the conformational transition of the stem RNAs; they do not seem to have a particular role in retrotransposition, however, because they have not been conserved.
[ "46", "46", "11", "20", "11" ]
198
1,072
0
false
These bulges probably also facilitate the conformational transition of the stem RNAs; they do not seem to have a particular role in retrotransposition, however, because they have not been conserved.
[]
These bulges probably also facilitate the conformational transition of the stem RNAs; they do not seem to have a particular role in retrotransposition, however, because they have not been conserved.
true
true
true
true
true
186
2
DISCUSSION
1
46
[ "b46", "b46", "b11", "b20", "b11" ]
17,000,640
pmid-12419252|pmid-9461397|pmid-15548748|pmid-12897783|pmid-15890192|pmid-9398517|pmid-9398517|pmid-12419252|pmid-15273327|pmid-12419252
The dynamic stability of these stem RNAs is an elegant example of the ability of an RNA structure to dictate biological function based on two distinct conformational states.
[ "46", "46", "11", "20", "11" ]
173
1,073
0
false
The dynamic stability of these stem RNAs is an elegant example of the ability of an RNA structure to dictate biological function based on two distinct conformational states.
[]
The dynamic stability of these stem RNAs is an elegant example of the ability of an RNA structure to dictate biological function based on two distinct conformational states.
true
true
true
true
true
186
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
The most intuitive decomposition of the binding free energy involves four terms (1–3): van der Waals (vdW) interactions, electrostatic, hydrophobicity and configurational entropy.
[ "1–3", "1", "1", "4", "2", "5–8" ]
179
1,074
1
false
The most intuitive decomposition of the binding free energy involves four terms : van der Waals (vdW) interactions, electrostatic, hydrophobicity and configurational entropy.
[ "1–3" ]
The most intuitive decomposition of the binding free energy involves four terms : van der Waals (vdW) interactions, electrostatic, hydrophobicity and configurational entropy.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
The relative contribution of the changes between the bound and free states of these four terms is not the same.
[ "1–3", "1", "1", "4", "2", "5–8" ]
111
1,075
0
false
The relative contribution of the changes between the bound and free states of these four terms is not the same.
[]
The relative contribution of the changes between the bound and free states of these four terms is not the same.
true
true
true
true
true
187
0
INTRODUCTION
1
1
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
For stability (1), the main contributions appear to be electrostatic and desolvation interactions.
[ "1–3", "1", "1", "4", "2", "5–8" ]
98
1,076
1
false
For stability, the main contributions appear to be electrostatic and desolvation interactions.
[ "1" ]
For stability, the main contributions appear to be electrostatic and desolvation interactions.
true
true
true
true
true
187
0
INTRODUCTION
1
1
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
For refined docked conformations, vdW interactions are expected to balance between the bound and unbound state, as they seemingly do in protein folding (1).
[ "1–3", "1", "1", "4", "2", "5–8" ]
156
1,077
1
false
For refined docked conformations, vdW interactions are expected to balance between the bound and unbound state, as they seemingly do in protein folding.
[ "1" ]
For refined docked conformations, vdW interactions are expected to balance between the bound and unbound state, as they seemingly do in protein folding.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
This is good news, since it is not yet possible to readily estimate solute–solvent interactions.
[ "1–3", "1", "1", "4", "2", "5–8" ]
96
1,078
0
false
This is good news, since it is not yet possible to readily estimate solute–solvent interactions.
[]
This is good news, since it is not yet possible to readily estimate solute–solvent interactions.
true
true
true
true
true
187
0
INTRODUCTION
1
4
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
It should be noted, however, that solute–solute vdW has been shown to be an important consideration for complex refinement (4).
[ "1–3", "1", "1", "4", "2", "5–8" ]
127
1,079
1
false
It should be noted, however, that solute–solute vdW has been shown to be an important consideration for complex refinement.
[ "4" ]
It should be noted, however, that solute–solute vdW has been shown to be an important consideration for complex refinement.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
Configurational entropy loss upon binding, including rotational and translational degrees of freedom, is always important, rough estimates based on crystal complexes varying between 5 and 15 kcal/mol (2,5–8).
[ "1–3", "1", "1", "4", "2", "5–8" ]
208
1,080
0
false
Configurational entropy loss upon binding, including rotational and translational degrees of freedom, is always important, rough estimates based on crystal complexes varying between 5 and 15 kcal/mol.
[ "2,5–8" ]
Configurational entropy loss upon binding, including rotational and translational degrees of freedom, is always important, rough estimates based on crystal complexes varying between 5 and 15 kcal/mol.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
For the most part, this entropy depends on the flexibility of the unbound or free state with respect to the bound, with smaller corrections depending on the docking geometry.
[ "1–3", "1", "1", "4", "2", "5–8" ]
174
1,081
0
false
For the most part, this entropy depends on the flexibility of the unbound or free state with respect to the bound, with smaller corrections depending on the docking geometry.
[]
For the most part, this entropy depends on the flexibility of the unbound or free state with respect to the bound, with smaller corrections depending on the docking geometry.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
Since there is no robust estimate of entropy for a given protein, empirical free energy estimates, like ‘FastContact’, are always subject to an entropic correction.
[ "1–3", "1", "1", "4", "2", "5–8" ]
164
1,082
0
false
Since there is no robust estimate of entropy for a given protein, empirical free energy estimates, like ‘FastContact’, are always subject to an entropic correction.
[]
Since there is no robust estimate of entropy for a given protein, empirical free energy estimates, like ‘FastContact’, are always subject to an entropic correction.
true
true
true
true
true
187
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B1", "B1", "B4", "B2", "B5 B6 B7 B8" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
Hence, the server is most useful for discrimination between protein–protein docked complexes, and, more generally, for identifying energetically important contacts at the interface.
[ "1–3", "1", "1", "4", "2", "5–8" ]
181
1,083
0
false
Hence, the server is most useful for discrimination between protein–protein docked complexes, and, more generally, for identifying energetically important contacts at the interface.
[]
Hence, the server is most useful for discrimination between protein–protein docked complexes, and, more generally, for identifying energetically important contacts at the interface.
true
true
true
true
true
187
1
INTRODUCTION
1
11
[ "B9", "B10", "B11", "B7" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
‘FastContact’, originally published in (9,10) rapidly estimates the electrostatic and desolvation component of the free energy based on a classic distance dependent dielectric 4r (11) and an empirical contact potential for the desolvation contribution (7) developed using a database of crystal (no complexes) structures ...
[ "9", "10", "11", "7" ]
333
1,084
1
false
‘FastContact’, originally published in rapidly estimates the electrostatic and desolvation component of the free energy based on a classic distance dependent dielectric 4r and an empirical contact potential for the desolvation contribution developed using a database of crystal (no complexes) structures from the PDB.
[ "9,10", "11", "7" ]
‘FastContact’, originally published in rapidly estimates the electrostatic and desolvation component of the free energy based on a classic distance dependent dielectric 4r and an empirical contact potential for the desolvation contribution developed using a database of crystal (no complexes) structures from the PDB.
false
false
true
true
false
188
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B7" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
Because of the pairwise nature of the empirical interactions, ‘FastContact’ is also able to report the contribution of individual residues and pairs of residues to the free energy.
[ "9", "10", "11", "7" ]
180
1,085
0
false
Because of the pairwise nature of the empirical interactions, ‘FastContact’ is also able to report the contribution of individual residues and pairs of residues to the free energy.
[]
Because of the pairwise nature of the empirical interactions, ‘FastContact’ is also able to report the contribution of individual residues and pairs of residues to the free energy.
true
true
true
true
true
188
1
INTRODUCTION
1
9
[ "B9", "B10", "B11", "B7" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
The latter should prove useful for site-directed mutagenesis studies since rankings of these interactions consistently identify the hot spots in the interface.
[ "9", "10", "11", "7" ]
159
1,086
0
false
The latter should prove useful for site-directed mutagenesis studies since rankings of these interactions consistently identify the hot spots in the interface.
[]
The latter should prove useful for site-directed mutagenesis studies since rankings of these interactions consistently identify the hot spots in the interface.
true
true
true
true
true
188
0
DISCUSSION
1
14
[ "B14", "B4", "B17", "B18", "B19", "B15", "B20" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
The method implemented in ‘FastContact’ has been successfully applied in the CAPRI experiment both as a free energy filtering procedure of the ‘ClusPro’ server (14) that predicts protein complexes and in protein–protein refinement (4) (using a 9 and 6 Å desolvation range, respectively).
[ "14", "4", "17", "18", "19", "15", "20" ]
287
1,087
1
false
The method implemented in ‘FastContact’ has been successfully applied in the CAPRI experiment both as a free energy filtering procedure of the ‘ClusPro’ server that predicts protein complexes and in protein–protein refinement (using a 9 and 6 Å desolvation range, respectively).
[ "14", "4" ]
The method implemented in ‘FastContact’ has been successfully applied in the CAPRI experiment both as a free energy filtering procedure of the ‘ClusPro’ server that predicts protein complexes and in protein–protein refinement (using a 9 and 6 Å desolvation range, respectively).
true
true
true
true
true
189
0
DISCUSSION
1
14
[ "B14", "B4", "B17", "B18", "B19", "B15", "B20" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
‘FastContact’ has been instrumental in the success of our group in blind predictions (17,18).
[ "14", "4", "17", "18", "19", "15", "20" ]
93
1,088
0
false
‘FastContact’ has been instrumental in the success of our group in blind predictions.
[ "17,18" ]
‘FastContact’ has been instrumental in the success of our group in blind predictions.
false
false
true
true
false
189
0
DISCUSSION
1
19
[ "B14", "B4", "B17", "B18", "B19", "B15", "B20" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
In rounds 1 and 2 of CAPRI, Camacho and Gatchell (19) produced some of the best model structures, appropriately distinguishing between near-native and false positive structures for three targets.
[ "14", "4", "17", "18", "19", "15", "20" ]
195
1,089
1
false
In rounds 1 and 2 of CAPRI, Camacho and Gatchell produced some of the best model structures, appropriately distinguishing between near-native and false positive structures for three targets.
[ "19" ]
In rounds 1 and 2 of CAPRI, Camacho and Gatchell produced some of the best model structures, appropriately distinguishing between near-native and false positive structures for three targets.
true
true
true
true
true
189
0
DISCUSSION
1
15
[ "B14", "B4", "B17", "B18", "B19", "B15", "B20" ]
17,537,824
NA|pmid-2475171|pmid-8819974|NA|NA|pmid-11517309|pmid-2475171|pmid-11159432|pmid-7947806|pmid-9126848|pmid-15162489|pmid-15215358|pmid-11517309|pmid-12784368|pmid-15981261|pmid-12784373|pmid-15981265|pmid-15981253
In rounds 3–5, the automated server ‘ClusPro’ (the only server participating in CAPRI) predicted good models for 5 targets (15), while our manual predictions resulted in good predictions for 6 targets (20) (missing the 3 targets that had a significant structural rearrangement upon binding).
[ "14", "4", "17", "18", "19", "15", "20" ]
291
1,090
1
false
In rounds 3–5, the automated server ‘ClusPro’ (the only server participating in CAPRI) predicted good models for 5 targets, while our manual predictions resulted in good predictions for 6 targets (missing the 3 targets that had a significant structural rearrangement upon binding).
[ "15", "20" ]
In rounds 3–5, the automated server ‘ClusPro’ (the only server participating in CAPRI) predicted good models for 5 targets, while our manual predictions resulted in good predictions for 6 targets (missing the 3 targets that had a significant structural rearrangement upon binding).
true
true
true
true
true
189
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
The robustness of our method was further supported by the analysis of the full set of models submitted for CAPRI (rounds 3–5) for the 6 targets that did not undergo a large structural rearrangement upon binding (18).
[ "18", "10", "23–33", "10" ]
216
1,091
1
false
The robustness of our method was further supported by the analysis of the full set of models submitted for CAPRI (rounds 3–5) for the 6 targets that did not undergo a large structural rearrangement upon binding.
[ "18" ]
The robustness of our method was further supported by the analysis of the full set of models submitted for CAPRI (rounds 3–5) for the 6 targets that did not undergo a large structural rearrangement upon binding.
true
true
true
true
true
190
1
DISCUSSION
1
10
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For these targets, we showed that ‘FastContact’ was able to discriminate near-native predictions from docked conformations far from the binding site for 5 of the targets (10), and for all but one of the manual predictions submitted to CAPRI.
[ "18", "10", "23–33", "10" ]
241
1,092
1
false
For these targets, we showed that ‘FastContact’ was able to discriminate near-native predictions from docked conformations far from the binding site for 5 of the targets, and for all but one of the manual predictions submitted to CAPRI.
[ "10" ]
For these targets, we showed that ‘FastContact’ was able to discriminate near-native predictions from docked conformations far from the binding site for 5 of the targets, and for all but one of the manual predictions submitted to CAPRI.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For instance, Figure 3 shows the re-scoring of models submitted for targets 8 and 12 by 13 different groups around the world.
[ "18", "10", "23–33", "10" ]
125
1,093
0
false
For instance, Figure 3 shows the re-scoring of models submitted for targets 8 and 12 by 13 different groups around the world.
[]
For instance, Figure 3 shows the re-scoring of models submitted for targets 8 and 12 by 13 different groups around the world.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
In all cases, ‘FastContact’ correctly identified the near-native conformation, even when the modeler failed to do so.
[ "18", "10", "23–33", "10" ]
117
1,094
0
false
In all cases, ‘FastContact’ correctly identified the near-native conformation, even when the modeler failed to do so.
[]
In all cases, ‘FastContact’ correctly identified the near-native conformation, even when the modeler failed to do so.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
Figure 3.Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
[ "18", "10", "23–33", "10" ]
175
1,095
0
false
Figure 3.Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
[]
Figure 3.Examples of ‘FastContact’ scoring for a subset of high quality docked models from eight groups for targets 8 and 12 of CAPRI rounds 3–5, from http://capri.ebi.ac.uk/.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For each of these targets, we run the models in our server and re-rank the models accordingly.
[ "18", "10", "23–33", "10" ]
94
1,096
0
false
For each of these targets, we run the models in our server and re-rank the models accordingly.
[]
For each of these targets, we run the models in our server and re-rank the models accordingly.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
[ "18", "10", "23–33", "10" ]
114
1,097
0
false
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
[]
In all cases, the server was able to correctly rank a low RMSD model as the one with the lowest free energy score.
true
true
true
true
true
190
1
DISCUSSION
1
23–33
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler (23–33).
[ "18", "10", "23–33", "10" ]
102
1,098
1
false
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler.
[ "23–33" ]
For comparison, we also marked with a diamond symbol the model ranked number 1 by the modeler.
true
true
true
true
true
190
1
DISCUSSION
1
18
[ "B18", "B10", "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32 B33", "B10" ]
17,537,824
pmid-15713734|pmid-16506242|pmid-3237687|pmid-9126848|pmid-15981261|pmid-16506242|pmid-15981273|pmid-15981272|pmid-15981271|pmid-15981270|pmid-15981266|pmid-15981262|pmid-15981258|pmid-15981255|pmid-15981251|pmid-15981249|pmid-15981246|pmid-16506242
(A) target 8; (B) target 12.
[ "18", "10", "23–33", "10" ]
28
1,099
0
false
(A) target 8; (B) target 12.
[]
(A) target 8; (B) target 12.
false
false
true
true
false
190