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
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
Figure 8.Repair of deaminated cytosine; model illustrating distinct coordination of BER initiated by SMUG1 and UNG2 in non-replicating chromatin and in replicating chromatin (foci), respectively.
[ "13", "8", "15", "8" ]
195
6,200
0
false
Figure 8.Repair of deaminated cytosine; model illustrating distinct coordination of BER initiated by SMUG1 and UNG2 in non-replicating chromatin and in replicating chromatin (foci), respectively.
[]
Figure 8.Repair of deaminated cytosine; model illustrating distinct coordination of BER initiated by SMUG1 and UNG2 in non-replicating chromatin and in replicating chromatin (foci), respectively.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
SMUG1 binds to the lesion and interacts with both strands in the DNA-helix.
[ "13", "8", "15", "8" ]
75
6,201
0
false
SMUG1 binds to the lesion and interacts with both strands in the DNA-helix.
[]
SMUG1 binds to the lesion and interacts with both strands in the DNA-helix.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
Uracil is probably flipped out of the helix and into the active site.
[ "13", "8", "15", "8" ]
69
6,202
0
false
Uracil is probably flipped out of the helix and into the active site.
[]
Uracil is probably flipped out of the helix and into the active site.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
The catalysis is not very efficient because the active site is relaxed to be able to bind several other lesions.
[ "13", "8", "15", "8" ]
112
6,203
0
false
The catalysis is not very efficient because the active site is relaxed to be able to bind several other lesions.
[]
The catalysis is not very efficient because the active site is relaxed to be able to bind several other lesions.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
SMUG1 stays bound to the AP-site after excision.
[ "13", "8", "15", "8" ]
48
6,204
0
false
SMUG1 stays bound to the AP-site after excision.
[]
SMUG1 stays bound to the AP-site after excision.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
APE1 competes with SMUG1 for AP-site binding.
[ "13", "8", "15", "8" ]
45
6,205
0
false
APE1 competes with SMUG1 for AP-site binding.
[]
APE1 competes with SMUG1 for AP-site binding.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
SMUG1 is released form the product and is free to bind new lesions.
[ "13", "8", "15", "8" ]
67
6,206
0
false
SMUG1 is released form the product and is free to bind new lesions.
[]
SMUG1 is released form the product and is free to bind new lesions.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
APE1 cuts the DNA strand, and Polβ/XRCC1/LigIIIα is recruited and completes BER.
[ "13", "8", "15", "8" ]
80
6,207
0
false
APE1 cuts the DNA strand, and Polβ/XRCC1/LigIIIα is recruited and completes BER.
[]
APE1 cuts the DNA strand, and Polβ/XRCC1/LigIIIα is recruited and completes BER.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
UNG2 is likely part of a highly coordinated and efficient repair complex scanning for lesions (U:G) in front of the replication fork (UNG2 is localized in replication foci).
[ "13", "8", "15", "8" ]
173
6,208
0
false
UNG2 is likely part of a highly coordinated and efficient repair complex scanning for lesions (U:G) in front of the replication fork (UNG2 is localized in replication foci).
[]
UNG2 is likely part of a highly coordinated and efficient repair complex scanning for lesions (U:G) in front of the replication fork (UNG2 is localized in replication foci).
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
Encountering the lesion uracil is flipped out of the DNA-helix and into the highly specific catalytic pocket of UNG2.
[ "13", "8", "15", "8" ]
117
6,209
0
false
Encountering the lesion uracil is flipped out of the DNA-helix and into the highly specific catalytic pocket of UNG2.
[]
Encountering the lesion uracil is flipped out of the DNA-helix and into the highly specific catalytic pocket of UNG2.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
Uracil is released by efficient hydrolysis of the N-glycosidic bond.
[ "13", "8", "15", "8" ]
68
6,210
0
false
Uracil is released by efficient hydrolysis of the N-glycosidic bond.
[]
Uracil is released by efficient hydrolysis of the N-glycosidic bond.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
Note, UNG2 interacts only with the uracil-containing DNA strand.
[ "13", "8", "15", "8" ]
64
6,211
0
false
Note, UNG2 interacts only with the uracil-containing DNA strand.
[]
Note, UNG2 interacts only with the uracil-containing DNA strand.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
UNG2 is immediately released from the AP-site and APE1 binds.
[ "13", "8", "15", "8" ]
61
6,212
0
false
UNG2 is immediately released from the AP-site and APE1 binds.
[]
UNG2 is immediately released from the AP-site and APE1 binds.
true
true
true
true
true
1,023
7
DISCUSSION
1
13
[ "B13", "B8", "B15", "B8" ]
17,537,817
pmid-10393198|pmid-15902269|pmid-9490791|pmid-15902269
UNG2 stimulates APE1 cleavage of the AP-site and BER is completed.
[ "13", "8", "15", "8" ]
66
6,213
0
false
UNG2 stimulates APE1 cleavage of the AP-site and BER is completed.
[]
UNG2 stimulates APE1 cleavage of the AP-site and BER is completed.
true
true
true
true
true
1,023
8
DISCUSSION
0
null
null
17,537,817
null
Repair of deaminated cytosine; model illustrating distinct coordination of BER initiated by SMUG1 and UNG2 in non-replicating chromatin and in replicating chromatin (foci), respectively.
null
186
6,214
0
false
null
null
Repair of deaminated cytosine; model illustrating distinct coordination of BER initiated by SMUG1 and UNG2 in non-replicating chromatin and in replicating chromatin (foci), respectively.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
SMUG1 binds to the lesion and interacts with both strands in the DNA-helix.
null
75
6,215
0
false
null
null
SMUG1 binds to the lesion and interacts with both strands in the DNA-helix.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
Uracil is probably flipped out of the helix and into the active site.
null
69
6,216
0
false
null
null
Uracil is probably flipped out of the helix and into the active site.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
The catalysis is not very efficient because the active site is relaxed to be able to bind several other lesions.
null
112
6,217
0
false
null
null
The catalysis is not very efficient because the active site is relaxed to be able to bind several other lesions.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
SMUG1 stays bound to the AP-site after excision.
null
48
6,218
0
false
null
null
SMUG1 stays bound to the AP-site after excision.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
APE1 competes with SMUG1 for AP-site binding.
null
45
6,219
0
false
null
null
APE1 competes with SMUG1 for AP-site binding.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
SMUG1 is released form the product and is free to bind new lesions.
null
67
6,220
0
false
null
null
SMUG1 is released form the product and is free to bind new lesions.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
APE1 cuts the DNA strand, and Polβ/XRCC1/LigIIIα is recruited and completes BER.
null
80
6,221
0
false
null
null
APE1 cuts the DNA strand, and Polβ/XRCC1/LigIIIα is recruited and completes BER.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
UNG2 is likely part of a highly coordinated and efficient repair complex scanning for lesions (U:G) in front of the replication fork (UNG2 is localized in replication foci).
null
173
6,222
0
false
null
null
UNG2 is likely part of a highly coordinated and efficient repair complex scanning for lesions (U:G) in front of the replication fork (UNG2 is localized in replication foci).
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
Encountering the lesion uracil is flipped out of the DNA-helix and into the highly specific catalytic pocket of UNG2.
null
117
6,223
0
false
null
null
Encountering the lesion uracil is flipped out of the DNA-helix and into the highly specific catalytic pocket of UNG2.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
Uracil is released by efficient hydrolysis of the N-glycosidic bond.
null
68
6,224
0
false
null
null
Uracil is released by efficient hydrolysis of the N-glycosidic bond.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
Note, UNG2 interacts only with the uracil-containing DNA strand.
null
64
6,225
0
false
null
null
Note, UNG2 interacts only with the uracil-containing DNA strand.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
UNG2 is immediately released from the AP-site and APE1 binds.
null
61
6,226
0
false
null
null
UNG2 is immediately released from the AP-site and APE1 binds.
true
true
true
true
true
1,024
8
DISCUSSION
0
null
null
17,537,817
null
UNG2 stimulates APE1 cleavage of the AP-site and BER is completed.
null
66
6,227
0
false
null
null
UNG2 stimulates APE1 cleavage of the AP-site and BER is completed.
true
true
true
true
true
1,024
9
DISCUSSION
1
6
[ "B6", "B7" ]
17,537,817
pmid-11483530|pmid-12161446
Notably, in mouse SMUG1, the residue corresponding to the conserved Pro245 in the hSMUG1 wedge motif is alanine (Figure 4A).
[ "6", "7" ]
124
6,228
0
false
Notably, in mouse SMUG1, the residue corresponding to the conserved Pro245 in the hSMUG1 wedge motif is alanine (Figure 4A).
[]
Notably, in mouse SMUG1, the residue corresponding to the conserved Pro245 in the hSMUG1 wedge motif is alanine (Figure 4A).
true
true
true
true
true
1,025
9
DISCUSSION
1
6
[ "B6", "B7" ]
17,537,817
pmid-11483530|pmid-12161446
Kinetic analysis of the hSMUG1-P245A mutant, mimicking mouse SMUG1, revealed that this mutant has more than a 7-fold increased turnover number (kcat) on U:G substrate compared with WT (Figure 7A).
[ "6", "7" ]
196
6,229
0
false
Kinetic analysis of the hSMUG1-P245A mutant, mimicking mouse SMUG1, revealed that this mutant has more than a 7-fold increased turnover number (kcat) on U:G substrate compared with WT.
[ "Figure 7A" ]
Kinetic analysis of the hSMUG1-P245A mutant, mimicking mouse SMUG1, revealed that this mutant has more than a 7-fold increased turnover number (kcat) on U:G substrate compared with WT.
true
true
true
true
true
1,025
9
DISCUSSION
1
6
[ "B6", "B7" ]
17,537,817
pmid-11483530|pmid-12161446
The increased U:G activity of this mouse SMUG1 mimicking mutant could thus provide a mechanistic explanation for the apparently higher SMUG1 activity in extracts from mouse cells than from human cells (6,7).
[ "6", "7" ]
207
6,230
0
false
The increased U:G activity of this mouse SMUG1 mimicking mutant could thus provide a mechanistic explanation for the apparently higher SMUG1 activity in extracts from mouse cells than from human cells.
[ "6,7" ]
The increased U:G activity of this mouse SMUG1 mimicking mutant could thus provide a mechanistic explanation for the apparently higher SMUG1 activity in extracts from mouse cells than from human cells.
true
true
true
true
true
1,025
9
DISCUSSION
1
6
[ "B6", "B7" ]
17,537,817
pmid-11483530|pmid-12161446
This observation should be kept in mind when using mice as model organisms for uracil repair in mammals.
[ "6", "7" ]
104
6,231
0
false
This observation should be kept in mind when using mice as model organisms for uracil repair in mammals.
[]
This observation should be kept in mind when using mice as model organisms for uracil repair in mammals.
true
true
true
true
true
1,025
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
The presence of at least one family member of the uracil-removing glycosylases in all known organisms points to the importance of this repair mechanism.
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
152
6,232
0
false
The presence of at least one family member of the uracil-removing glycosylases in all known organisms points to the importance of this repair mechanism.
[]
The presence of at least one family member of the uracil-removing glycosylases in all known organisms points to the importance of this repair mechanism.
true
true
true
true
true
1,026
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
The present article demonstrates new distinct properties of SMUG1 and UNG2 that point to different mechanisms for coordination of the initial steps in BER.
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
155
6,233
0
false
The present article demonstrates new distinct properties of SMUG1 and UNG2 that point to different mechanisms for coordination of the initial steps in BER.
[]
The present article demonstrates new distinct properties of SMUG1 and UNG2 that point to different mechanisms for coordination of the initial steps in BER.
true
true
true
true
true
1,026
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
Considering functional differences, SMUG1 still seems to be able to compensate for UNG-deficiency in most somatic tissues (6), and is apparently sufficient to maintain genomic stability in some organisms.
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
204
6,234
1
false
Considering functional differences, SMUG1 still seems to be able to compensate for UNG-deficiency in most somatic tissues, and is apparently sufficient to maintain genomic stability in some organisms.
[ "6" ]
Considering functional differences, SMUG1 still seems to be able to compensate for UNG-deficiency in most somatic tissues, and is apparently sufficient to maintain genomic stability in some organisms.
true
true
true
true
true
1,026
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
However, from Ung−/− mice and human UNG-deficient patients it is evident that SMUG1 is not able to compensate for UNG2 in Ig diversification in B-cells (10,11,50,51).
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
166
6,235
0
false
However, from Ung−/− mice and human UNG-deficient patients it is evident that SMUG1 is not able to compensate for UNG2 in Ig diversification in B-cells.
[ "10,11,50,51" ]
However, from Ung−/− mice and human UNG-deficient patients it is evident that SMUG1 is not able to compensate for UNG2 in Ig diversification in B-cells.
true
true
true
true
true
1,026
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
Furthermore, old Ung−/− mice develop B-cell lymphomas (52,53).
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
62
6,236
0
false
Furthermore, old Ung−/− mice develop B-cell lymphomas.
[ "52,53" ]
Furthermore, old Ung−/− mice develop B-cell lymphomas.
true
true
true
true
true
1,026
10
DISCUSSION
1
51
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
Whether human individuals lacking UNG will develop malignancies remain unknown since they are yet too few identified and too young for conclusions to be made (51).
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
163
6,237
1
false
Whether human individuals lacking UNG will develop malignancies remain unknown since they are yet too few identified and too young for conclusions to be made.
[ "51" ]
Whether human individuals lacking UNG will develop malignancies remain unknown since they are yet too few identified and too young for conclusions to be made.
true
true
true
true
true
1,026
10
DISCUSSION
1
6
[ "B6", "B10", "B11", "B50", "B51", "B52", "B53", "B51" ]
17,537,817
pmid-11483530|pmid-15967827|pmid-16407970|pmid-12401169|pmid-12958596|pmid-12934097|pmid-16174566|pmid-12958596
A more comprehensive knowledge of the short-term and long-term consequences of deficient uracil removal require further studies of the Ung−/− mice and generation and characterization of Smug1−/− mice and Ung/Smug1 double knockout mice.
[ "6", "10", "11", "50", "51", "52", "53", "51" ]
235
6,238
0
false
A more comprehensive knowledge of the short-term and long-term consequences of deficient uracil removal require further studies of the Ung−/− mice and generation and characterization of Smug1−/− mice and Ung/Smug1 double knockout mice.
[]
A more comprehensive knowledge of the short-term and long-term consequences of deficient uracil removal require further studies of the Ung−/− mice and generation and characterization of Smug1−/− mice and Ung/Smug1 double knockout mice.
true
true
true
true
true
1,026
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5 B6 B7 B8", "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14" ]
17,537,808
pmid-7761829|pmid-3914833|pmid-7563096|pmid-9571027|pmid-2726810|pmid-12589754|pmid-16284202|pmid-14654694|pmid-12589754|pmid-16284202|pmid-14654694|pmid-15356290|pmid-15146487|pmid-15613393|pmid-9299343|pmid-10753808|pmid-16919296
The surface of a protein is the region where the protein interacts with other molecules such as other proteins, nucleic acids, membrane receptors and small ligands.
[ "1", "2", "3", "4", "5–8", "6", "7", "8–11", "12", "13", "14" ]
164
6,239
0
false
The surface of a protein is the region where the protein interacts with other molecules such as other proteins, nucleic acids, membrane receptors and small ligands.
[]
The surface of a protein is the region where the protein interacts with other molecules such as other proteins, nucleic acids, membrane receptors and small ligands.
true
true
true
true
true
1,027
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4", "B5 B6 B7 B8", "B6", "B7", "B8 B9 B10 B11", "B12", "B13", "B14" ]
17,537,808
pmid-7761829|pmid-3914833|pmid-7563096|pmid-9571027|pmid-2726810|pmid-12589754|pmid-16284202|pmid-14654694|pmid-12589754|pmid-16284202|pmid-14654694|pmid-15356290|pmid-15146487|pmid-15613393|pmid-9299343|pmid-10753808|pmid-16919296
The electrostatic potential is a fundamental property of the protein surface, playing a central role in recognition of other macromolecules (1).
[ "1", "2", "3", "4", "5–8", "6", "7", "8–11", "12", "13", "14" ]
144
6,240
1
false
The electrostatic potential is a fundamental property of the protein surface, playing a central role in recognition of other macromolecules.
[ "1" ]
The electrostatic potential is a fundamental property of the protein surface, playing a central role in recognition of other macromolecules.
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INTRODUCTION
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When the first 3D structures of protein–DNA complexes were solved it was noticed that charges are distributed asymmetrically on the protein surface, creating a patch of positive charges which complements the negative charge of the DNA (2).
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When the first 3D structures of protein–DNA complexes were solved it was noticed that charges are distributed asymmetrically on the protein surface, creating a patch of positive charges which complements the negative charge of the DNA.
[ "2" ]
When the first 3D structures of protein–DNA complexes were solved it was noticed that charges are distributed asymmetrically on the protein surface, creating a patch of positive charges which complements the negative charge of the DNA.
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1,027
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INTRODUCTION
1
1
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It was further suggested that charge complementarity is one of the first steps of recognition between proteins and DNA (3,4).
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It was further suggested that charge complementarity is one of the first steps of recognition between proteins and DNA.
[ "3,4" ]
It was further suggested that charge complementarity is one of the first steps of recognition between proteins and DNA.
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1,027
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INTRODUCTION
1
5–8
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Indeed, large patches of positive charges have been suggested to be characteristic of protein–nucleic acid interfaces (5–8).
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Indeed, large patches of positive charges have been suggested to be characteristic of protein–nucleic acid interfaces.
[ "5–8" ]
Indeed, large patches of positive charges have been suggested to be characteristic of protein–nucleic acid interfaces.
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1,027
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INTRODUCTION
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Recently, several methods have been developed for automatic prediction of DNA-binding proteins based on the existence of large positive patches on the protein surface (6,7,8–11)
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Recently, several methods have been developed for automatic prediction of DNA-binding proteins based on the existence of large positive patches on the protein surface
[ "6,7,8–11" ]
Recently, several methods have been developed for automatic prediction of DNA-binding proteins based on the existence of large positive patches on the protein surface
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1,027
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INTRODUCTION
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In addition to nucleic acid binding, other essential protein functions could be dependent on the presence of large patches of positive charges on the protein surface (12).
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In addition to nucleic acid binding, other essential protein functions could be dependent on the presence of large patches of positive charges on the protein surface.
[ "12" ]
In addition to nucleic acid binding, other essential protein functions could be dependent on the presence of large patches of positive charges on the protein surface.
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1,027
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INTRODUCTION
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Among these are proteins which bind negatively charged membranes and receptor-binding ligands.
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Among these are proteins which bind negatively charged membranes and receptor-binding ligands.
[]
Among these are proteins which bind negatively charged membranes and receptor-binding ligands.
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1,027
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INTRODUCTION
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Furthermore, although protein–protein interactions are usually known to be stabilized by a net neutral charge, different studies have revealed that positive and negative patches are commonly involved in protein–protein interfaces (13,14).
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Furthermore, although protein–protein interactions are usually known to be stabilized by a net neutral charge, different studies have revealed that positive and negative patches are commonly involved in protein–protein interfaces.
[ "13,14" ]
Furthermore, although protein–protein interactions are usually known to be stabilized by a net neutral charge, different studies have revealed that positive and negative patches are commonly involved in protein–protein interfaces.
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INTRODUCTION
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15
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In general, positively charged surfaces can be detected by visualizing the electrostatic properties of the protein surface with graphical programs such as GRASP or GRASS (15,16).
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In general, positively charged surfaces can be detected by visualizing the electrostatic properties of the protein surface with graphical programs such as GRASP or GRASS.
[ "15,16" ]
In general, positively charged surfaces can be detected by visualizing the electrostatic properties of the protein surface with graphical programs such as GRASP or GRASS.
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1,028
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INTRODUCTION
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15
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The first program for graphical representation and analysis of surface properties of macromolecules was the GRASP software (Graphical Representation and Analysis of Surface Properties), developed by Nicholls et al.
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The first program for graphical representation and analysis of surface properties of macromolecules was the GRASP software (Graphical Representation and Analysis of Surface Properties), developed by Nicholls et al.
[]
The first program for graphical representation and analysis of surface properties of macromolecules was the GRASP software (Graphical Representation and Analysis of Surface Properties), developed by Nicholls et al.
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1,028
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INTRODUCTION
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Among the features which are calculated and displayed by GRASP are the electrostatic potential and surface accessibility.
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Among the features which are calculated and displayed by GRASP are the electrostatic potential and surface accessibility.
[]
Among the features which are calculated and displayed by GRASP are the electrostatic potential and surface accessibility.
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1,028
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INTRODUCTION
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15
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The electrostatic potential displayed by GRASP is calculated using the finite-difference Poisson–Boltzmann equation (FDPB).
[ "15", "16", "17", "16", "15" ]
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The electrostatic potential displayed by GRASP is calculated using the finite-difference Poisson–Boltzmann equation (FDPB).
[]
The electrostatic potential displayed by GRASP is calculated using the finite-difference Poisson–Boltzmann equation (FDPB).
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1,028
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INTRODUCTION
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16
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A newer version of the GRASP program, GRASP2, was published more recently (16).
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A newer version of the GRASP program, GRASP2, was published more recently.
[ "16" ]
A newer version of the GRASP program, GRASP2, was published more recently.
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1,028
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INTRODUCTION
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15
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In addition, the GRASS web server was developed (15) to exploit many of the features calculated by the previous programs on a simple interface over the World Wide Web.
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In addition, the GRASS web server was developed to exploit many of the features calculated by the previous programs on a simple interface over the World Wide Web.
[ "15" ]
In addition, the GRASS web server was developed to exploit many of the features calculated by the previous programs on a simple interface over the World Wide Web.
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INTRODUCTION
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These programs, however, are not designed to capture isolated patches on the protein surface.
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These programs, however, are not designed to capture isolated patches on the protein surface.
[]
These programs, however, are not designed to capture isolated patches on the protein surface.
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INTRODUCTION
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In order to specifically detect continuous regions on the protein surface that could be indicative of the protein function, we have previously developed an in-house program named PatchFinder (6), similar approaches have been developed later by several groups (7,8,18).
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In order to specifically detect continuous regions on the protein surface that could be indicative of the protein function, we have previously developed an in-house program named PatchFinder, similar approaches have been developed later by several groups.
[ "6", "7,8,18" ]
In order to specifically detect continuous regions on the protein surface that could be indicative of the protein function, we have previously developed an in-house program named PatchFinder, similar approaches have been developed later by several groups.
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INTRODUCTION
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PatchFinder was designed to calculate the Poisson–Boltzmann electrostatic potential of the protein and to construct the largest continuous positive patch on the protein surface.
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PatchFinder was designed to calculate the Poisson–Boltzmann electrostatic potential of the protein and to construct the largest continuous positive patch on the protein surface.
[]
PatchFinder was designed to calculate the Poisson–Boltzmann electrostatic potential of the protein and to construct the largest continuous positive patch on the protein surface.
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INTRODUCTION
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6
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Earlier, we have shown that there is a high overlap between the largest electrostatic positive patches on protein surfaces and the DNA-binding interfaces (6).
[ "6", "7", "8", "18", "6", "6" ]
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Earlier, we have shown that there is a high overlap between the largest electrostatic positive patches on protein surfaces and the DNA-binding interfaces.
[ "6" ]
Earlier, we have shown that there is a high overlap between the largest electrostatic positive patches on protein surfaces and the DNA-binding interfaces.
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1,029
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INTRODUCTION
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6
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17,537,808
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Figure 1 and Supplementary Figure S1 demonstrate the overlap (colored in green) between the largest positive patch, calculated with the PatchFinder algorithm (blue) and the real nucleic acid-binding interface (yellow) extracted from six selected co-crystal structures of DNA and RNA-binding proteins.
[ "6", "7", "8", "18", "6", "6" ]
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Figure 1 and Supplementary Figure S1 demonstrate the overlap (colored in green) between the largest positive patch, calculated with the PatchFinder algorithm (blue) and the real nucleic acid-binding interface (yellow) extracted from six selected co-crystal structures of DNA and RNA-binding proteins.
[]
Figure 1 and Supplementary Figure S1 demonstrate the overlap (colored in green) between the largest positive patch, calculated with the PatchFinder algorithm (blue) and the real nucleic acid-binding interface (yellow) extracted from six selected co-crystal structures of DNA and RNA-binding proteins.
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INTRODUCTION
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Furthermore, the percent overlap between the patch and the interface for a randomly selected set of DNA–protein complexes is given in Supplementary Table S1 (the average percent-overlap for the random set was 75%).
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Furthermore, the percent overlap between the patch and the interface for a randomly selected set of DNA–protein complexes is given in Supplementary Table S1.
[ "the average percent-overlap for the random set was 75%" ]
Furthermore, the percent overlap between the patch and the interface for a randomly selected set of DNA–protein complexes is given in Supplementary Table S1.
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INTRODUCTION
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As shown in the figures, though the percent overlap varies between the different structures in all cases the calculated patch coincides with the binding site of the nucleic acids.
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As shown in the figures, though the percent overlap varies between the different structures in all cases the calculated patch coincides with the binding site of the nucleic acids.
[]
As shown in the figures, though the percent overlap varies between the different structures in all cases the calculated patch coincides with the binding site of the nucleic acids.
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1,029
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INTRODUCTION
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Figure 1.Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
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Figure 1.Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
[]
Figure 1.Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
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INTRODUCTION
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The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
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The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
[]
The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
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INTRODUCTION
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Yellow represents the interface which was missed by the patch calculation.
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Yellow represents the interface which was missed by the patch calculation.
[]
Yellow represents the interface which was missed by the patch calculation.
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1,029
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INTRODUCTION
1
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[ "B6", "B7", "B8", "B18", "B6", "B6" ]
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Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
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Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
[]
Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
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INTRODUCTION
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Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
[ "6" ]
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Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
[]
Overlap between the largest positive patch of the HIV-1 nucleocapsid protein (calculated with the PatchFinder algorithm) and the experimentally defined RNA-interface (1a1t).
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true
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1,030
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INTRODUCTION
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[ "B6" ]
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The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
[ "6" ]
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The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
[]
The overlap is shown in green, while the calculated patch that did not overlap with the real interface is colored in blue.
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INTRODUCTION
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Yellow represents the interface which was missed by the patch calculation.
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Yellow represents the interface which was missed by the patch calculation.
[]
Yellow represents the interface which was missed by the patch calculation.
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INTRODUCTION
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[ "B6" ]
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Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
[ "6" ]
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Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
[]
Overall, a high degree of overlap is observed between the largest positive patch calculated with the PFplus server and the actual RNA-binding interface calculated as described in Stawiski et al.
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INTRODUCTION
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18
[ "B18" ]
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pmid-15215360
Recently, Ahmad and Sarai (18) have developed the Qgrid web server which identifies charge and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html).
[ "18" ]
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Recently, Ahmad and Sarai have developed the Qgrid web server which identifies charge and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html).
[ "18" ]
Recently, Ahmad and Sarai have developed the Qgrid web server which identifies charge and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html).
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1,031
4
INTRODUCTION
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18
[ "B18" ]
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The Qgrid program calculates the distribution of charge and hydrophobic regions throughout the protein and applies a hierarchical clustering algorithm for clustering the atoms based on their charge.
[ "18" ]
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The Qgrid program calculates the distribution of charge and hydrophobic regions throughout the protein and applies a hierarchical clustering algorithm for clustering the atoms based on their charge.
[]
The Qgrid program calculates the distribution of charge and hydrophobic regions throughout the protein and applies a hierarchical clustering algorithm for clustering the atoms based on their charge.
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1,031
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INTRODUCTION
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18
[ "B18" ]
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The output of Qgrid is a tree diagram of all grid points from which the user can interpret the different charge and hydrophobic clusters within the whole protein and the relationship between the different clusters.
[ "18" ]
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The output of Qgrid is a tree diagram of all grid points from which the user can interpret the different charge and hydrophobic clusters within the whole protein and the relationship between the different clusters.
[]
The output of Qgrid is a tree diagram of all grid points from which the user can interpret the different charge and hydrophobic clusters within the whole protein and the relationship between the different clusters.
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1,031
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INTRODUCTION
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18
[ "B18" ]
17,537,808
pmid-15215360
Here we describe a new web server, PatchFinderPlus (PFplus), for extracting electrostatic patches on the protein surface.
[ "18" ]
121
6,272
0
false
Here we describe a new web server, PatchFinderPlus (PFplus), for extracting electrostatic patches on the protein surface.
[]
Here we describe a new web server, PatchFinderPlus (PFplus), for extracting electrostatic patches on the protein surface.
true
true
true
true
true
1,031
4
INTRODUCTION
1
18
[ "B18" ]
17,537,808
pmid-15215360
Different than the Qgrid algorithm, PFplus is designed to map only the largest continuous positive patch on the protein surface.
[ "18" ]
128
6,273
0
false
Different than the Qgrid algorithm, PFplus is designed to map only the largest continuous positive patch on the protein surface.
[]
Different than the Qgrid algorithm, PFplus is designed to map only the largest continuous positive patch on the protein surface.
true
true
true
true
true
1,031
4
INTRODUCTION
1
18
[ "B18" ]
17,537,808
pmid-15215360
Furthermore, the PFplus algorithm searches for adjacent grid points above a given cutoff, and thus does not require any heuristic calculations, such as clustering.
[ "18" ]
163
6,274
0
false
Furthermore, the PFplus algorithm searches for adjacent grid points above a given cutoff, and thus does not require any heuristic calculations, such as clustering.
[]
Furthermore, the PFplus algorithm searches for adjacent grid points above a given cutoff, and thus does not require any heuristic calculations, such as clustering.
true
true
true
true
true
1,031
4
INTRODUCTION
1
18
[ "B18" ]
17,537,808
pmid-15215360
Our server provides a graphical output of the surface patch which presumably corresponds to the region on the protein surface involved in interaction with other molecules.
[ "18" ]
171
6,275
0
false
Our server provides a graphical output of the surface patch which presumably corresponds to the region on the protein surface involved in interaction with other molecules.
[]
Our server provides a graphical output of the surface patch which presumably corresponds to the region on the protein surface involved in interaction with other molecules.
true
true
true
true
true
1,031
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b16" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
Protein structure comparison (PSC) has been a staple method for obtaining information about a protein when its 3D structure is determined experimentally or predicted computationally.
[ "1", "6", "7", "8", "9", "10", "11", "12", "13", "14", "16" ]
182
6,276
0
false
Protein structure comparison (PSC) has been a staple method for obtaining information about a protein when its 3D structure is determined experimentally or predicted computationally.
[]
Protein structure comparison (PSC) has been a staple method for obtaining information about a protein when its 3D structure is determined experimentally or predicted computationally.
true
true
true
true
true
1,032
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b16" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
It is therefore not surprising that the development of new PSC algorithms has been continuing for more than two decades with no sign of ceasing (1–6).
[ "1", "6", "7", "8", "9", "10", "11", "12", "13", "14", "16" ]
150
6,277
0
false
It is therefore not surprising that the development of new PSC algorithms has been continuing for more than two decades with no sign of ceasing.
[ "1–6" ]
It is therefore not surprising that the development of new PSC algorithms has been continuing for more than two decades with no sign of ceasing.
true
true
true
true
true
1,032
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b16" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
These efforts are needed not only to meet new scientific challenges but also to benefit maximally from the large number of new structures now pouring in from structural genomics projects (7,8).
[ "1", "6", "7", "8", "9", "10", "11", "12", "13", "14", "16" ]
193
6,278
0
false
These efforts are needed not only to meet new scientific challenges but also to benefit maximally from the large number of new structures now pouring in from structural genomics projects.
[ "7,8" ]
These efforts are needed not only to meet new scientific challenges but also to benefit maximally from the large number of new structures now pouring in from structural genomics projects.
true
true
true
true
true
1,032
0
INTRODUCTION
1
1
[ "b1", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b16" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
To these ends, a number of laboratories have created PSC servers in recent years to provide information beyond the basic PSC operations, including, e.g.
[ "1", "6", "7", "8", "9", "10", "11", "12", "13", "14", "16" ]
152
6,279
0
false
To these ends, a number of laboratories have created PSC servers in recent years to provide information beyond the basic PSC operations, including, e.g.
[]
To these ends, a number of laboratories have created PSC servers in recent years to provide information beyond the basic PSC operations, including, e.g.
true
true
true
true
true
1,032
0
INTRODUCTION
1
13
[ "b1", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b16" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
those that do flexible alignment (9,10), those that discover recurring substructures or motifs (11,12), those that perform multiple structure alignment (13) and those that focus on fast structure feature extraction (14–16).
[ "1", "6", "7", "8", "9", "10", "11", "12", "13", "14", "16" ]
223
6,280
1
false
those that do flexible alignment, those that discover recurring substructures or motifs, those that perform multiple structure alignment and those that focus on fast structure feature extraction.
[ "9,10", "11,12", "13", "14–16" ]
those that do flexible alignment, those that discover recurring substructures or motifs, those that perform multiple structure alignment and those that focus on fast structure feature extraction.
false
true
true
true
false
1,032
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
Here we offer a new PSC server with the functionality to report statistically significant alternative alignments (17,18) and structural permutations (19,20) at all levels of complexity.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
185
6,281
0
false
Here we offer a new PSC server with the functionality to report statistically significant alternative alignments and structural permutations at all levels of complexity.
[ "17,18", "19,20" ]
Here we offer a new PSC server with the functionality to report statistically significant alternative alignments and structural permutations at all levels of complexity.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
Our method, named OPAAS, which has been detailed elsewhere (21,22), deduces the probabilities of aligning every possible pair of secondary structure elements (SSEs) between two protein structures prior to the search for a solution of their alignment.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
250
6,282
0
false
Our method, named OPAAS, which has been detailed elsewhere, deduces the probabilities of aligning every possible pair of secondary structure elements (SSEs) between two protein structures prior to the search for a solution of their alignment.
[ "21,22" ]
Our method, named OPAAS, which has been detailed elsewhere, deduces the probabilities of aligning every possible pair of secondary structure elements (SSEs) between two protein structures prior to the search for a solution of their alignment.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
This deduction allows the ready identification of most, though not all, statistically significant alignment solutions, many of which being distinct alternatives to the ‘optimal’ solution, the target of conventional PSC operations.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
230
6,283
0
false
This deduction allows the ready identification of most, though not all, statistically significant alignment solutions, many of which being distinct alternatives to the ‘optimal’ solution, the target of conventional PSC operations.
[]
This deduction allows the ready identification of most, though not all, statistically significant alignment solutions, many of which being distinct alternatives to the ‘optimal’ solution, the target of conventional PSC operations.
true
true
true
true
true
1,033
1
INTRODUCTION
1
22
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
As we reported previously from a study of all-against-all database comparisons (22), about half of the alternative alignments were detectable only when permutation, i.e.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
169
6,284
1
false
As we reported previously from a study of all-against-all database comparisons, about half of the alternative alignments were detectable only when permutation, i.e.
[ "22" ]
As we reported previously from a study of all-against-all database comparisons, about half of the alternative alignments were detectable only when permutation, i.e.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
non-topological alignment, was allowed.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
39
6,285
0
false
non-topological alignment, was allowed.
[]
non-topological alignment, was allowed.
false
true
true
true
false
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
Moreover, many of the permuted alignments exhibited a permutation complexity higher than that of circular permutation, meaning that more than two separable regions of the protein structure could be aligned non-sequentially.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
223
6,286
0
false
Moreover, many of the permuted alignments exhibited a permutation complexity higher than that of circular permutation, meaning that more than two separable regions of the protein structure could be aligned non-sequentially.
[]
Moreover, many of the permuted alignments exhibited a permutation complexity higher than that of circular permutation, meaning that more than two separable regions of the protein structure could be aligned non-sequentially.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
To quantitatively measure the level of permutation complexity for all the alignments, we devised a permutation index (PI) as follows: PI=(∑i=1nSi)2∑i=1nSi2, where Si is the size (number of aligned amino acid residues) of the aligned region i and n is the total number of aligned regions.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
287
6,287
0
false
To quantitatively measure the level of permutation complexity for all the alignments, we devised a permutation index (PI) as follows: PI=(∑i=1nSi)2∑i=1nSi2, where Si is the size (number of aligned amino acid residues) of the aligned region i and n is the total number of aligned regions.
[]
To quantitatively measure the level of permutation complexity for all the alignments, we devised a permutation index (PI) as follows: PI=2∑i=1nSi2, where Si is the size (number of aligned amino acid residues) of the aligned region i and n is the total number of aligned regions.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
A region is an independently, and, within the region itself, topologically aligned part of an alignment.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
104
6,288
0
false
A region is an independently, and, within the region itself, topologically aligned part of an alignment.
[]
A region is an independently, and, within the region itself, topologically aligned part of an alignment.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
That is, within a region, all the aligned residues are ordered sequentially, which may or may not be interrupted by gaps, but these regions, if there are more than one, are aligned non-sequentially.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
198
6,289
0
false
That is, within a region, all the aligned residues are ordered sequentially, which may or may not be interrupted by gaps, but these regions, if there are more than one, are aligned non-sequentially.
[]
That is, within a region, all the aligned residues are ordered sequentially, which may or may not be interrupted by gaps, but these regions, if there are more than one, are aligned non-sequentially.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
It follows that an alignment without any permutation will have just one region, and will have, by definition, a PI value of 1.0.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
128
6,290
0
false
It follows that an alignment without any permutation will have just one region, and will have, by definition, a PI value of 1.0.
[]
It follows that an alignment without any permutation will have just one region, and will have, by definition, a PI value of 1.0.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
Also by definition, a circular permutation, which involves swapping two regions in a non-topological alignment (19,20), will receive a PI value >1.0 but not >2.0.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
162
6,291
0
false
Also by definition, a circular permutation, which involves swapping two regions in a non-topological alignment, will receive a PI value >1.0 but not >2.0.
[ "19,20" ]
Also by definition, a circular permutation, which involves swapping two regions in a non-topological alignment, will receive a PI value >1.0 but not >2.0.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
PI hence furthermore let us know how much the sizes of the separately aligned regions differ.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
93
6,292
0
false
PI hence furthermore let us know how much the sizes of the separately aligned regions differ.
[]
PI hence furthermore let us know how much the sizes of the separately aligned regions differ.
true
true
true
true
true
1,033
1
INTRODUCTION
1
17
[ "b17", "b18", "b19", "b20", "b21", "b22", "b22", "b19", "b20" ]
16,845,117
pmid-9079372|pmid-8819165|pmid-16592676|pmid-8987381|pmid-12691985|pmid-15229884|pmid-15229884|pmid-16592676|pmid-8987381
For example, given two permuted protein pairs having PI 3.0 and 2.5, respectively, we will know that they both have three aligned regions, but the sizes of the three regions are equal for the former and vary significantly for the latter.
[ "17", "18", "19", "20", "21", "22", "22", "19", "20" ]
237
6,293
0
false
For example, given two permuted protein pairs having PI 3.0 and 2.5, respectively, we will know that they both have three aligned regions, but the sizes of the three regions are equal for the former and vary significantly for the latter.
[]
For example, given two permuted protein pairs having PI 3.0 and 2.5, respectively, we will know that they both have three aligned regions, but the sizes of the three regions are equal for the former and vary significantly for the latter.
true
true
true
true
true
1,033
2
INTRODUCTION
0
null
null
16,845,117
null
Both permuted and non-permuted alternative alignments are reported by the OPAAS server in a fashion that is easy for a non-specialist user to grasp the main significance of the comparison as one would with the ‘optimal’ alignment featured by other PSC servers.
null
260
6,294
0
false
null
null
Both permuted and non-permuted alternative alignments are reported by the OPAAS server in a fashion that is easy for a non-specialist user to grasp the main significance of the comparison as one would with the ‘optimal’ alignment featured by other PSC servers.
true
true
true
true
true
1,034
2
INTRODUCTION
0
null
null
16,845,117
null
This is aided by the server's user-friendly interfaces described below, which use intuitive viewing directions, informative tables that can be sorted by different parameters, cascading information windows, and a structured user guide with examples.
null
248
6,295
0
false
null
null
This is aided by the server's user-friendly interfaces described below, which use intuitive viewing directions, informative tables that can be sorted by different parameters, cascading information windows, and a structured user guide with examples.
true
true
true
true
true
1,034
0
DISCUSSION
1
6
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
The best way to compare two protein structures often depends on the question being asked (6), so having a server like OPAAS that can simultaneously analyze solutions beyond the ‘optimal’ alignment is useful.
[ "6", "25", "26", "21", "22", "27" ]
207
6,296
1
false
The best way to compare two protein structures often depends on the question being asked, so having a server like OPAAS that can simultaneously analyze solutions beyond the ‘optimal’ alignment is useful.
[ "6" ]
The best way to compare two protein structures often depends on the question being asked, so having a server like OPAAS that can simultaneously analyze solutions beyond the ‘optimal’ alignment is useful.
true
true
true
true
true
1,035
0
DISCUSSION
1
25
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
Although most of the published PSC algorithms can be modified to offer similar capability, to our knowledge, only two PSC servers give user the option to see alternative alignments: Prosup (25) and SARF2 (26), but Prosup is limited to topological alignments and neither offers one-against-all database searching service.
[ "6", "25", "26", "21", "22", "27" ]
320
6,297
1
false
Although most of the published PSC algorithms can be modified to offer similar capability, to our knowledge, only two PSC servers give user the option to see alternative alignments: Prosup and SARF2, but Prosup is limited to topological alignments and neither offers one-against-all database searching service.
[ "25", "26" ]
Although most of the published PSC algorithms can be modified to offer similar capability, to our knowledge, only two PSC servers give user the option to see alternative alignments: Prosup and SARF2, but Prosup is limited to topological alignments and neither offers one-against-all database searching service.
true
true
true
true
true
1,035
0
DISCUSSION
1
6
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
Moreover, with an intuitive hierarchical layout of the comparison results and optional parameter settings to view most significant alignments (e.g.
[ "6", "25", "26", "21", "22", "27" ]
147
6,298
0
false
Moreover, with an intuitive hierarchical layout of the comparison results and optional parameter settings to view most significant alignments (e.g.
[]
Moreover, with an intuitive hierarchical layout of the comparison results and optional parameter settings to view most significant alignments (e.g.
true
true
true
true
true
1,035
0
DISCUSSION
1
6
[ "b6", "b25", "b26", "b21", "b22", "b27" ]
16,845,117
NA|pmid-15576025|pmid-15854658|pmid-16424331|pmid-12112693|pmid-15215455|pmid-15215355|pmid-15215444|pmid-15215359|pmid-15215453|pmid-15980464|pmid-15576025|pmid-11161105|pmid-8844870|pmid-12691985|pmid-15229884|pmid-9796821
with similarity P-value set at 10−5, a typical comparison usually resulted in <5 such solutions), an informative summary that could lead to unexpected insight from unexpected alternative alignments is effectively produced.
[ "6", "25", "26", "21", "22", "27" ]
222
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0
false
with similarity P-value set at 10−5, a typical comparison usually resulted in <5 such solutions), an informative summary that could lead to unexpected insight from unexpected alternative alignments is effectively produced.
[]
with similarity P-value set at 10−5, a typical comparison usually resulted in <5 such solutions), an informative summary that could lead to unexpected insight from unexpected alternative alignments is effectively produced.
false
true
true
true
false
1,035