-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402 (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
25444460232
-
Dimerization of doublesex is mediated by a cryptic ubiquitin-associated domain fold: Implications for sex-specific gene regulation
-
DOI 10.1074/jbc.M507990200
-
J.R. Bayrer, W. Zhang, and M.A. Weiss Dimerization of doublesex is mediated by a cryptic ubiquitin-associated domain fold: implications for sex-specific gene regulation J. Biol. Chem. 280 2005 32989 32996 (Pubitemid 41368348)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.38
, pp. 32989-32996
-
-
Bayrer, J.R.1
Zhang, W.2
Weiss, M.A.3
-
3
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
J.U. Bowie, R. Luthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 253 1991 164 170 (Pubitemid 21917131)
-
(1991)
Science
, vol.253
, Issue.5016
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
4
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
J. Cheng, and P. Baldi Improved residue contact prediction using support vector machines and a large feature set BMC Bioinformatics 8 2007 113
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
5
-
-
74249108517
-
Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
-
I. Ezkurdia, O. Grana, J.M. Izarzugaza, and M.L. Tress Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8 Proteins 77 Suppl 9 2009 196 209
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 196-209
-
-
Ezkurdia, I.1
Grana, O.2
Izarzugaza, J.M.3
Tress, M.L.4
-
6
-
-
0028295169
-
Correlated mutations and residue contacts in proteins
-
U. Gobel, C. Sander, R. Schneider, and A. Valencia Correlated mutations and residue contacts in proteins Proteins 18 1994 309 317 (Pubitemid 24111530)
-
(1994)
Proteins: Structure, Function and Genetics
, vol.18
, Issue.4
, pp. 309-317
-
-
Gobel, U.1
Sander, C.2
Schneider, R.3
Valencia, A.4
-
8
-
-
33646766064
-
Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families
-
DOI 10.1002/prot.20933
-
I. Halperin, H. Wolfson, and R. Nussinov Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families Proteins 63 2006 832 845 (Pubitemid 43765137)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.63
, Issue.4
, pp. 832-845
-
-
Halperin, I.1
Wolfson, H.2
Nussinov, R.3
-
9
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
DOI 10.1093/bioinformatics/14.10.846
-
K. Karplus, C. Barrett, and R. Hughey Hidden Markov models for detecting remote protein homologies Bioinformatics 14 1998 846 856 (Pubitemid 29041540)
-
(1998)
Bioinformatics
, vol.14
, Issue.10
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
10
-
-
33751219893
-
Predicting residue contacts using pragmatic correlated mutations method: Reducing the false positives
-
P.J. Kundrotas, and E.G. Alexov Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives BMC Bioinformatics 7 2006 503
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 503
-
-
Kundrotas, P.J.1
Alexov, E.G.2
-
11
-
-
0036223323
-
The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: The 'double wing' motif
-
DOI 10.1046/j.1365-2958.2002.02809.x
-
N. Li, E.A. Sickmier, R. Zhang, A. Joachimiak, and S.W. White The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif Mol. Microbiol. 43 2002 1079 1088 (Pubitemid 34304528)
-
(2002)
Molecular Microbiology
, vol.43
, Issue.5
, pp. 1079-1088
-
-
Li, N.1
Sickmier, E.A.2
Zhang, R.3
Joachimiak, A.4
White, S.W.5
-
12
-
-
4143110064
-
Application of sparse NMR restraints to large-scale protein structure prediction
-
DOI 10.1529/biophysj.104.044750
-
W. Li, Y. Zhang, and J. Skolnick Application of sparse NMR restraints to large-scale protein structure prediction Biophys. J. 87 2004 1241 1248 (Pubitemid 39095100)
-
(2004)
Biophysical Journal
, vol.87
, Issue.2
, pp. 1241-1248
-
-
Li, W.1
Zhang, Y.2
Skolnick, J.3
-
13
-
-
0033545962
-
Protein structure prediction by global optimization of a potential energy function
-
DOI 10.1073/pnas.96.10.5482
-
A. Liwo, J. Lee, D.R. Ripoll, J. Pillardy, and H.A. Scheraga Protein structure prediction by global optimization of a potential energy function Proc. Natl. Acad. Sci. USA 96 1999 5482 5485 (Pubitemid 29234643)
-
(1999)
Proceedings of the National Academy of Sciences of the United States of America
, vol.96
, Issue.10
, pp. 5482-5485
-
-
Liwo, A.1
Lee, J.2
Ripoll, D.R.3
Pillardy, J.4
Scheraga, H.A.5
-
14
-
-
33645792604
-
Physically realistic homology models built with ROSETTA can be more accurate than their templates
-
K.M. Misura, D. Chivian, C.A. Rohl, D.E. Kim, and D. Baker Physically realistic homology models built with ROSETTA can be more accurate than their templates Proc. Natl. Acad. Sci. USA 103 2006 5361 5366
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 5361-5366
-
-
Misura, K.M.1
Chivian, D.2
Rohl, C.A.3
Kim, D.E.4
Baker, D.5
-
15
-
-
0030627941
-
Improving contact predictions by the combination of correlated mutations and other sources of sequence information
-
O. Olmea, and A. Valencia Improving contact predictions by the combination of correlated mutations and other sources of sequence information Fold. Des. 2 1997 S25 S32
-
(1997)
Fold. Des.
, vol.2
-
-
Olmea, O.1
Valencia, A.2
-
16
-
-
67849110427
-
Structure prediction for CASP8 with all-atom refinement using Rosetta
-
S. Raman, R. Vernon, J. Thompson, M. Tyka, R. Sadreyev, J. Pei, D. Kim, E. Kellogg, F. DiMaio, and O. Lange Structure prediction for CASP8 with all-atom refinement using Rosetta Proteins 77 Suppl 9 2009 89 99
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 89-99
-
-
Raman, S.1
Vernon, R.2
Thompson, J.3
Tyka, M.4
Sadreyev, R.5
Pei, J.6
Kim, D.7
Kellogg, E.8
Dimaio, F.9
Lange, O.10
-
17
-
-
77954065271
-
I-TASSER: A unified platform for automated protein structure and function prediction
-
A. Roy, A. Kucukural, and Y. Zhang I-TASSER: a unified platform for automated protein structure and function prediction Nat. Protoc. 5 2010 725 738
-
(2010)
Nat. Protoc.
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
18
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
DOI 10.1006/jmbi.1993.1626
-
A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815 (Pubitemid 24007801)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
19
-
-
36749031067
-
Contact prediction using mutual information and neural nets
-
DOI 10.1002/prot.21791
-
G. Shackelford, and K. Karplus Contact prediction using mutual information and neural nets Proteins 69 2007 159 164 (Pubitemid 350210123)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.69
, Issue.SUPPL. 8
, pp. 159-164
-
-
Shackelford, G.1
Karplus, K.2
-
20
-
-
0042721397
-
Predicting Interresidue Contacts Using Templates and Pathways
-
DOI 10.1002/prot.10539
-
Y. Shao, and C. Bystroff Predicting interresidue contacts using templates and pathways Proteins 53 Suppl 6 2003 497 502 (Pubitemid 37352209)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.53
, Issue.SUPPL. 6
, pp. 497-502
-
-
Shao, Y.1
Bystroff, C.2
-
21
-
-
0031585984
-
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
-
DOI 10.1006/jmbi.1997.0959
-
K.T. Simons, C. Kooperberg, E. Huang, and D. Baker Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions J. Mol. Biol. 268 1997 209 225 (Pubitemid 27192690)
-
(1997)
Journal of Molecular Biology
, vol.268
, Issue.1
, pp. 209-225
-
-
Simons, K.T.1
Kooperberg, C.2
Huang, E.3
Baker, D.4
-
22
-
-
3142764482
-
Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm
-
DOI 10.1002/prot.20106
-
J. Skolnick, D. Kihara, and Y. Zhang Development and large scale benchmark testing of the PROSPECTOR-3 threading algorithm Proteins 56 2004 502 518 (Pubitemid 38924963)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.3
, pp. 502-518
-
-
Skolnick, J.1
Kihara, D.2
Zhang, Y.3
-
23
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
DOI 10.1093/bioinformatics/bti125
-
J. Soding Protein homology detection by HMM-HMM comparison Bioinformatics 21 2005 951 960 (Pubitemid 40467915)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
24
-
-
67849110005
-
NNcon: Improved protein contact map prediction using 2D-recursive neural networks
-
A.N. Tegge, Z. Wang, J. Eickholt, and J. Cheng NNcon: improved protein contact map prediction using 2D-recursive neural networks Nucleic Acids Res. 37 2009 W515 W518
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Tegge, A.N.1
Wang, Z.2
Eickholt, J.3
Cheng, J.4
-
26
-
-
0043180474
-
PISCES: A protein sequence culling server
-
DOI 10.1093/bioinformatics/btg224
-
G. Wang, and R.L. Dunbrack Jr. PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591 (Pubitemid 37038881)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
27
-
-
34250851687
-
LOMETS: A local meta-threading-server for protein structure prediction
-
DOI 10.1093/nar/gkm251
-
S. Wu, and Y. Zhang LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res. 35 2007 3375 3382 (Pubitemid 47073600)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.10
, pp. 3375-3382
-
-
Wu, S.1
Zhang, Y.2
-
28
-
-
41349114023
-
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
-
DOI 10.1093/bioinformatics/btn069
-
S. Wu, and Y. Zhang A comprehensive assessment of sequence-based and template-based methods for protein contact prediction Bioinformatics 24 2008 924 931 (Pubitemid 351448026)
-
(2008)
Bioinformatics
, vol.24
, Issue.7
, pp. 924-931
-
-
Wu, S.1
Zhang, Y.2
-
29
-
-
46449123146
-
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
-
DOI 10.1002/prot.21945
-
S. Wu, and Y. Zhang MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information Proteins 72 2008 547 556 (Pubitemid 351928511)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.72
, Issue.2
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
30
-
-
34249869832
-
Ab initio modeling of small proteins by iterative TASSER simulations
-
S. Wu, J. Skolnick, and Y. Zhang Ab initio modeling of small proteins by iterative TASSER simulations BMC Biol. 5 2007 17
-
(2007)
BMC Biol.
, vol.5
, pp. 17
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
31
-
-
77951961719
-
How significant is a protein structure similarity with TM-score = 0.5?
-
J. Xu, and Y. Zhang How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26 2010 889 895
-
(2010)
Bioinformatics
, vol.26
, pp. 889-895
-
-
Xu, J.1
Zhang, Y.2
-
32
-
-
74249106219
-
I-TASSER: Fully automated protein structure prediction in CASP8
-
Y. Zhang I-TASSER: fully automated protein structure prediction in CASP8 Proteins 77 2009 100 113
-
(2009)
Proteins
, vol.77
, pp. 100-113
-
-
Zhang, Y.1
-
34
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
DOI 10.1002/prot.20264
-
Y. Zhang, and J. Skolnick Scoring function for automated assessment of protein structure template quality Proteins 57 2004 702 710 (Pubitemid 39626992)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
35
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
DOI 10.1093/nar/gki524
-
Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309 (Pubitemid 41439897)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
36
-
-
0041843696
-
TOUCHSTONE II: A new approach to ab initio protein structure prediction
-
Y. Zhang, A. Kolinski, and J. Skolnick TOUCHSTONE II: a new approach to ab initio protein structure prediction Biophys. J. 85 2003 1145 1164 (Pubitemid 36909676)
-
(2003)
Biophysical Journal
, vol.85
, Issue.2
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
|