-
1
-
-
0014693695
-
A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme
-
Browne WJ, North AC, Phillips DC, Brew K, Vanaman TC, Hill RL. A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J Mol Biol 1969;42:65–86.
-
(1969)
J Mol Biol
, vol.42
, pp. 65-86.
-
-
Browne, W.J.1
North, A.C.2
Phillips, D.C.3
Brew, K.4
Vanaman, T.C.5
Hill, R.L.6
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389–3402.
-
(1997)
Nucleic Acids Res
, vol.25
, 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
-
3
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie JU, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991;253:164–170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Luthy, R.2
Eisenberg, D.3
-
4
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951–960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Soding, J.1
-
5
-
-
46449123146
-
MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information
-
Wu S, Zhang Y. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 2008;72:547–556.
-
(2008)
Proteins
, vol.72
, pp. 547-556
-
-
Wu, S.1
Zhang, Y.2
-
7
-
-
34250851687
-
LOMETS: a local meta-threading-server for protein structure prediction
-
Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucl Acids Res 2007;35:3375–3382.
-
(2007)
Nucl Acids Res
, vol.35
, pp. 3375-3382
-
-
Wu, S.1
Zhang, Y.2
-
8
-
-
2442676589
-
Automated structure prediction of weakly homologous proteins on a genomic scale
-
Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594–7599.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7594-7599
-
-
Zhang, Y.1
Skolnick, J.2
-
9
-
-
84925156346
-
The I-TASSER Suite: protein structure and function prediction
-
Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods 2015;12:7–8.
-
(2015)
Nature Methods
, vol.12
, pp. 7-8
-
-
Yang, J.1
Yan, R.2
Roy, A.3
Xu, D.4
Poisson, J.5
Zhang, Y.6
-
10
-
-
84893009061
-
Protein structure modeling for CASP10 by multiple layers of global optimization
-
Joo K, Lee J, Sim S, Lee SY, Lee K, Heo S, Lee IH, Lee SJ, Lee J. Protein structure modeling for CASP10 by multiple layers of global optimization. Proteins 2014;82 Suppl 2:188–195.
-
(2014)
Proteins
, vol.82
, pp. 188-195
-
-
Joo, K.1
Lee, J.2
Sim, S.3
Lee, S.Y.4
Lee, K.5
Heo, S.6
Lee, I.H.7
Lee, S.J.8
Lee, J.9
-
11
-
-
74249120024
-
Prediction of global and local quality of CASP8 models by MULTICOM series
-
Cheng J, Wang Z, Tegge AN, Eickholt J. Prediction of global and local quality of CASP8 models by MULTICOM series. Proteins 2009;77 Suppl 9:181–184.
-
(2009)
Proteins
, vol.77
, pp. 181-184
-
-
Cheng, J.1
Wang, Z.2
Tegge, A.N.3
Eickholt, J.4
-
12
-
-
33645792604
-
Physically realistic homology models built with ROSETTA can be more accurate than their templates
-
Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 2006;103:5361–5366.
-
(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
-
13
-
-
77954065271
-
ITASSER: a unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y. ITASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 2010;5:725–738.
-
(2010)
Nat Protoc
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
14
-
-
84862225232
-
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field
-
Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 2012;80:1715–1735.
-
(2012)
Proteins
, vol.80
, pp. 1715-1735
-
-
Xu, D.1
Zhang, Y.2
-
15
-
-
84892968997
-
CASP10 results compared to those of previous CASP experiments
-
Kryshtafovych A, Fidelis K, Moult J. CASP10 results compared to those of previous CASP experiments. Proteins 2014;82 Suppl 2:164–174.
-
(2014)
Proteins
, vol.82
, pp. 164-174
-
-
Kryshtafovych, A.1
Fidelis, K.2
Moult, J.3
-
17
-
-
84879988025
-
ThreaDom: extracting protein domain boundary information from multiple threading alignments
-
Xue Z, Xu D, Wang Y, Zhang Y. ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics 2013;29:i247–i256.
-
(2013)
Bioinformatics
, vol.29
, pp. i247-i256
-
-
Xue, Z.1
Xu, D.2
Wang, Y.3
Zhang, Y.4
-
18
-
-
0030777303
-
CATH–a hierarchic classification of protein domain structures
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH–a hierarchic classification of protein domain structures. Structure 1997;5:1093–1108.
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
19
-
-
84893010893
-
Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10
-
Zhang Y. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10. Proteins 2014;82 Suppl 2:175–187.
-
(2014)
Proteins
, vol.82 Suppl 2
, pp. 175-187
-
-
Zhang, Y.1
-
20
-
-
34249869832
-
Ab initio modeling of small proteins by iterative TASSER simulations
-
Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 2007;5:17
-
(2007)
BMC Biol
, vol.5
, pp. 17
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
21
-
-
0041843696
-
TOUCHSTONE II: a new approach to ab initio protein structure prediction
-
Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 2003;85:1145–1164.
-
(2003)
Biophys J
, vol.85
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
-
22
-
-
84872600524
-
Toward optimal fragment generations for ab initio protein structure assembly
-
Xu D, Zhang Y. Toward optimal fragment generations for ab initio protein structure assembly. Proteins 2013;81:229–239.
-
(2013)
Proteins
, vol.81
, pp. 229-239
-
-
Xu, D.1
Zhang, Y.2
-
23
-
-
1942519275
-
SPICKER: a clustering approach to identify near-native protein folds
-
Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865–871.
-
(2004)
J Comput Chem
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
24
-
-
82955239912
-
Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
-
Zhang J, Liang Y, Zhang Y. Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 2011;19:1784–1795.
-
(2011)
Structure
, vol.19
, pp. 1784-1795
-
-
Zhang, J.1
Liang, Y.2
Zhang, Y.3
-
25
-
-
10344232638
-
Scoring function for automated assessment of protein structure template quality
-
Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702–710.
-
(2004)
Proteins
, vol.57
, pp. 702-710
-
-
Zhang, Y.1
Skolnick, J.2
-
26
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci 2006;15:2507–2524.
-
(2006)
Protein Sci
, vol.15
, pp. 2507-2524
-
-
Shen, M.Y.1
Sali, A.2
-
27
-
-
80054694711
-
GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
-
Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 2011;101:2043–2052.
-
(2011)
Biophys J
, vol.101
, pp. 2043-2052
-
-
Zhou, H.1
Skolnick, J.2
-
28
-
-
78149453870
-
A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction
-
Zhang J, Zhang Y. A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction. PloS One 2010;5:e15386
-
(2010)
PloS One
, vol.5
-
-
Zhang, J.1
Zhang, Y.2
-
29
-
-
39449115394
-
ITASSER server for protein 3D structure prediction
-
Zhang Y. ITASSER server for protein 3D structure prediction. BMC Bioinformatics 2008;9:40
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
30
-
-
68049138029
-
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks
-
Li Y, Zhang Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 2009;76:665–676.
-
(2009)
Proteins
, vol.76
, pp. 665-676
-
-
Li, Y.1
Zhang, Y.2
-
31
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov GG, Shapovalov MV, Dunbrack RL. Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009;77:778–795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack, R.L.3
-
32
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302–2309.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
33
-
-
77951961719
-
How significant is a protein structure similarity with TM-score = 0.5?
-
Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 2010;26:889–895.
-
(2010)
Bioinformatics
, vol.26
, pp. 889-895
-
-
Xu, J.1
Zhang, Y.2
-
34
-
-
74249092329
-
The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models
-
Keedy DA, Williams CJ, Headd JJ, Arendall WB, 3rd, Chen VB, Kapral GJ, Gillespie RA, Block JN, Zemla A, Richardson DC, Richardson JS. The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models. Proteins 2009;77 Suppl 9:29–49.
-
(2009)
Proteins
, vol.77
, pp. 29-49
-
-
Keedy, D.A.1
Williams, C.J.2
Headd, J.J.3
Arendall, W.B.4
Chen, V.B.5
Kapral, G.J.6
Gillespie, R.A.7
Block, J.N.8
Zemla, A.9
Richardson, D.C.10
Richardson, J.S.11
-
35
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB, 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D 2010;66(Pt 1):12–21.
-
(2010)
Acta Crystallogr D
, vol.66Pt 1
, pp. 12-21
-
-
Chen, V.B.1
Arendall, W.B.2
Headd, J.J.3
Keedy, D.A.4
Immormino, R.M.5
Kapral, G.J.6
Murray, L.W.7
Richardson, J.S.8
Richardson, D.C.9
-
36
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195–202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
37
-
-
79960418213
-
Structure of Burkholderia cepacia UDP-glucose dehydrogenase (UGD) BceC and role of Tyr10 in final hydrolysis of UGD thioester intermediate
-
Rocha J, Popescu AO, Borges P, Mil-Homens D, Moreira LM, Sa-Correia I, Fialho AM, Frazao C. Structure of Burkholderia cepacia UDP-glucose dehydrogenase (UGD) BceC and role of Tyr10 in final hydrolysis of UGD thioester intermediate. J Bacteriol 2011;193:3978–3987.
-
(2011)
J Bacteriol
, vol.193
, pp. 3978-3987
-
-
Rocha, J.1
Popescu, A.O.2
Borges, P.3
Mil-Homens, D.4
Moreira, L.M.5
Sa-Correia, I.6
Fialho, A.M.7
Frazao, C.8
-
38
-
-
74249106219
-
ITASSER: Fully automated protein structure prediction in CASP8
-
Zhang Y. ITASSER: Fully automated protein structure prediction in CASP8. Proteins 2009;77:100–113.
-
(2009)
Proteins
, vol.77
, pp. 100-113
-
-
Zhang, Y.1
-
39
-
-
80855147432
-
Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement
-
Xu D, Zhang J, Roy A, Zhang Y. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins 2011;79 (Suppl 10):147–160.
-
(2011)
Proteins
, vol.79
, pp. 147-160
-
-
Xu, D.1
Zhang, J.2
Roy, A.3
Zhang, Y.4
-
40
-
-
84901271941
-
A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction
-
Yan R, Xu D, Yang J, Walker S, Zhang Y. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Sci Rep 2013;3:2619
-
(2013)
Sci Rep
, vol.3
, pp. 2619
-
-
Yan, R.1
Xu, D.2
Yang, J.3
Walker, S.4
Zhang, Y.5
|