-
1
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001; 294: 93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
2
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234: 779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
3
-
-
3242887695
-
Protein structure prediction and analysis using the Robetta server
-
Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004; 32: W526-W531.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
-
4
-
-
30344488120
-
TASSER: an automated method for the prediction of protein tertiary structures in CASP6
-
Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005; 61(Suppl 7): 91-98.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 91-98
-
-
Zhang, Y.1
Arakaki, A.K.2
Skolnick, J.3
-
5
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Soding J, Biegert A, Lupas AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 2005; 33: W244-W248.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Soding, J.1
Biegert, A.2
Lupas, A.N.3
-
6
-
-
34249824268
-
Computational methods in protein structure prediction
-
Floudas CA. Computational methods in protein structure prediction. Biotechnol Bioeng 2007; 97: 207-213.
-
(2007)
Biotechnol Bioeng
, vol.97
, pp. 207-213
-
-
Floudas, C.A.1
-
7
-
-
69449084152
-
Quality assessment of protein structure models
-
Kihara D, Chen H, Yang YD. Quality assessment of protein structure models. Curr Protein Pept Sci 2009; 10: 216-228.
-
(2009)
Curr Protein Pept Sci
, vol.10
, pp. 216-228
-
-
Kihara, D.1
Chen, H.2
Yang, Y.D.3
-
8
-
-
0033531959
-
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
-
Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol 1999; 288: 477-487.
-
(1999)
J Mol Biol
, vol.288
, pp. 477-487
-
-
Lazaridis, T.1
Karplus, M.2
-
9
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990; 112: 6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
10
-
-
0035882533
-
A distance-dependent atomic knowledge-based potential for improved protein structure selection
-
Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001; 44: 223-232.
-
(2001)
Proteins
, vol.44
, pp. 223-232
-
-
Lu, H.1
Skolnick, J.2
-
11
-
-
34250829219
-
OPUS-Ca: a knowledge-based potential function requiring only Calpha positions
-
Wu Y, Lu M, Chen M, Li J, Ma J. OPUS-Ca: a knowledge-based potential function requiring only Calpha positions. Protein Sci 2007; 16: 1449-1463.
-
(2007)
Protein Sci
, vol.16
, pp. 1449-1463
-
-
Wu, Y.1
Lu, M.2
Chen, M.3
Li, J.4
Ma, J.5
-
12
-
-
38049051121
-
OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing
-
Lu M, Dousis AD, Ma J. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing. J Mol Biol 2008; 376: 288-301.
-
(2008)
J Mol Biol
, vol.376
, pp. 288-301
-
-
Lu, M.1
Dousis, A.D.2
Ma, J.3
-
13
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002; 11: 2714-2726.
-
(2002)
Protein Sci
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
14
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998; 275: 895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
15
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
Wang Z, Tegge AN, Cheng J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins 2009; 75: 638-647.
-
(2009)
Proteins
, vol.75
, pp. 638-647
-
-
Wang, Z.1
Tegge, A.N.2
Cheng, J.3
-
16
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle D, Simons KT, Baker D. Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci U S A 1998; 95: 11158-11162.
-
(1998)
Proc Natl Acad Sci U S A
, vol.95
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
17
-
-
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
-
18
-
-
30544448408
-
Exploring protein energy landscapes with hierarchical clustering
-
Gront D, Hansmann UH, Kolinski A. Exploring protein energy landscapes with hierarchical clustering. Int J Quantum Chem 2005; 105: 826-830.
-
(2005)
Int J Quantum Chem
, vol.105
, pp. 826-830
-
-
Gront, D.1
Hansmann, U.H.2
Kolinski, A.3
-
19
-
-
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
, Issue.SUPPL. 9
, pp. 181-184
-
-
Cheng, J.1
Wang, Z.2
Tegge, A.N.3
Eickholt, J.4
-
20
-
-
74249103622
-
Assessment of global and local model quality in CASP8 using Pcons and ProQ
-
Larsson P, Skwark MJ, Wallner B, Elofsson A. Assessment of global and local model quality in CASP8 using Pcons and ProQ. Proteins 2009; 77(Suppl 9): 167-172.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 167-172
-
-
Larsson, P.1
Skwark, M.J.2
Wallner, B.3
Elofsson, A.4
-
21
-
-
74249088516
-
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
-
Benkert P, Tosatto SC, Schwede T. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins 2009; 77(Suppl 9): 173-180.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 173-180
-
-
Benkert, P.1
Tosatto, S.C.2
Schwede, T.3
-
22
-
-
79959415779
-
-
editors. Protein structure selection based on consensus. In: 2010 IEEE Congress on Evolutionary Computation (CEC), July 18-23
-
Wang Q, Shang Y, Xu D, editors. Protein structure selection based on consensus. In: 2010 IEEE Congress on Evolutionary Computation (CEC), July 18-23, 2010.
-
(2010)
-
-
Wang, Q.1
Shang, Y.2
Xu, D.3
-
23
-
-
74249102516
-
Evaluation of CASP8 model quality predictions
-
Cozzetto D, Kryshtafovych A, Tramontano A. Evaluation of CASP8 model quality predictions. Proteins 2009; 77(Suppl 9): 157-166.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 157-166
-
-
Cozzetto, D.1
Kryshtafovych, A.2
Tramontano, A.3
-
24
-
-
80855131663
-
Evaluation of model quality predictions in CASP9
-
Kryshtafovych A, Fidelis K, Tramontano A. Evaluation of model quality predictions in CASP9. Proteins 2011. 79 (Suppl 10): 91-106.
-
(2011)
Proteins
, vol.79
, Issue.SUPPL. 10
, pp. 91-106
-
-
Kryshtafovych, A.1
Fidelis, K.2
Tramontano, A.3
-
25
-
-
77951234057
-
MUFOLD: a new solution for protein 3D structure prediction
-
Zhang J, Wang Q, Barz B, He Z, Kosztin I, Shang Y, Xu D. MUFOLD: a new solution for protein 3D structure prediction. Proteins 2010; 78: 1137-1152.
-
(2010)
Proteins
, vol.78
, pp. 1137-1152
-
-
Zhang, J.1
Wang, Q.2
Barz, B.3
He, Z.4
Kosztin, I.5
Shang, Y.6
Xu, D.7
-
26
-
-
17744387920
-
All are not equal: a benchmark of different homology modeling programs
-
Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci 2005; 14: 1315-1327.
-
(2005)
Protein Sci
, vol.14
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
-
27
-
-
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
-
28
-
-
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
-
29
-
-
0034663738
-
Protein threading using PROSPECT: design and evaluation
-
Xu Y, Xu D. Protein threading using PROSPECT: design and evaluation. Proteins 2000; 40: 343-354.
-
(2000)
Proteins
, vol.40
, pp. 343-354
-
-
Xu, Y.1
Xu, D.2
-
30
-
-
0042622381
-
LGA: a method for finding 3D similarities in protein structures
-
Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003; 31: 3370-3374.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3370-3374
-
-
Zemla, A.1
-
31
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
32
-
-
84970096342
-
Transitivity in structural models of small groups
-
Holland PW, Leinhardt S. Transitivity in structural models of small groups. Small Group Res 1971; 2: 107-124.
-
(1971)
Small Group Res
, vol.2
, pp. 107-124
-
-
Holland, P.W.1
Leinhardt, S.2
-
33
-
-
0032482432
-
Collective dynamics of /'small-world/' networks
-
Watts DJ, Strogatz SH. Collective dynamics of /'small-world/' networks. Nature 1998; 393: 440-442.
-
(1998)
Nature
, vol.393
, pp. 440-442
-
-
Watts, D.J.1
Strogatz, S.H.2
-
34
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB. Principles that govern the folding of protein chains. Science 1973; 181: 223-230.
-
(1973)
Science
, vol.181
, pp. 223-230
-
-
Anfinsen, C.B.1
-
35
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks BR, Brooks CL, III, Mackerell AD, Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009; 30: 1545-1614.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
36
-
-
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
-
37
-
-
77950478720
-
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
-
McGuffin LJ, Roche DB. Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics 2010; 26: 182-188.
-
(2010)
Bioinformatics
, vol.26
, pp. 182-188
-
-
McGuffin, L.J.1
Roche, D.B.2
-
38
-
-
74249107702
-
Assessment of CASP8 structure predictions for template free targets
-
Ben-David M, Noivirt-Brik O, Paz A, Prilusky J, Sussman JL, Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins 2009; 77(Suppl 9): 50-65.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 50-65
-
-
Ben-David, M.1
Noivirt-Brik, O.2
Paz, A.3
Prilusky, J.4
Sussman, J.L.5
Levy, Y.6
-
39
-
-
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
-
40
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998; 275: 895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
41
-
-
67650465659
-
QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
-
Benkert P, Schwede T, Tosatto SC. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol 2009; 9: 35.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 35
-
-
Benkert, P.1
Schwede, T.2
Tosatto, S.C.3
-
42
-
-
0033670439
-
MaxSub: an automated measure for the assessment of protein structure prediction quality
-
Siew N, Elofsson A, Rychlewski L, Fischer D. MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000; 16: 776-785.
-
(2000)
Bioinformatics
, vol.16
, pp. 776-785
-
-
Siew, N.1
Elofsson, A.2
Rychlewski, L.3
Fischer, D.4
-
43
-
-
44449124693
-
Fast procedure for reconstruction of full-atom protein models from reduced representations
-
Rotkiewicz P, Skolnick J. Fast procedure for reconstruction of full-atom protein models from reduced representations. J Comput Chem 2008; 29: 1460-1465.
-
(2008)
J Comput Chem
, vol.29
, pp. 1460-1465
-
-
Rotkiewicz, P.1
Skolnick, J.2
|