-
1
-
-
79960394811
-
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
-
Yang Y, Faraggi E, Zhao H, Zhou Y. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates Bioinformatics 2011;27:2076-2082.
-
(2011)
Bioinformatics
, vol.27
, pp. 2076-2082
-
-
Yang, Y.1
Faraggi, E.2
Zhao, H.3
Zhou, Y.4
-
2
-
-
77954065271
-
I-tasser: a unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y. I-tasser: 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
-
3
-
-
77951941264
-
Multicom: a multi-level combination approach to protein structure prediction and its assessments in casp8
-
Wang Z, Eickholt J, Cheng J. Multicom: a multi-level combination approach to protein structure prediction and its assessments in casp8 Bioinformatics 2010;26:882-888.
-
(2010)
Bioinformatics
, vol.26
, pp. 882-888
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
4
-
-
78650905964
-
Rosetta3 an object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A, Tyka M, Lewis S, Lange O, Thompson J, Jacak R, Kaufman K, Renfrew D, Smith C, Sheffler W, Davis I, Cooper S, Treuille A, Mandell D, Richter F, Ban YEA, Fleishman S, Corn J, Kim D, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek J, Karanicolas J, Das R, Meiler J, Kortemme T, Gray J, Kuhlman B, Baker D, Bradley P. Rosetta3 an object-oriented software suite for the simulation and design of macromolecules Methods Enzymol 2011;487:545-574.
-
(2011)
Methods Enzymol
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.3
Lange, O.4
Thompson, J.5
Jacak, R.6
Kaufman, K.7
Renfrew, D.8
Smith, C.9
Sheffler, W.10
Davis, I.11
Cooper, S.12
Treuille, A.13
Mandell, D.14
Richter, F.15
Ban, Y.E.A.16
Fleishman, S.17
Corn, J.18
Kim, D.19
Lyskov, S.20
Berrondo, M.21
Mentzer, S.22
Popovic, Z.23
Havranek, J.24
Karanicolas, J.25
Das, R.26
Meiler, J.27
Kortemme, T.28
Gray, J.29
Kuhlman, B.30
Baker, D.31
Bradley, P.32
more..
-
5
-
-
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
-
6
-
-
0141642142
-
Astro-fold: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
-
Klepeis JL, Floudas CA. Astro-fold: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence Biophys J 2003;85:2119-2146.
-
(2003)
Biophys J
, vol.85
, pp. 2119-2146
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
7
-
-
84857946670
-
Astro-fold 2.0: an enhanced framework for protein structure prediction
-
Subramani A, Wei Y, Floudas CA. Astro-fold 2.0: an enhanced framework for protein structure prediction AIChE J 2012;58:1619-1637.
-
(2012)
AIChE J
, vol.58
, pp. 1619-1637
-
-
Subramani, A.1
Wei, Y.2
Floudas, C.A.3
-
8
-
-
27844505722
-
Advances in protein structure prediction and de novo protein design: a review
-
Floudas CA, Fung H, McAllister S, Mönnigmann M, Rajgaria R. Advances in protein structure prediction and de novo protein design: a review. Chem Eng Sci 2006;61:966-988.
-
(2006)
Chem Eng Sci
, vol.61
, pp. 966-988
-
-
Floudas, C.A.1
Fung, H.2
McAllister, S.3
Mönnigmann, M.4
Rajgaria, R.5
-
9
-
-
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
-
10
-
-
84869761071
-
The protein-folding problem, 50 years on
-
Dill KA, MacCallum JL. The protein-folding problem, 50 years on. Science 2012;338:1042-1046.
-
(2012)
Science
, vol.338
, pp. 1042-1046
-
-
Dill, K.A.1
MacCallum, J.L.2
-
11
-
-
80855147416
-
Assessment of protein structure refinement in casp9
-
MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in casp9. Proteins 2011;79:74-90.
-
(2011)
Proteins
, vol.79
, pp. 74-90
-
-
MacCallum, J.L.1
Pérez, A.2
Schnieders, M.J.3
Hua, L.4
Jacobson, M.P.5
Dill, K.A.6
-
12
-
-
74249121740
-
Assessment of the protein-structure refinement category in casp8
-
MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in casp8. Proteins 2009;77(Suppl 9):66-80.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL 9
, pp. 66-80
-
-
MacCallum, J.L.1
Hua, L.2
Schnieders, M.J.3
Pande, V.S.4
Jacobson, M.P.5
Dill, K.A.6
-
13
-
-
1642575364
-
Accurate and efficient loop selections by the dfire-based all-atom statistical potential
-
Zhang C, Liu S, Zhou Y. Accurate and efficient loop selections by the dfire-based all-atom statistical potential. Protein Sci 2004;13:391-399.
-
(2004)
Protein Sci
, vol.13
, pp. 391-399
-
-
Zhang, C.1
Liu, S.2
Zhou, Y.3
-
14
-
-
84873657174
-
Protein structure refinement through structure selection and averaging from molecular dynamics ensembles
-
Mirjalili V, Feig M. Protein structure refinement through structure selection and averaging from molecular dynamics ensembles. J Chem Theory Comput 2013;9:1294-1303.
-
(2013)
J Chem Theory Comput
, vol.9
, pp. 1294-1303
-
-
Mirjalili, V.1
Feig, M.2
-
15
-
-
84864436301
-
Kobamin: a knowledge-based minimization web server for protein structure refinement
-
Rodrigues JPGLM, Levitt M, Chopra G. Kobamin: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res 2012;40:W323-W328.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Rodrigues, J.P.1
Levitt, M.2
Chopra, G.3
-
16
-
-
77955792980
-
Consistent refinement of submitted models at casp using a knowledge-based potential
-
Chopra G, Kalisman N, Levitt M. Consistent refinement of submitted models at casp using a knowledge-based potential. Proteins 2010;78:2668-2678.
-
(2010)
Proteins
, vol.78
, pp. 2668-2678
-
-
Chopra, G.1
Kalisman, N.2
Levitt, M.3
-
17
-
-
58149479285
-
Solvent dramatically affects protein structure refinement
-
Chopra G, Summa CM, Levitt M. Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci USA 2008;105:20239-20244.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 20239-20244
-
-
Chopra, G.1
Summa, C.M.2
Levitt, M.3
-
18
-
-
84871034858
-
3drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization
-
Bhattacharya D, Cheng J. 3drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization. Proteins 2013;81:119-131.
-
(2013)
Proteins
, vol.81
, pp. 119-131
-
-
Bhattacharya, D.1
Cheng, J.2
-
19
-
-
84883590772
-
Galaxyrefine: protein structure refinement driven by side-chain repacking
-
Heo L, Park H, Seok C. Galaxyrefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 2013;41:W384-W388.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Heo, L.1
Park, H.2
Seok, C.3
-
20
-
-
84863783282
-
Refinement of unreliable local regions in template-based protein models
-
Park H, Seok C. Refinement of unreliable local regions in template-based protein models. Proteins 2012;80:1974-1986.
-
(2012)
Proteins
, vol.80
, pp. 1974-1986
-
-
Park, H.1
Seok, C.2
-
21
-
-
80051556272
-
Refinement of protein termini in template-based modeling using conformational space annealing
-
Park H, Ko J, Joo K, Lee J, Seok C, Lee J. Refinement of protein termini in template-based modeling using conformational space annealing. Proteins 2011;79:2725-2734.
-
(2011)
Proteins
, vol.79
, pp. 2725-2734
-
-
Park, H.1
Ko, J.2
Joo, K.3
Lee, J.4
Seok, C.5
Lee, J.6
-
22
-
-
77951234057
-
-
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)
Mufold: a new solution for protein 3d structure prediction 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
-
23
-
-
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
-
24
-
-
0035914481
-
Molecular dynamics in the endgame of protein structure prediction
-
Lee MR, Tsai J, Baker D, Kollman PA. Molecular dynamics in the endgame of protein structure prediction J Mol Biol 2001;313:417-430.
-
(2001)
J Mol Biol
, vol.313
, pp. 417-430
-
-
Lee, M.R.1
Tsai, J.2
Baker, D.3
Kollman, P.A.4
-
25
-
-
34248549547
-
Can molecular dynamics simulations provide high-resolution refinement of protein structure?
-
Chen J, Brooks III CL. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007;67:922-930.
-
(2007)
Proteins
, vol.67
, pp. 922-930
-
-
Chen, J.1
Brooks III, C.L.2
-
26
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
Misura KMS, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 2005;59:15-29.
-
(2005)
Proteins
, vol.59
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
27
-
-
4644340524
-
Automated nmr structure calculation with cyana
-
Güntert P. Automated nmr structure calculation with cyana. Methods Mol Biol 2004;278:353-378.
-
(2004)
Methods Mol Biol
, vol.278
, pp. 353-378
-
-
Güntert, P.1
-
28
-
-
67650500988
-
Charmm: the biomolecular simulation program
-
Brooks BR, Brooks III CL, Mackerell A 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.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..
-
29
-
-
46449132707
-
Specific interactions for ab initio folding of protein terminal regions with secondary structures
-
Yang Y, Zhou Y. Specific interactions for ab initio folding of protein terminal regions with secondary structures. Proteins 2008;72:793-803.
-
(2008)
Proteins
, vol.72
, pp. 793-803
-
-
Yang, Y.1
Zhou, Y.2
-
30
-
-
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
-
31
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P. Knowledge-based protein secondary structure assignment Proteins 1995;23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
32
-
-
84859738455
-
A simple and efficient statistical potential for scoring ensembles of protein structures
-
Cossio P, Granata D, Laio A, Seno F, Trovato A. A simple and efficient statistical potential for scoring ensembles of protein structures. Sci Rep 2012;2.
-
(2012)
Sci Rep
, vol.2
-
-
Cossio, P.1
Granata, D.2
Laio, A.3
Seno, F.4
Trovato, A.5
-
33
-
-
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
-
34
-
-
79958078892
-
Apollo: a quality assessment service for single and multiple protein models
-
Wang Z, Eickholt J, Cheng J. Apollo: a quality assessment service for single and multiple protein models. Bioinformatics 2011;27:1715-1716.
-
(2011)
Bioinformatics
, vol.27
, pp. 1715-1716
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
35
-
-
42449122271
-
Ranking predicted protein structures with support vector regression
-
Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support vector regression. Proteins 2008;71:1175-1182.
-
(2008)
Proteins
, vol.71
, pp. 1175-1182
-
-
Qiu, J.1
Sheffler, W.2
Baker, D.3
Noble, W.S.4
-
37
-
-
79952673719
-
A machine learning-based method for protein global model quality assessment
-
Dong Q, Chen Y, Zhou S. A machine learning-based method for protein global model quality assessment. Int J Gen Syst 2011;40:417-425.
-
(2011)
Int J Gen Syst
, vol.40
, pp. 417-425
-
-
Dong, Q.1
Chen, Y.2
Zhou, S.3
-
38
-
-
34249753618
-
Support-vector networks
-
Cortes C, Vapnik V. Support-vector networks. Mach Learn 1995;20:273-297.
-
(1995)
Mach Learn
, vol.20
, pp. 273-297
-
-
Cortes, C.1
Vapnik, V.2
-
39
-
-
85076265982
-
Class imbalance learning methods for support vector machines
-
Batuwita R, Palade V. Class imbalance learning methods for support vector machines. Imbalanced Learn 2013;83:83-96.
-
(2013)
Imbalanced Learn
, vol.83
, pp. 83-96
-
-
Batuwita, R.1
Palade, V.2
-
40
-
-
33646358186
-
The application of support vector machines to medical decision support: a case study
-
Veropoulos K, Cristianini N, Campbell C. The application of support vector machines to medical decision support: a case study. Adv Course Artif Intell 1999;1-6.
-
(1999)
Adv Course Artif Intell
, pp. 1-6
-
-
Veropoulos, K.1
Cristianini, N.2
Campbell, C.3
-
41
-
-
4444221565
-
Ucsf chimera-a visualization system for exploratory research and analysis
-
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. Ucsf chimera-a visualization system for exploratory research and analysis J Comput Chem 2004;25:1605-1612.
-
(2004)
J Comput Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
42
-
-
35748935079
-
Wordom: a program for efficient analysis of molecular dynamics simulations
-
Seeber M, Cecchini M, Rao F, Settanni G, Caflisch A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics 2007;23:2625-2627.
-
(2007)
Bioinformatics
, vol.23
, pp. 2625-2627
-
-
Seeber, M.1
Cecchini, M.2
Rao, F.3
Settanni, G.4
Caflisch, A.5
-
43
-
-
0345306764
-
Design of a novel globular protein fold with atomic-level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science 2003;302:1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
45
-
-
34247247779
-
Improved residue contact prediction using support vector machines and a large feature set
-
Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007;8:113.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 113
-
-
Cheng, J.1
Baldi, P.2
-
46
-
-
40549111613
-
Facts: fast analytical continuum treatment of solvation
-
Haberthür U, Caflisch A. Facts: fast analytical continuum treatment of solvation J Comput Chem 2008;29:701-715.
-
(2008)
J Comput Chem
, vol.29
, pp. 701-715
-
-
Haberthür, U.1
Caflisch, A.2
-
47
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems. J Chem Phys 1996;105:1902.
-
(1996)
J Chem Phys
, vol.105
, pp. 1902
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
48
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert J, Ciccotti G, Berendsen H. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
49
-
-
76549089189
-
Sphericity of a protein via the β-complex
-
Kim DS, Kim JK, Won CI, Kim CM, Park JY, Bhak J. Sphericity of a protein via the β-complex. J Mol Graph Model 2010;28:636-649.
-
(2010)
J Mol Graph Model
, vol.28
, pp. 636-649
-
-
Kim, D.S.1
Kim, J.K.2
Won, C.I.3
Kim, C.M.4
Park, J.Y.5
Bhak, J.6
-
50
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott Dunbrack, R.L.3
Evanseck, J.D.4
Field, M.J.5
Fischer, S.6
Gao, J.7
Guo, H.8
Ha, S.9
Joseph-McCarthy, D.10
Kuchnir, L.11
Kuczera, K.12
Lau, F.T.K.13
Mattos, C.14
Michnick, S.15
Ngo, T.16
Nguyen, D.T.17
Prodhom, B.18
Reiher, W.E.19
Roux, B.20
Schlenkrich, M.21
Smith, J.C.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiorkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
51
-
-
4444351490
-
Empirical force fields for biological macromolecules: overview and issues
-
MacKerell AD. Empirical force fields for biological macromolecules: overview and issues J Comput Chem 2004;25:1584-1604.
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
MacKerell, A.D.1
-
53
-
-
84893010893
-
Interplay of i-tasser and quark for template-based and ab initio protein structure prediction in casp10
-
in press, doi: 10.1002/prot.24341
-
Zhang Y. Interplay of i-tasser and quark for template-based and ab initio protein structure prediction in casp10. Proteins, in press, doi: 10.1002/prot.24341.
-
Proteins
-
-
Zhang, Y.1
-
54
-
-
84893009061
-
Protein structure modeling for casp10 by multiple layers of global optimization
-
in press, doi: 10.1002/prot.24397
-
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, in press, doi: 10.1002/prot.24397.
-
Proteins
-
-
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
-
55
-
-
23144452044
-
The hhpred interactive server for protein homology detection and structure prediction
-
Söding 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
-
-
Söding, J.1
Biegert, A.2
Lupas, A.N.3
-
56
-
-
84864448769
-
Template-based protein structure modeling using the raptorx web server
-
Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, Xu J. Template-based protein structure modeling using the raptorx web server. Nat Protoc 2012;7:1511-1522.
-
(2012)
Nat Protoc
, vol.7
, pp. 1511-1522
-
-
Källberg, M.1
Wang, H.2
Wang, S.3
Peng, J.4
Wang, Z.5
Lu, H.6
Xu, J.7
-
58
-
-
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
-
59
-
-
71649114292
-
Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: insights from molecular dynamics simulations
-
Tamamis P, Kasotakis E, Mitraki A, Archontis G. Amyloid-like self-assembly of peptide sequences from the adenovirus fiber shaft: insights from molecular dynamics simulations. J Phys Chem B 2009;113:15639-15647.
-
(2009)
J Phys Chem B
, vol.113
, pp. 15639-15647
-
-
Tamamis, P.1
Kasotakis, E.2
Mitraki, A.3
Archontis, G.4
-
60
-
-
78751580537
-
Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: perspectives from molecular dynamics simulations
-
Tamamis P, Archontis G. Amyloid-like self-assembly of a dodecapeptide sequence from the adenovirus fiber shaft: perspectives from molecular dynamics simulations. J Non-Cryst Solids 2011;357:717-722.
-
(2011)
J Non-Cryst Solids
, vol.357
, pp. 717-722
-
-
Tamamis, P.1
Archontis, G.2
-
61
-
-
33645786604
-
Importance of the cmap correction to the charmm22 protein force field: dynamics of hen lysozyme
-
Buck M, Bouguet-Bonnet S, Pastor RW, MacKerell AD Jr. Importance of the cmap correction to the charmm22 protein force field: dynamics of hen lysozyme. Biophys J 2006;90:L36-L38.
-
(2006)
Biophys J
, vol.90
-
-
Buck, M.1
Bouguet-Bonnet, S.2
Pastor, R.W.3
MacKerell Jr., A.D.4
-
62
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell AD Jr, Feig M, Brooks III CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
63
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im W, Lee MS, Brooks III CL. Generalized born model with a simple smoothing function J Comput Chem 2003;24:1691-702.
-
(2003)
J Comput Chem
, vol.24
, pp. 1691-1702
-
-
Im, W.1
Lee, M.S.2
Brooks III, C.L.3
-
65
-
-
0038792211
-
New analytic approximation to the standard molecular volume definition and its application to generalized born calculations
-
Lee MS, Feig M, Salsbury FR, Brooks III CL. New analytic approximation to the standard molecular volume definition and its application to generalized born calculations J Comput Chem 2003;24:1348-1356.
-
(2003)
J Comput Chem
, vol.24
, pp. 1348-1356
-
-
Lee, M.S.1
Feig, M.2
Salsbury, F.R.3
Brooks III, C.L.4
-
66
-
-
0346971105
-
Performance comparison of generalized born and poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks III CL. Performance comparison of generalized born and poisson methods in the calculation of electrostatic solvation energies for protein structures J Comput Chem 2004;25:265-284.
-
(2004)
J Comput Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
-
67
-
-
84860767348
-
Routine microsecond molecular dynamics simulations with amber on gpus. 1
-
Gotz AW, Williamson MJ, Xu D, Poole D, Le Grand S, Walker RC. Routine microsecond molecular dynamics simulations with amber on gpus. 1. Generalized born J Chem Theory Comput 2012;8:1542-1555.
-
(2012)
Generalized born J Chem Theory Comput
, vol.8
, pp. 1542-1555
-
-
Gotz, A.W.1
Williamson, M.J.2
Xu, D.3
Poole, D.4
Le Grand, S.5
Walker, R.C.6
-
68
-
-
84863775602
-
Refinement of protein structure homology models via long, all-atom molecular dynamics simulations
-
Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations Proteins 2012;80:2071-2079.
-
(2012)
Proteins
, vol.80
, pp. 2071-2079
-
-
Raval, A.1
Piana, S.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
69
-
-
43149099005
-
Development of a physics-based force field for the scoring and refinement of protein models
-
Wroblewska L, Jagielska A, Skolnick J. Development of a physics-based force field for the scoring and refinement of protein models. Biophys J 2008;94:3227-3240.
-
(2008)
Biophys J
, vol.94
, pp. 3227-3240
-
-
Wroblewska, L.1
Jagielska, A.2
Skolnick, J.3
-
70
-
-
46149096463
-
Protein model refinement using an optimized physics-based all-atom force field
-
Jagielska A, Wroblewska L, Skolnick J. Protein model refinement using an optimized physics-based all-atom force field. Proc Natl Acad Sci USA 2008;105:8268-8273.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 8268-8273
-
-
Jagielska, A.1
Wroblewska, L.2
Skolnick, J.3
|