-
1
-
-
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
, Issue.SUPPL 10
, pp. 147-160
-
-
Xu, D.1
Zhang, J.2
Roy, A.3
Zhang, Y.4
-
2
-
-
79251513288
-
Reliable protein structure refinement using a physical energy function
-
Lin MS, Head-Gordon T. Reliable protein structure refinement using a physical energy function. J Comput Chem 2011;32:709-717.
-
(2011)
J Comput Chem
, vol.32
, pp. 709-717
-
-
Lin, M.S.1
Head-Gordon, T.2
-
3
-
-
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
-
4
-
-
80052027212
-
Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations
-
Olson MA, Chaudhury S, Lee MS. Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations. J Comput Chem 2011;32:3014-3022.
-
(2011)
J Comput Chem
, vol.32
, pp. 3014-3022
-
-
Olson, M.A.1
Chaudhury, S.2
Lee, M.S.3
-
5
-
-
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(12):1784-1795.
-
(2011)
Structure
, vol.19
, Issue.12
, pp. 1784-1795
-
-
Zhang, J.1
Liang, Y.2
Zhang, Y.3
-
6
-
-
84857737248
-
Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method
-
Park I-H, Gangupomu V, Wagner J, Jain A, Vaidehi N. Structure refinement of protein low resolution models using the GNEIMO constrained dynamics method. J Phys Chem B 2012;116:2365-2375.
-
(2012)
J Phys Chem B
, vol.116
, pp. 2365-2375
-
-
Park, I.-H.1
Gangupomu, V.2
Wagner, J.3
Jain, A.4
Vaidehi, N.5
-
7
-
-
84861668666
-
Elastic network normal modes provide a basis for protein structure refinement
-
Gniewek P, Kolinski A, Jernigan RL, Kloczkowski A. Elastic network normal modes provide a basis for protein structure refinement. J Chem Phys 2012;136:195101.
-
(2012)
J Chem Phys
, vol.136
, pp. 195101
-
-
Gniewek, P.1
Kolinski, A.2
Jernigan, R.L.3
Kloczkowski, A.4
-
8
-
-
84862167980
-
Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models
-
Fan H, Periole X, Mark AE. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models. Proteins 2012;80:1744-1754.
-
(2012)
Proteins
, vol.80
, pp. 1744-1754
-
-
Fan, H.1
Periole, X.2
Mark, A.E.3
-
9
-
-
84864461950
-
Galaxy WEB server for protein structure prediction and refinement
-
Web Server issue
-
Ko J, Park H, Heo L, Seok C. Galaxy WEB server for protein structure prediction and refinement. Nucleic Acids Res 2012;40(Web Server issue):W294-W297.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Ko, J.1
Park, H.2
Heo, L.3
Seok, C.4
-
10
-
-
84864436301
-
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
-
Web Server issue
-
Rodrigues JPGLM, Levitt M, Chopra G. KoBaMIN: a knowledge-based minimization web server for protein structure refinement. Nucleic Acids Res 2012;40(Web Server issue):W323-W328.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Rodrigues, J.P.1
Levitt, M.2
Chopra, G.3
-
11
-
-
84864882089
-
Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX
-
Bell JA, Ho KL, Farid R. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. Acta Crystallogr D Biol Crystallogr 2012;68(Pt 8):935-952.
-
(2012)
Acta Crystallogr D Biol Crystallogr
, vol.68
, Issue.PART 8
, pp. 935-952
-
-
Bell, J.A.1
Ho, K.L.2
Farid, R.3
-
12
-
-
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
-
13
-
-
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
-
14
-
-
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
-
15
-
-
84873094319
-
Structure refinement of protein model decoys requires accurate side chain placement
-
Olson MA, Lee MS. Structure refinement of protein model decoys requires accurate side chain placement. Proteins 2013;81:469-478.
-
(2013)
Proteins
, vol.81
, pp. 469-478
-
-
Olson, M.A.1
Lee, M.S.2
-
16
-
-
84873478862
-
GRID: a high-resolution protein structure refinement algorithm
-
Chitsaz M, Mayo SL. GRID: a high-resolution protein structure refinement algorithm. J Comput Chem 2013;34:445-450.
-
(2013)
J Comput Chem
, vol.34
, pp. 445-450
-
-
Chitsaz, M.1
Mayo, S.L.2
-
17
-
-
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
-
18
-
-
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 Suppl 10:74-90.
-
(2011)
Proteins
, vol.79
, Issue.SUPPL 10
, 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
-
19
-
-
74549178560
-
MolProbity: all-atom structure validation for macromolecular crystallography
-
Chen VB, Arendall WB III, 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 Biol Crystallogr 2010;66(Pt 1):12-21.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, Issue.PART 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
-
20
-
-
34547566446
-
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Web Server issue
-
Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007;35(Web Server issue):W407-W410.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wiederstein, M.1
Sippl, M.J.2
-
21
-
-
36749099341
-
Assessment of CASP7 predictions for template-based modeling targets
-
Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007;69(Suppl 8):38-56.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL 8
, pp. 38-56
-
-
Kopp, J.1
Bordoli, L.2
Battey, J.N.3
Kiefer, F.4
Schwede, T.5
-
22
-
-
84867347204
-
FlexE: using elastic network models to compare models of protein structure
-
Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. FlexE: using elastic network models to compare models of protein structure. J Chem Theory Comput 2012;8:3985-3991.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 3985-3991
-
-
Perez, A.1
Yang, Z.2
Bahar, I.3
Dill, K.A.4
MacCallum, J.L.5
-
23
-
-
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
-
24
-
-
84876529328
-
The RCSB Protein Data Bank: new resources for research and education
-
Database issue
-
Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, Green RK, Goodsell DS, Prlic A, Quesada M, Quinn GB, Ramos AG, Westbrook JD, Young J, Zardecki C, Berman HM, Bourne PE. The RCSB Protein Data Bank: new resources for research and education. Nucleic Acids Res 2013;41(Database issue):D475-D482.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Rose, P.W.1
Bi, C.2
Bluhm, W.F.3
Christie, C.H.4
Dimitropoulos, D.5
Dutta, S.6
Green, R.K.7
Goodsell, D.S.8
Prlic, A.9
Quesada, M.10
Quinn, G.B.11
Ramos, A.G.12
Westbrook, J.D.13
Young, J.14
Zardecki, C.15
Berman, H.M.16
Bourne, P.E.17
-
25
-
-
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 III, 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
, Issue.SUPPL 9
, 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
-
26
-
-
84893010856
-
CASP Prediction center infrastructure and evaluation measires in CASP10 and CASP ROLL
-
Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP Prediction center infrastructure and evaluation measires in CASP10 and CASP ROLL. Proteins 2014;82(Suppl 2):7-13.
-
(2014)
Proteins
, vol.82
, Issue.SUPPL 2
, pp. 7-13
-
-
Kryshtafovych, A.1
Monastyrskyy, B.2
Fidelis, K.3
-
27
-
-
84927694907
-
-
R Development Core Team. Vienna, Austria: R Foundation for Statistical Computing; ; Version 2.11.1.
-
R Development Core Team. R: a language and environment for statistical computing, Vol. 1. Vienna, Austria: R Foundation for Statistical Computing; 2011; Version 2.11.1. p 409.
-
(2011)
R: a language and environment for statistical computing
, vol.1
, pp. 409
-
-
-
28
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr 2007;40(Pt 4):658-674.
-
(2007)
J Appl Crystallogr
, vol.40
, Issue.PART 4
, pp. 658-674
-
-
McCoy, A.J.1
Grosse-Kunstleve, R.W.2
Adams, P.D.3
Winn, M.D.4
Storoni, L.C.5
Read, R.J.6
-
29
-
-
0035788107
-
Pushing the boundaries of molecular replacement with maximum likelihood
-
Read RJ. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr 2001;57(Pt 10):1373-1382.
-
(2001)
Acta Crystallogr D Biol Crystallogr
, vol.57
, Issue.PART 10
, pp. 1373-1382
-
-
Read, R.J.1
-
30
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald IK, Thornton JM. Satisfying hydrogen bonding potential in proteins. J MolBiol 1994;238:777-793.
-
(1994)
J MolBiol
, vol.238
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
31
-
-
84864115802
-
Evaluation of protein structure prediction methods: issues and strategies
-
Kolinski A, editor. New York: Springer;
-
Tramontano A, Cozzetto D. Evaluation of protein structure prediction methods: issues and strategies. In: Kolinski A, editor. Multiscale approaches to protein modeling. New York: Springer; 2011. pp 315-339.
-
(2011)
Multiscale approaches to protein modeling
, pp. 315-339
-
-
Tramontano, A.1
Cozzetto, D.2
-
32
-
-
36749099341
-
Assessment of CASP7 predictions for template-based modeling targets
-
Kopp J, Bordoli L, Battey JND, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007;69(Suppl 8):38-56.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL 8
, pp. 38-56
-
-
Kopp, J.1
Bordoli, L.2
Battey, J.N.D.3
Kiefer, F.4
Schwede, T.5
-
33
-
-
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
|