Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Edoardo Sarti; Ivan Gladich; Stefano Zamuner; Bruno E. Correia; Alessandro Laio

doi:10.1002/prot.25079

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25079 ◽

2016 ◽

Vol 84 (9) ◽

pp. 1312-1320 ◽

Cited By ~ 6

Author(s):

Edoardo Sarti ◽

Ivan Gladich ◽

Stefano Zamuner ◽

Bruno E. Correia ◽

Alessandro Laio

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction

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De novo protein structure prediction using ultra-fast molecular dynamics simulation

PLoS ONE ◽

10.1371/journal.pone.0205819 ◽

2018 ◽

Vol 13 (11) ◽

pp. e0205819 ◽

Cited By ~ 6

Author(s):

Ngaam J. Cheung ◽

Wookyung Yu

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Protein Structure Prediction ◽

Structure Prediction ◽

De Novo ◽

Dynamics Simulation

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Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

Journal of Chemical Theory and Computation ◽

10.1021/ct500995d ◽

2015 ◽

Vol 11 (3) ◽

pp. 1337-1346 ◽

Cited By ~ 24

Author(s):

Steffen Lindert ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

High Precision ◽

Structure Prediction ◽

Structure Refinement ◽

Protein Structure Refinement

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A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2008.02.048 ◽

2008 ◽

Vol 369 (2) ◽

pp. 500-506 ◽

Cited By ~ 7

Author(s):

Takeshi N. Sasaki ◽

Hikmet Cetin ◽

Masaki Sasai

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

De Novo ◽

Coarse Grained

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State of the art in studying protein folding and protein structure prediction using molecular dynamics methods

Journal of Molecular Graphics and Modelling ◽

10.1016/s1093-3263(00)00126-1 ◽

2001 ◽

Vol 19 (1) ◽

pp. 146-149 ◽

Cited By ~ 7

Author(s):

M.R Lee ◽

Y Duan ◽

P.A Kollman

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

State Of The Art ◽

Molecular Dynamics Methods

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Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations

Bulletin of the Korean Chemical Society ◽

10.5012/bkcs.2008.29.11.2172 ◽

2008 ◽

Vol 29 (11) ◽

pp. 2172-2182 ◽

Cited By ~ 4

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Dynamics Simulations

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Molecular dynamics in the endgame of protein structure prediction

Journal of Molecular Biology ◽

10.1006/jmbi.2001.5032 ◽

2001 ◽

Vol 313 (2) ◽

pp. 417-430 ◽

Cited By ~ 102

Author(s):

Matthew R. Lee ◽

Jerry Tsai ◽

David Baker ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction

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A study of simulated annealing protocols for use with molecular dynamics in protein structure prediction

Protein Engineering Design and Selection ◽

10.1093/protein/7.2.235 ◽

1994 ◽

Vol 7 (2) ◽

pp. 235-241 ◽

Cited By ~ 17

Author(s):

C. A. Laughton

Keyword(s):

Molecular Dynamics ◽

Simulated Annealing ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction

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Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2014.994188 ◽

2015 ◽

Vol 33 (10) ◽

pp. 2173-2179 ◽

Cited By ~ 17

Author(s):

Nicole Balasco ◽

Daniela Barone ◽

Luigi Vitagliano

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Structural Conversion ◽

Dynamics Simulations

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Self-consistently optimized energy functions for protein structure prediction by molecular dynamics

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.95.6.2932 ◽

1998 ◽

Vol 95 (6) ◽

pp. 2932-2937 ◽

Cited By ~ 54

Author(s):

K. K. Koretke ◽

Z. Luthey-Schulten ◽

P. G. Wolynes

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Energy Functions

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Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction

Biophysical Journal ◽

10.1016/j.bpj.2009.11.031 ◽

2010 ◽

Vol 98 (6) ◽

pp. 1046-1054 ◽

Cited By ~ 6

Author(s):

Tyler J. Glembo ◽

S. Banu Ozkan

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Geometric Constraint

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