pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

Bioinformatics ◽

10.1093/bioinformatics/btt262 ◽

2013 ◽

Vol 29 (13) ◽

pp. 1698-1699 ◽

Author(s):

Brian Jiménez-García ◽

Carles Pons ◽

Juan Fernández-Recio

Keyword(s):

Protein Docking ◽

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Effect of local shape modifications of molecular surfaces on rigid-body protein–protein docking

Protein Engineering Design and Selection ◽

10.1093/proeng/gzg021 ◽

2003 ◽

Vol 16 (3) ◽

pp. 179-185 ◽

Author(s):

A. Heifetz ◽

M. Eisenstein

Keyword(s):

Protein Docking ◽

Body Protein ◽

Local Shape ◽

Molecular Surfaces

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Performance and Its Limits in Rigid Body Protein-Protein Docking

Structure ◽

10.1016/j.str.2020.06.006 ◽

2020 ◽

Vol 28 (9) ◽

pp. 1071-1081.e3 ◽

Author(s):

Israel T. Desta ◽

Kathryn A. Porter ◽

Bing Xia ◽

Dima Kozakov ◽

Sandor Vajda

Keyword(s):

Protein Docking ◽

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Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization

Protein Science ◽

10.1110/ps.072847207 ◽

2007 ◽

Vol 16 (12) ◽

pp. 2716-2725 ◽

Author(s):

Stephan Lorenzen ◽

Yang Zhang

Keyword(s):

Monte Carlo ◽

Protein Docking ◽

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RDOCK: Refinement of rigid-body protein docking predictions

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10460 ◽

2003 ◽

Vol 53 (3) ◽

pp. 693-707 ◽

Author(s):

Li Li ◽

Rong Chen ◽

Zhiping Weng

Keyword(s):

Protein Docking ◽

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1E1536 Representative Interaction FingerPrint from decoys generated by rigid-body protein-protein docking(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s41_2 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S41

Author(s):

Nobuyuki Uchikoga ◽

Yuri Matsuzaki ◽

Masahito Ohue ◽

Takatsugu Hirokawa ◽

Yutaka Akiyama

Keyword(s):

Annual Meeting ◽

Protein Docking ◽

Genome Biology ◽

Body Protein ◽

Biophysical Society

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Refinement of rigid-body protein–protein docking using backbone and side-chain minimization with a coarse-grained model

Open Access Bioinformatics ◽

10.2147/oab.s7183 ◽

2010 ◽

pp. 19

Author(s):

Juan Fernandez-Recio ◽

Solernou ◽

Juan Fernandez-Recio

Keyword(s):

Protein Docking ◽

Coarse Grained ◽

Body Protein ◽

Coarse Grained Model

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A systematic analysis of scoring functions in rigid-body protein docking: The delicate balance between the predictive rate improvement and the risk of overtraining

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25289 ◽

2017 ◽

Vol 85 (7) ◽

pp. 1287-1297 ◽

Author(s):

Didier Barradas-Bautista ◽

Iain H. Moal ◽

Juan Fernández-Recio

Keyword(s):

Protein Docking ◽

Scoring Functions ◽

Systematic Analysis ◽

Body Protein ◽

Delicate Balance ◽

Rate Improvement ◽

Predictive Rate

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CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24252 ◽

2013 ◽

Vol 81 (6) ◽

pp. 1005-1016 ◽

Author(s):

Satoshi Omori ◽

Akio Kitao

Keyword(s):

Protein Docking ◽

Body Protein ◽

Cylindrical Interface

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Scoring docked conformations generated by rigid-body protein-protein docking

Proteins Structure Function and Bioinformatics ◽

10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-f ◽

2000 ◽

Vol 40 (3) ◽

pp. 525-537 ◽

Author(s):

Carlos J. Camacho ◽

David W. Gatchell ◽

S. Roy Kimura ◽

Sandor Vajda

Keyword(s):

Protein Docking ◽

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Applying Constraint Programming to Rigid Body Protein Docking

Principles and Practice of Constraint Programming - CP 2005 - Lecture Notes in Computer Science ◽

10.1007/11564751_29 ◽

2005 ◽

pp. 373-387 ◽

Author(s):

Ludwig Krippahl ◽

Pedro Barahona

Keyword(s):

Constraint Programming ◽

Protein Docking ◽

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