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

Brian JiménezGarcía | Zendy; Carles Pons | Zendy; Juan FernándezRecio | Zendy

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

Author(s) -

Brian JiménezGarcía,

Carles Pons,

Juan FernándezRecio

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt262

Subject(s) - docking (animal) , computer science , web server , electrostatics , fast fourier transform , grid , computational science , maple , software , algorithm , the internet , chemistry , operating system , mathematics , biology , geometry , medicine , nursing , botany

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy.

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