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

Bioinformatics (Oxford, England) - Tập 29 Số 13 - Trang 1698-1699 - 2013
Brian Jiménez‐García1, Carles Pons2, Juan Fernández‐Recio3
1Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center, National Institute of Bioinformatics, Jordi Girona 29, 08034 Barcelona, Spain.
2Computer Science and Engineering
31Joint BSC-IRB Research Programme in Computational Biology, Department of Life Sciences, Barcelona Supercomputing Center and 2Computational Bioinformatics, National Institute of Bioinformatics (INB), Jordi Girona 29, 08034 Barcelona, Spain

Tóm tắt

Abstract Summary: 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. Availability and implementation: The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock Contact:  [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.

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Tài liệu tham khảo

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Thông tin xuất bản

Bioinformatics (Oxford, England)

Tập 29 Số 13

1698-1699

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