articleNucleic Acids ResearchJul 1, 2006GOLD OA

GRAMM-X public web server for protein-protein docking

ATAndrey TovchigrechkoIAIlya A. Vakser

University of Kansas · Institute of Bioinformatics

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Abstract

Protein docking software GRAMM-X and its web interface (http://vakser.bioinformatics.ku.edu/resources/gramm/grammx) extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track.

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Topics & keywords

Topics
Keywords
  • Docking (animal)
  • Web server
  • Software
  • Biology
  • Computer science
  • Benchmarking
  • Operating system
  • Macromolecular docking
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