ClusPro: a fully automated algorithm for protein-protein docking | Zendy

Stephen R. Comeau | Zendy; David Gatchell | Zendy; Sándor Vajda | Zendy; Carlos J. Camacho | Zendy

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ClusPro: a fully automated algorithm for protein-protein docking

Author(s) -

Stephen R. Comeau,

David Gatchell,

Sándor Vajda,

Carlos J. Camacho

Publication year - 2004

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkh354

Subject(s) - protein data bank (rcsb pdb) , upload , docking (animal) , cluster analysis , web server , computer science , structural bioinformatics , protein data bank , interface (matter) , biology , protein structure , algorithm , data mining , bioinformatics , database , the internet , artificial intelligence , operating system , biochemistry , medicine , nursing , bubble , maximum bubble pressure method

ClusPro (http://nrc.bu.edu/cluster) represents the first fully automated, web-based program for the computational docking of protein structures. Users may upload the coordinate files of two protein structures through ClusPro's web interface, or enter the PDB codes of the respective structures, which ClusPro will then download from the PDB server (http://www.rcsb.org/pdb/). The docking algorithms evaluate billions of putative complexes, retaining a preset number with favorable surface complementarities. A filtering method is then applied to this set of structures, selecting those with good electrostatic and desolvation free energies for further clustering. The program output is a short list of putative complexes ranked according to their clustering properties, which is automatically sent back to the user via email.

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