ClusPro: A fully automated algorithm for protein-protein docking

Stephen R. Comeau; David W. Gatchell; Sandor Vajda; Carlos J. Camacho

doi:10.1093/nar/gkh354

ClusPro: A fully automated algorithm for protein-protein docking

Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho^*

^*Corresponding author for this work

Segal Design Institute

Research output: Contribution to journal › Article › peer-review

679 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	W96-W99
Journal	Nucleic acids research
Volume	32
Issue number	WEB SERVER ISS.
DOIs	https://doi.org/10.1093/nar/gkh354
State	Published - Jul 1 2004

Funding

We are grateful to J. C. Prasad for helping set up the server. This research has been supported by grants GM61867 from the National Institute of Health and P42 ES07381 from the National Institute of Environmental Health.

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkh354

Cite this

@article{8f60583474ba43f7ab8e64db83e4add3,

title = "ClusPro: A fully automated algorithm for protein-protein docking",

abstract = "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.",

author = "Comeau, {Stephen R.} and Gatchell, {David W.} and Sandor Vajda and Camacho, {Carlos J.}",

note = "Funding Information: We are grateful to J. C. Prasad for helping set up the server. This research has been supported by grants GM61867 from the National Institute of Health and P42 ES07381 from the National Institute of Environmental Health.",

year = "2004",

month = jul,

day = "1",

doi = "10.1093/nar/gkh354",

language = "English (US)",

volume = "32",

pages = "W96--W99",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "WEB SERVER ISS.",

}

TY - JOUR

T1 - ClusPro

T2 - A fully automated algorithm for protein-protein docking

AU - Comeau, Stephen R.

AU - Gatchell, David W.

AU - Vajda, Sandor

AU - Camacho, Carlos J.

N1 - Funding Information: We are grateful to J. C. Prasad for helping set up the server. This research has been supported by grants GM61867 from the National Institute of Health and P42 ES07381 from the National Institute of Environmental Health.

PY - 2004/7/1

Y1 - 2004/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=3242877815&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=3242877815&partnerID=8YFLogxK

U2 - 10.1093/nar/gkh354

DO - 10.1093/nar/gkh354

M3 - Article

C2 - 15215358

AN - SCOPUS:3242877815

SN - 0305-1048

VL - 32

SP - W96-W99

JO - Nucleic acids research

JF - Nucleic acids research

IS - WEB SERVER ISS.

ER -

ClusPro: A fully automated algorithm for protein-protein docking

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this