Tools for comparative protein structure modeling and analysis

Narayanan Eswar; Bino John; Nebojsa Mirkovic; Andras Fiser; Valentin A. Ilyin; Ursula Pieper; Ashley C. Stuart; Marc A. Marti-Renom; M. S. Madhusudhan; Bozidar Yerkovich; Andrej Sali

doi:10.1093/nar/gkg543

Tools for comparative protein structure modeling and analysis

Narayanan Eswar, Bino John, Nebojsa Mirkovic, Andras Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Marti-Renom, M. S. Madhusudhan, Bozidar Yerkovich, Andrej Sali

Systems & Computational Biology

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

400 Scopus citations

Abstract

The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

Original language	English (US)
Pages (from-to)	3375-3380
Number of pages	6
Journal	Nucleic acids research
Volume	31
Issue number	13
DOIs	https://doi.org/10.1093/nar/gkg543
State	Published - Jul 1 2003

ASJC Scopus subject areas

Genetics

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title = "Tools for comparative protein structure modeling and analysis",

abstract = "The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.",

author = "Narayanan Eswar and Bino John and Nebojsa Mirkovic and Andras Fiser and Ilyin, {Valentin A.} and Ursula Pieper and Stuart, {Ashley C.} and Marti-Renom, {Marc A.} and Madhusudhan, {M. S.} and Bozidar Yerkovich and Andrej Sali",

note = "Funding Information: This research was supported by the grants NIH/NIGMS R01 GM 54762, NIH/NIGMS P50 GM62529, NIH/NCI R33 CA84699, Merck Genome Research Institute Award, Mathers Foundation Award and Sun Academic Equipment Grant EDUD-7824-020257-US. A.S. is an Irma T. Hirschl Trust Career Scientist.",

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doi = "10.1093/nar/gkg543",

language = "English (US)",

volume = "31",

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T1 - Tools for comparative protein structure modeling and analysis

AU - Eswar, Narayanan

AU - John, Bino

AU - Mirkovic, Nebojsa

AU - Fiser, Andras

AU - Ilyin, Valentin A.

AU - Pieper, Ursula

AU - Stuart, Ashley C.

AU - Marti-Renom, Marc A.

AU - Madhusudhan, M. S.

AU - Yerkovich, Bozidar

AU - Sali, Andrej

N1 - Funding Information: This research was supported by the grants NIH/NIGMS R01 GM 54762, NIH/NIGMS P50 GM62529, NIH/NCI R33 CA84699, Merck Genome Research Institute Award, Mathers Foundation Award and Sun Academic Equipment Grant EDUD-7824-020257-US. A.S. is an Irma T. Hirschl Trust Career Scientist.

PY - 2003/7/1

Y1 - 2003/7/1

N2 - The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

AB - The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

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Tools for comparative protein structure modeling and analysis

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