Tools for comparative protein structure modeling and analysis

TitleTools for comparative protein structure modeling and analysis
Publication TypeJournal Article
Year of Publication2003
AuthorsEswar, N, John, B, Mirkovic, N, Fiser, A, Ilyin, VA, Pieper, U, Stuart, AC, Marti-Renom, MA, Madhusudhan, MS, Yerkovich, B, Sali, A
JournalNucleic Acids Res
KeywordsAmino Acid *Software *Structural Homology; Internet Models; Molecular Protein Folding Proteins/chemistry Reproducibility of Results Sequence Alignment Sequence Homology; Protein Systems Integration

The following resources for comparative protein structure modeling and analysis are described ( 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.


Eswar, Narayanan John, Bino Mirkovic, Nebojsa Fiser, Andras Ilyin, Valentin A Pieper, Ursula Stuart, Ashley C Marti-Renom, Marc A Madhusudhan, M S Yerkovich, Bozidar Sali, Andrej P50 GM62529/GM/NIGMS NIH HHS/United States R01 GM 54762/GM/NIGMS NIH HHS/United States R33 CA84699/CA/NCI NIH HHS/United States Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, P.H.S. England Nucleic acids research Nucleic Acids Res. 2003 Jul 1;31(13):3375-80.