Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations

Authors

Hongyi Zhou, State University of New York at Buffalo
Chi Zhang, University of Nebraska-LincolnFollow
Song Liu, State University of New York at BuffaloFollow
Yaoqi Zhou, State University of New York at BuffaloFollow

Date of this Version

2005

Citation

Zhou, Zhang, Liu & Zhou in Nucelic Acids Research (2005) 33 (Special issue); doi:10.1093/nar/gki360

Comments

Copyright 2005, Oxford University Press. Used by permission.

Abstract

We have developed the following web servers for protein structural modeling and analysis at http:// theory.med.buffalo.edu: THUMBUP, UMDHMM^TMHP and TUPS, predictors of trans-membrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMM^TMHP) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile– profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP³); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity of protein–protein/ peptide/DNA complexes (DCOMPLEX & DDNA); TCD, a program for protein-folding rate and transition-state analysis of small globular proteins; and DOGMA, a web-server that allows comparative analysis of domain combinations between plant and other 55 organisms. These servers provide tools for prediction and/or analysis of proteins on the secondary structure, tertiary structure and interaction levels, respectively.