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

Document Type

Article

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.