Authors: Zhou, Hongyi; Zhang, Chi; Liu, Song; Zhou, Yaoqi

Source: Nucleic Acids Research, Volume 33, Supplement 1, 1 July 2005 , pp. W193-W197(5)

Publisher: Oxford University Press

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 transmembrane 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.

Document Type: Research article

DOI: http://dx.doi.org/10.1093/nar/gki360

Publication date: 2005-07-01

More about this publication?

• Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
  in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.

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