TY - JOUR
T1 - 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
AU - Zhou, Hongyi
AU - Zhang, Chi
AU - Liu, Song
AU - Zhou, Yaoqi
N1 - Funding Information:
This work was supported by NIH (R01 GM 966049 and R01 GM 068530), a grant from HHMI to SUNY Buffalo and by the Center for Computational Research and the Keck Center for Computational Biology at SUNY Buffalo. Y.Z. is also in part supported by a two-base fund (No. 203240420391) from National Science Foundation of China. Funding to pay the Open Access publication charges for this article was provided by NIH.
PY - 2005/7
Y1 - 2005/7
N2 - We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMMTMHP and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMMTMHP) 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.
AB - We have developed the following web servers for protein structural modeling and analysis at http://theory.med.buffalo.edu: THUMBUP, UMDHMMTMHP and TUPS, predictors of transmembrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMMTMHP) 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.
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U2 - 10.1093/nar/gki360
DO - 10.1093/nar/gki360
M3 - Article
C2 - 15980453
AN - SCOPUS:23144454057
VL - 33
SP - W193-W197
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - SUPPL. 2
ER -