Document Detail

Distance dependency and minimum amino acid alphabets for decoy scoring potentials.
MedLine Citation:
PMID:  22941794     Owner:  NLM     Status:  Publisher    
The validity and accuracy of a proposed tertiary structure of a protein can be assessed in several ways. Scoring such a structure by a knowledge-based potential is a well-known approach in molecular biophysics, an important task in structure prediction and refinement, and a key step in several experiments on protein structures. Although several parameterizations for such models have been derived over the course of time, improvements in accuracy by explicitly using continuous distance information have not been suggested yet. We close this methodological gap by formulating the parameterization of a protein structure model as a linear program. Optimization of the parameters was performed using amino acid distances calculated for the residues in topology rich 2830 protein structures. We show the capability of our derived model to discriminate between native structures and decoys for a diverse set of proteins. In addition, we discuss the effect of reduced amino acid alphabets on the model. In contrast to studies focusing on binary contact schemes (without considering distance dependencies and proposing five symbols as optimal alphabet size), we find an accurate protein alphabet size to contain at least five symbols, preferably more, to assure a satisfactory fold recognition capability. © 2012 Wiley Periodicals, Inc.
Susanne Pape; Franziska Hoffgaard; Mirjam Dür; Kay Hamacher
Related Documents :
24658274 - Roles of f-box proteins in cancer.
10677424 - Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings a...
24389104 - Ubiquitin ligase trapping identifies an scf(saf1) pathway targeting unprocessed vacuola...
25288364 - Colloidal pen lithography.
23013244 - Thermophysical characterization of the seeds of invasive chinese tallow tree: importanc...
16836974 - Mitochondria as the target of the pro-apoptotic protein bax.
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-9-1
Journal Detail:
Title:  Journal of computational chemistry     Volume:  -     ISSN:  1096-987X     ISO Abbreviation:  J Comput Chem     Publication Date:  2012 Sep 
Date Detail:
Created Date:  2012-9-3     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
Department of Mathematics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Previous Document:  Acquired Hemophilia A.
Next Document:  The Power of a Smile to Move You: Complementary Submissiveness in Women's Posture as a Function of G...