Extension of the pairwise-contact energy parameters for proteins with the local environments of amino acids

Muyoung Heo, Mookyung Cheon, Eun-Joung Moon, Suhkmann Kim, Kwanghoon Chung, Haejin Kim and Iksoo Chang

Physica A: Statistical Mechanics and its Applications, 2005, vol. 351, issue 2, 439-447

Abstract: After parameterizing the local environments of amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (solvation) of amino acids, we could design and construct the 16,290 pairwise-contact energy parameters of amino acids by the quasi-chemical approximation using the 937 test proteins with 30% homology, which include all representatives of the different classes of proteins. The capability of the energy parameters for recognizing the native folds of proteins is checked by the protein threading. These could recognize the 911 (97.2%) native folds of the 937 test proteins simultaneously. When these parameters are tested on the new distinct 382 proteins with 90% homology, the 372 (97.4%) proteins could recognize their native folds. Although the quasi-chemical approximation is simple, we showed that it is possible to achieve the high success ratio of recognizing the native folds of many proteins as long as all representative proteins of the different classes of proteins were considered and the local environments such as the hydrophobicity (solvation) and the secondary structures of amino acids were properly taken into account.

Keywords: Protein folding; Pairwise-contact energy; Protein threading; Native fold recognition (search for similar items in EconPapers)
Date: 2005
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0378437104016048
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:351:y:2005:i:2:p:439-447

DOI: 10.1016/j.physa.2004.12.044

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().