Journal
PROTEIN SCIENCE
Volume 19, Issue 3, Pages 603-616Publisher
WILEY
DOI: 10.1002/pro.339
Keywords
scoring matrices; secondary structure and contact based environment; hydrophobicity; accessible surface area
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Funding
- Supercomputer Education and Research Center (SERC)
- Indian Institute of Science, Bangalore, Mathematical Biology Project, Department of Science and Technology (DST), India
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Understanding the key factors that influence the interaction preferences of amino acids in the folding of proteins have remained a challenge. Here we present a knowledge-based approach for determining the effective interactions between amino acids based on amino acid type, their secondary structure, and the contact based environment that they find themselves in the native state structure as measured by their number of neighbors. We find that the optimal information is approximately encoded in a 60 x 60 matrix describing the 20 types of amino acids in three distinct secondary structures (helix, beta strand, and loop). We carry out a clustering scheme to understand the similarity between these interactions and to elucidate a nonredundant set. We demonstrate that the inferred energy parameters can be used for assessing the fit of a given sequence into a putative native state structure.
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