Highly designable protein structures and inter-monomer interactions

DOI10.1088/0305-4470/31/29/006MaRDI QIDQ4212379zbMATH OpenOpenAlexFDO

Authors M. R. Ejtehadi, N. Hamedani, Hamed Seyed-allaei, Vahid Shahrezaei, M. Yahyanejad

Publication date 31 January 1999

Published in Journal of Physics A: Mathematical and General (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/9710028

zbMATH Keywords

computer enumerationlattice hydrophobic-polar modelprotein folding

Mathematics Subject Classification ID

Exact enumeration problems, generating functions (05A15) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Abstract: By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.

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• scientific article; zbMATH DE number 2130520 (Why is no real title available?)
• Self-consistent ensemble optimization and its implementation for mutation analysis in proteins
• Minimum energy conformations of self-interacting polymer chains via multipopulation genetic algorithms (MpGA)
• Structural entropy to characterize small proteins (70 aa) and their interactions

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