Packing helices in proteins by global optimization of a potential energy function.
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ABSTRACT:
SUBMITTER: Nanias M
PROVIDER: S-EPMC149897 | biostudies-literature | 2003 Feb
REPOSITORIES: biostudies-literature
Publications
Packing helices in proteins by global optimization of a potential energy function.
Nanias Marian M Chinchio Maurizio M Pillardy Jarosław J Ripoll Daniel R DR Scheraga Harold A HA
Proceedings of the National Academy of Sciences of the United States of America 20030205 4
An efficient method has been developed for packing alpha-helices in proteins. It treats alpha-helices as rigid bodies and uses a simplified Lennard-Jones potential with Miyazawa-Jernigan contact-energy parameters to describe the interactions between the alpha-helical elements in this coarse-grained system. Global conformational searches to generate packing arrangements rapidly are carried out with a Monte Carlo-with-minimization type of approach. The results for 42 proteins show that the approac ...[more]
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