Linked Life Data

12116381

Source:http://linkedlifedata.com/resource/pubmed/id/12116381

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2002-7-12
pubmed:abstractText
The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across energy barriers thereby providing results for a wide range of temperatures. However, a MUCA simulation is based on weights (related to the density of states) that should be determined prior to a production run and their calculation is not straightforward. To overcome this difficulty a procedure has been developed by Berg that calculates the MUCA weights automatically. In a previous article (Ya?ar et al. J Comput Chem 2000, 14, 1251-1261) we extended this procedure to continuous systems and applied it successfully to the small pentapeptide Leu-enkephalin. To investigate the performance of the automated MUCA procedure for larger peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr(1)-D-Met(2)-Phe(3)-His(4)-Leu(5)-Met(6)-Asp(7)-NH(2)). As for Leu-enkephalin, deltorphin is modeled in vacuum by the potential energy function ECEPP. MUCA is found to perform well. A weak second peak is seen for the specific heat, which is given a special attention. By minimizing the energy of structures along the trajectory it is found that MUCA provides a good conformational coverage of the low energy region of the molecule. These latter results are compared with conformational coverage obtained by the Monte Carlo minimization method of Li and Scheraga.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0192-8651
pubmed:author
pubmed:copyrightInfo
Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1127-1134, 2002
pubmed:issnType
Print
pubmed:volume
23
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1127-34
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Efficiency of the multicanonical simulation method as applied to peptides of increasing size: the heptapeptide deltorphin.
pubmed:affiliation
Department of Physics Engineering, Hacettepe University, 06532, Ankara, Turkey.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't