Linked Life Data

15197271

Source:http://linkedlifedata.com/resource/pubmed/id/15197271

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
25
pubmed:dateCreated
2004-6-23
pubmed:abstractText
A method called complete hypothetical scanning Monte Carlo has been introduced for calculating the absolute entropy, S, and free energy, F, of fluids. Here, the method is extended to peptide chains in vacuum. Thus, S is calculated from a given sample by reconstructing each conformation step-by-step by using transition probabilities (TPs); at each step, part of the chain coordinates have already been determined (the "frozen past"), and the TP is obtained from a Monte Carlo simulation of the (future) part of the chain whose TPs as yet have not been calculated. Very accurate results for S and F are obtained for the helix, extended, and hairpin microstates of a simplified model of decaglycine (Gly)(10) and (Gly)(16). These results agree well with results obtained by the quasiharmonic approximation and the local states method. The complete HSMC method can be applied to a macromolecule with any degree of flexibility, ranging from local fluctuations to a random coil. Also, the difference in stability, Delta F(mn) = F(m) - F(n) between significantly different microstates m and n can be obtained from two simulations only without the need to resort to thermodynamic integration. Our long-term goal is to extend this method to any peptide and apply it to a peptide immersed in a box with explicit water.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
0027-8424
pubmed:author
pubmed:issnType
Print
pubmed:day
22
pubmed:volume
101
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
9241-6
pubmed:dateRevised
2010-9-21
pubmed:meshHeading
pubmed:year
2004
pubmed:articleTitle
Simulation method for calculating the entropy and free energy of peptides and proteins.
pubmed:affiliation
Center for Computational Biology and Bioinformatics and Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, W1058 BST, PA 15261, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S.