Linked Life Data

16604514

Source:http://linkedlifedata.com/resource/pubmed/id/16604514

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
8
pubmed:dateCreated
2006-4-27
pubmed:abstractText
The polarizable continuum model (PCM) for the description of solvent effects is combined with the fragment molecular orbital (FMO) method at several levels of theory, using a many-body expansion of the electron density and the corresponding electrostatic potential, thereby determining solute (FMO)-solvent (PCM) interactions. The resulting method, denoted FMO/PCM, is applied to a set of model systems, including alpha-helices and beta-strands of alanine consisting of 10, 20, and 40 residues and their mutants to charged arginine and glutamate residues. The FMO/PCM error in reproducing the PCM solvation energy for a full system is found to be below 1 kcal/mol in all cases if a two-body expansion of the electron density is used in the PCM potential calculation and two residues are assigned to each fragment. The scaling of the FMO/PCM method is demonstrated to be nearly linear at all levels for polyalanine systems. A study of the relative stabilities of alpha-helices and beta-strands is performed, and the magnitude of the contributing factors is determined. The method is applied to three proteins consisting of 20, 129, and 245 residues, and the solvation energy and computational efficiency are discussed.
pubmed:language
eng
pubmed:journal
pubmed:status
PubMed-not-MEDLINE
pubmed:month
Jun
pubmed:issn
0192-8651
pubmed:author
pubmed:issnType
Print
pubmed:volume
27
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
976-85
pubmed:year
2006
pubmed:articleTitle
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO).
pubmed:affiliation
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba, 305-8568 Ibaraki, Japan. d.g.fedorov@aist.go.jp
pubmed:publicationType
Journal Article