Linked Life Data

16942188

Source:http://linkedlifedata.com/resource/pubmed/id/16942188

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2006-8-31
pubmed:abstractText
Pairwise interaction correction (PIC) is introduced to account for electron density polarization due to short-range interactions such as hydrogen bonding and close contact between molecular fragments in the molecular fractionation with conjugated caps density matrix (MFCC-DM) approach for energy calculation of protein and other polymers [Chen et al., J. Chem. Phys. 122, 184105 (2005)]. With this PIC, the accuracy of the calculated protein energy and other electronic properties are improved, and the MFCC approach can be applied to study real proteins with short-range structural complexity. In the present MFCC-DM-PIC approach, the short-range interresidual interactions are represented by a pair of small molecules (interacting units) which are made from the two residues that fall within a certain distance criterion. The density matrices of fragments, concaps, interacting units and pairs are calculated by conventional Hartree-Fock or density functional theory methods and are combined to construct the full density matrix which is finally employed to calculate the total energy, electron density, electrostatic potential, dipole moment, etc., of the protein. Numerical tests on seven conformationally varied peptides are presented to demonstrate the accuracy of the MFCC-DM-PIC method.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jul
pubmed:issn
0021-9606
pubmed:author
pubmed:issnType
Print
pubmed:day
28
pubmed:volume
125
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
44903
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Molecular fractionation with conjugated caps density matrix with pairwise interaction correction for protein energy calculation.
pubmed:affiliation
Department of Chemistry, New York University, New York, New York 10003, USA.
pubmed:publicationType
Journal Article