Linked Life Data

16126228

Source:http://linkedlifedata.com/resource/pubmed/id/16126228

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2005-9-13
pubmed:abstractText
We describe the derivation and testing of a knowledge-based atomic environment potential for the modeling of protein structural energetics. An analysis of the probabilities of atomic interactions in a dataset of high-resolution protein structures shows that the probabilities of non-bonded inter-atomic contacts are not statistically independent events, and that the multi-body contact frequencies are poorly predicted from pairwise contact potentials. A pseudo-energy function is defined that measures the preferences for protein atoms to be in a given microenvironment defined by the number of contacting atoms in the environment and its atomic composition. This functional form is tested for its ability to recognize native protein structures amongst an ensemble of decoy structures and a detailed relative performance comparison is made with a number of common functions used in protein structure prediction.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
30
pubmed:volume
352
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
986-1001
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
An atomic environment potential for use in protein structure prediction.
pubmed:affiliation
Department of Biochemistry and Biophysics, The University of Pennsylvania Medical School, Philadelphia, PA 19104-6059, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S., Research Support, N.I.H., Extramural