Linked Life Data

16363875

Source:http://linkedlifedata.com/resource/pubmed/id/16363875

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2005-12-20
pubmed:abstractText
Arriving at the native conformation of a polypeptide chain characterized by minimum most free energy is a problem of long standing interest in protein structure prediction endeavors. Owing to the computational requirements in developing free energy estimates, scoring functions--energy based or statistical--have received considerable renewed attention in recent years for distinguishing native structures of proteins from non-native like structures. Several cleverly designed decoy sets, CASP (Critical Assessment of Techniques for Protein Structure Prediction) structures and homology based internet accessible three dimensional model builders are now available for validating the scoring functions. We describe here an all-atom energy based empirical scoring function and examine its performance on a wide series of publicly available decoys. Barring two protein sequences where native structure is ranked second and seventh, native is identified as the lowest energy structure in 67 protein sequences from among 61,659 decoys belonging to 12 different decoy sets. We further illustrate a potential application of the scoring function in bracketing native-like structures of two small mixed alpha/beta globular proteins starting from sequence and secondary structural information. The scoring function has been web enabled at www.scfbio-iitd.res.in/utility/proteomics/energy.jsp.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
0739-1102
pubmed:author
pubmed:issnType
Print
pubmed:volume
23
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
385-406
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Protein structure evaluation using an all-atom energy based empirical scoring function.
pubmed:affiliation
Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi - 110016, India. bjayaram@chemistry.iitd.ac.in.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't