Linked Life Data

11159328

Source:http://linkedlifedata.com/resource/pubmed/id/11159328

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2001-2-22
pubmed:abstractText
MOTIVATION: Automatic decomposition of a multi-domain protein into individual domains represents a highly interesting and unsolved problem. As the number of protein structures in PDB is growing at an exponential rate, there is clearly a need for more reliable and efficient methods for protein domain decomposition simply to keep the domain databases up-to-date. RESULTS: We present a new algorithm for solving the domain decomposition problem, using a graph-theoretic approach. We have formulated the problem as a network flow problem, in which each residue of a protein is represented as a node of the network and each residue--residue contact is represented as an edge with a particular capacity, depending on the type of the contact. A two-domain decomposition problem is solved by finding a bottleneck (or a minimum cut) of the network, which minimizes the total cross-edge capacity, using the classical Ford--Fulkerson algorithm. A multi-domain decomposition problem is solved through repeatedly solving a series of two-domain problems. The algorithm has been implemented as a computer program, called DomainParser. We have tested the program on a commonly used test set consisting of 55 proteins. The decomposition results are 78.2% in agreement with the literature on both the number of decomposed domains and the assignments of residues to each domain, which compares favorably to existing programs. On the subset of two-domain proteins (20 in number), the program assigned 96.7% of the residues correctly when we require that the number of decomposed domains is two.
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
1367-4803
pubmed:author
pubmed:issnType
Print
pubmed:volume
16
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1091-104
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2000
pubmed:articleTitle
Protein domain decomposition using a graph-theoretic approach.
pubmed:affiliation
Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830-6480, USA. xyn@ornl.gov
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S.