Abstract:
:Structural domains are considered as the basic units of protein folding, evolution, function and design. Automatic decomposition of protein structures into structural domains, though after many years of investigation, remains a challenging and unsolved problem. Manual inspection still plays a key role in domain decomposition of a protein structure. We have previously developed a computer program, DomainParser, using network flow algorithms. The algorithm partitions a protein structure into domains accurately when the number of domains to be partitioned is known. However the performance drops when this number is unclear (the overall performance is 74.5% over a set of 1317 protein chains). Through utilization of various types of structural information including hydrophobic moment profile, we have developed an effective method for assessing the most probable number of domains a structure may have. The core of this method is a neural network, which is trained to discriminate correctly partitioned domains from incorrectly partitioned domains. When compared with the manual decomposition results given in the SCOP database, our new algorithm achieves higher decomposition accuracy (81.9%) on the same data set.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Guo JT,Xu D,Kim D,Xu Ydoi
10.1093/nar/gkg189keywords:
subject
Has Abstractpub_date
2003-02-01 00:00:00pages
944-52issue
3eissn
0305-1048issn
1362-4962journal_volume
31pub_type
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