2003
DOI: 10.1093/nar/gkg189
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Improving the performance of DomainParser for structural domain partition using neural network

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 w… Show more

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Cited by 64 publications
(73 citation statements)
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“…Hence, methods for phylogenetic analyses and protein modelling usually perform better for single domains [58]. Automatic domain parsing generally makes the assumption that interdomain interaction (under a correct domain assignment) is weaker than the intradomain interaction (PUU [59], DOMAK [60] and 3Dee [61,62], DETECTIVE [63], DALI [64], STRUDL [65], DomainParser [66,67], Protein Domain Parser [68] and DDOMAIN [69]). These approaches maximize the number of contacts within a domain.…”
Section: Introductionmentioning
confidence: 99%
“…Hence, methods for phylogenetic analyses and protein modelling usually perform better for single domains [58]. Automatic domain parsing generally makes the assumption that interdomain interaction (under a correct domain assignment) is weaker than the intradomain interaction (PUU [59], DOMAK [60] and 3Dee [61,62], DETECTIVE [63], DALI [64], STRUDL [65], DomainParser [66,67], Protein Domain Parser [68] and DDOMAIN [69]). These approaches maximize the number of contacts within a domain.…”
Section: Introductionmentioning
confidence: 99%
“…(5) The DomainParser set. We downloaded the test data set used by DomainParser 2 (Guo et al 2003). It contains 1317 chains whose domains were assigned by SCOP 1.59.…”
Section: The Training and Test Data Setsmentioning
confidence: 99%
“…Dividing a protein into domains is useful for more accurate function and structure determination because the methods for phylogenetic analysis and protein modeling usually work best for single domains (Ponting and Russell 2002). Both sequencebased (Chivian et al 2003;Heger and Holm 2003;Linding et al 2003;Bateman et al 2004;Letunic et al 2004;Liu and Rost 2004;Nagarajan and Yona 2004;von Ohsen et al 2004;Sim et al 2005) and structure-based methods (Holm and Sander 1994;Siddiqui and Barton 1995;Sowdhamini and Blundell 1995;Swindells 1995;Holm and Sander 1998;Taylor 1999;Xu et al 2000;Alexandrov and Shindyalov 2003;Guo et al 2003;Kundu et al 2004) have been developed for identification of protein domains.The problem of dividing a protein structure into domains is not yet solved. This is in part due to the lack of an unambiguous definition of domains.…”
mentioning
confidence: 99%
See 1 more Smart Citation
“…Methods for phylogenetic analyses or protein modeling usually perform best for single domains [29]. The commonly used principle for automatic domain parsing is that interdomain interaction under a correct domain assignment is weaker than the intradomain interaction (PUU [30], DOMAK [31], 3Dee [32,33], DETECTIVE [34], DALI [35], STRUDL [36], DomainParser [37,38], Protein Domain Parser [39] and DDOMAIN [40]). Innovative approaches have been used in this context, e.g., graph theory [41] and Normal Mode Analysis approach [42].…”
Section: Introductionmentioning
confidence: 99%