TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers
Cao, Han; Ng, Marcus C. K.; Jusoh, Siti Azma; Tai, Hio Kuan; Siu, Shirley W. I.
2017-09
Source PublicationJOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
ISSN0920-654X
Volume31Issue:9Pages:855-865
Abstractalpha-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD < 2.0 angstrom) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.
KeywordStructure prediction Bitopic dimer Helix packing Helix assembly Scwrl4 Bioinformatics
DOI10.1007/s10822-017-0047-0
URLView the original
Indexed BySCIE
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biophysics ; Computer Science
WOS SubjectBiochemistry & Molecular Biology ; Biophysics ; Computer Science, Interdisciplinary Applications
WOS IDWOS:000412668900007
PublisherSPRINGER
The Source to ArticleWOS
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Cited Times [WOS]:2   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionDEPARTMENT OF COMPUTER AND INFORMATION SCIENCE
Recommended Citation
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Cao, Han,Ng, Marcus C. K.,Jusoh, Siti Azma,et al. TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers[J]. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,2017,31(9):855-865.
APA Cao, Han,Ng, Marcus C. K.,Jusoh, Siti Azma,Tai, Hio Kuan,&Siu, Shirley W. I..(2017).TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers.JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,31(9),855-865.
MLA Cao, Han,et al."TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers".JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 31.9(2017):855-865.
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