title: (PS)2: protein structure prediction server version 3.0.
abstract: Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)(2) web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)(2) server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)(2) is freely available at http://ps2v3.life.nctu.edu.tw/.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 30068, Taiwan.
authors.forename: Tsun-Tsao
authors.initials: TT
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 30068, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan.
authors.forename: Jenn-Kang
authors.initials: JK
authors.lastname: Hwang
authors.affiliation: Department of Vascular and Medicinal Research, Texas Heart Institute, Houston, TX 77030, USA Center for Lipid Biosciences, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan L5 Research Center, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Chu-Huang
authors.initials: CH
authors.lastname: Chen
authors.affiliation: Center for Lipid Biosciences, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors.forename: Chih-Sheng
authors.initials: CS
authors.lastname: Chu
authors.affiliation: Center for Bioinformatics Research, National Chiao Tung University, Hsinchu 30068, Taiwan Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan.
authors.forename: Chi-Wen
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Center for Lipid Biosciences, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan Center for Lipid and Glycomedicine Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan chieh.bi91g@nctu.edu.tw.
authors.forename: Chih-Chieh
authors.initials: CC
authors.lastname: Chen
mesh_terms: D020407:Internet; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D046912:Multiprotein Complexes