title: MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.
abstract: Modeling the three-dimensional (3D) structures of proteins assumes great significance because of its manifold applications in biomolecular research. Toward this goal, we present MaxMod, a graphical user interface (GUI) of the MODELLER program that combines profile hidden Markov model (profile HMM) method with Clustal Omega program to significantly improve the selection of homologous templates and target-template alignment for construction of accurate 3D protein models. MaxMod distinguishes itself from other existing GUIs of MODELLER software by implementing effortless modeling of proteins using templates that bear modified residues. Additionally, it provides various features such as loop optimization, express modeling (a feature where protein model can be generated directly from its sequence, without any further user intervention) and automatic update of PDB database, thus enhancing the user-friendly control of computational tasks. We find that HMM-based MaxMod performs better than other modeling packages in terms of execution time and model quality. MaxMod is freely available as a downloadable standalone tool for academic and non-commercial purpose at http://www.immt.res.in/maxmod/.
authors: Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar, 751013, India.
authors: Bikram K
authors: BK
authors: Parida
authors: Prasanna K
authors: PK
authors: Panda
authors: Namrata
authors: N
authors: Misra
authors: Barada K
authors: BK
authors: Mishra
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
references: J Mol Model. 2011 Oct;17(10):2601-7
references: 21258829
references: Mol Syst Biol. 2011 Oct 11;7:539
references: 21988835
references: J Mol Biol. 1994 Feb 4;235(5):1501-31
references: 8107089
references: FASEB J. 1995 Jun;9(9):708-17
references: 7601335
references: Sci Rep. 2013;3:2619
references: 24018415
references: Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 1):1139-46
references: 10089490
references: Nature. 1992 Mar 5;356(6364):83-5
references: 1538787
references: Methods Mol Biol. 2000;132:185-219
references: 10547837
references: Protein Sci. 2000 Sep;9(9):1753-73
references: 11045621
references: Indian J Pharm Sci. 2012 Jan;74(1):1-17
references: 23204616
references: Bioinformatics. 1998;14(9):755-63
references: 9918945
references: Bioinformatics. 2007 Aug 1;23(15):1901-8
references: 17510171
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Bioinformatics. 2004 May 22;20(8):1301-8
references: 14962936
references: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references: 22039361
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10
references: 17517781
references: Science. 1991 Jul 12;253(5016):164-70
references: 1853201
references: Proteins. 2000 Jul 1;40(1):6-22
references: 10813826
references: BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S2
references: 22536966
references: BMC Res Notes. 2010 Aug 16;3:226
references: 20712861
references: Curr Opin Struct Biol. 1995 Apr;5(2):229-35
references: 7648326
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: Drug Discov Today. 2009 Jul;14(13-14):676-83
references: 19422931
references: J Mol Biol. 1993 Dec 5;234(3):779-815
references: 8254673