caa a22 4500 605513481 CHVBK 20210128100700.0 cr unu---uuuuu 210128e20150201xx s 000 0 eng 10.1007/s00894-014-2563-3 doi (NATIONALLICENCE)springer-10.1007/s00894-014-2563-3 MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models [Elektronische Daten] [Bikram Parida, Prasanna Panda, Namrata Misra, Barada Mishra] 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/ . Graphical Abstract Overview of steps involved in protein modeling using MaxMod Springer-Verlag Berlin Heidelberg, 2015 Clustal omega nationallicence Graphical user interface nationallicence Hidden markov model nationallicence Homology modeling nationallicence Modified residues nationallicence Parida Bikram Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut Panda Prasanna Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut Misra Namrata Academy of Scientific & Innovative Research, CSIR- CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut Mishra Barada Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/2(2015-02-01), 1-10 1610-2940 21:2<1 2015 21 894 https://doi.org/10.1007/s00894-014-2563-3 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-014-2563-3 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Parida Bikram Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut NATIONALLICENCE 700 1- Panda Prasanna Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut NATIONALLICENCE 700 1- Misra Namrata Academy of Scientific & Innovative Research, CSIR- CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut NATIONALLICENCE 700 1- Mishra Barada Bioresources Engineering Department, CSIR-Institute of Minerals & Materials Technology, 751013, Bhubaneswar, India aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/2(2015-02-01), 1-10 1610-2940 21:2<1 2015 21 894