MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models

  • Bikram K. Parida
  • Prasanna K. Panda
  • Namrata Misra
  • Barada K. Mishra
Original Paper


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

Graphical Abstract

Overview of steps involved in protein modeling using MaxMod


Clustal omega Graphical user interface Hidden markov model Homology modeling Modified residues 



NM is grateful to Council of Scientific and Industrial Research, Govt. of India for the award of Senior Research Fellowship. The authors would also like to thank the members of CNeM department, CSIR-IMMT for providing server space and hosting the website of MaxMod.

Supplementary material

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(GIF 24 kb)

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High-resolution image (TIFF 173 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Bikram K. Parida
    • 1
  • Prasanna K. Panda
    • 1
    • 2
  • Namrata Misra
    • 2
  • Barada K. Mishra
    • 1
    • 2
  1. 1.Bioresources Engineering DepartmentCSIR-Institute of Minerals & Materials TechnologyBhubaneswarIndia
  2. 2.Academy of Scientific & Innovative ResearchCSIR- CSIR-Institute of Minerals & Materials TechnologyBhubaneswarIndia

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