MODELLER 9.16 – Comparative Protein Structure Modeling

MODELLER 9.16

:: DESCRIPTION

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  MODELLER

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1137:1-15. doi: 10.1007/978-1-4939-0366-5_1.
Protein structure modeling with MODELLER.
Webb B1, Sali A.

N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali.
Comparative Protein Structure Modeling With MODELLER.
Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.

MaxMod 1.0.0.1 – Improved Prediction of Protein 3D Models

MaxMod 1.0.0.1

:: DESCRIPTION

MaxMod is a standalone Graphical User Interface (GUI) of the MODELLER program which combines profile Hidden Markov Model (profile HMM) method with Clustal Omega for the construction of protein homology models.

::DEVELOPER

MaxMod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • MODELLER
  • Python
  • .NET Framework 2.0 or higher

:: DOWNLOAD

 MaxMod

:: MORE INFORMATION

Citation:

J Mol Model. 2015 Feb;21(2):30. doi: 10.1007/s00894-014-2563-3. Epub 2015 Jan 31.
MaxMod: a hidden Markov model based novel interface to MODELLER for improved prediction of protein 3D models.
Parida BK1, Panda PK, Misra N, Mishra BK.

modplus – script for Modeller to perform Sequence-structure Alignment

modplus

:: DESCRIPTION

modplus is a wrapper script for Modeller; it performs sequence-structure alignment and preprocessing steps to model target sequence. The input to the program is a multiple alignment of target and template sequences in the FASTA format. The template structures will be supposed to be accessible in a given location.

::DEVELOPER

Laboratory of Bioinformatics, VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 modplus

:: MORE INFORMATION

MINT 3.2 – User Interface to Modeller

MINT 3.2

:: DESCRIPTION

MINT is a graphical user interface to Andrej Sali’s Modeller program. It allows only the basic homology modelling functions of Modeller to be used, but saves you from having to use the Modeller control language.

::DEVELOPER

Dr. Andrew C.R. Martin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  MINT

:: MORE INFORMATION