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(!) Please edit this page to link to your own resources or interfaces using Modeller, so that Modeller users can easily find them!

Graphical and web interfaces

  • MINT, a graphical interface to simple Modeller comparative modeling functions

  • EasyModeller, a windows based GUI (graphical user interface) to Modeller developed using PerlTk


  • Chimera has a Modeller interface in version 1.5 or later. A video tutorial is also available.

  • PyMod, a simple graphical interface between PyMOL and other tools like BLAST, ClustalW, Muscle, CEalign and MODELLER (Workflow Example Video).

  • Modelface, an interface to Modeller 9.10 and higher, Capable of making single point mutaion in a PDB structure, password=yazdpharmacy

  • Structuropedia, a simple yet powerful and versatile web interface with capabilities for modeling and rendering of proteins alone and in complex with peptides and DNA. Powered by a wide array of engines including Biopython, Blast, Clustal, JSmol, Modeller, Refsense and VMD.

Usage of Modeller in other systems

  • Friend, an integrated multiple structure visualization and multiple sequence alignment application (see "extended capabilities")

  • Structure SNP, which compares structural nsSNP distributions in many proteins or protein complexes, and allows mapping onto protein structures by comparative modeling with Modeller

  • M4T, Multiple Mapping Method with Multiple Templates: Comparative protein structure modeling by combining of multiple templates and optimizing sequence-to-structure alignments

  • MMM, Multiple Mapping Method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling

  • ArchPred, template based loop structure prediction server that delivers a full comparative model with the predicted loop using Modeller

  • Flex-EM, a method for protein structure fitting and refinement guided by cryoEM density.

Frameworks and other interfaces

  • Biskit, a modular, object-oriented Python library for structural bioinformatics research.