Links: Difference between revisions

Revision as of 23:35, 23 October 2012

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

MINT, a graphical interface to simple Modeller comparative modeling functions
EasyModeller, a windows based GUI (graphical user interface) to Modeller developed using PerlTk
SWIFT MODELLER, a JAVA based GUI to MODELLER
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).

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.

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

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 * [http://www.cgl.ucsf.edu/chimera/ Chimera] has a Modeller interface in version 1.5 or later. A [http://plato.cgl.ucsf.edu/chimera/videodoc/Modeller/ video tutorial] is also available.
 * [http://schubert.bio.uniroma1.it/pymod/index.html PyMod], a simple graphical interface between PyMOL and other tools like BLAST, ClustalW, Muscle, CEalign and MODELLER ([http://www.youtube.com/watch?v=VCcqEU0-xrU/ Workflow Example Video]).
-* [http://visual-table-modeller-interface.googlecode.com/files/vitamin.tar ViTaMIn], a Python based graphical interface with customized modeling, mutations and refinement options. ([http://www.youtube.com/watch?feature=player_embedded&v=3DRM4HUmBBA  Basic and Loop Refinement], [http://www.youtube.com/watch?feature=player_embedded&v=KPpRlg8quo0  Mutated Modeling])
 === Usage of Modeller in other systems ===