Links: Difference between revisions

Revision as of 02:41, 29 April 2022

Links to other resources and people using Modeller

(!) 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
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).
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

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.
homelette, a unified and modular interface to homology modelling software.

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 === Graphical and web interfaces ===
 * [http://www.bioinf.org.uk/software/mint/index.html MINT], a graphical interface to simple Modeller comparative modeling functions
-* [http://www.uohyd.ernet.in/modellergui/index.html EasyModeller], a windows based GUI (graphical user interface)  to Modeller developed using [[PerlTk]]
-* [http://bitmesra.ac.in/swift-modeller/swift.htm SWIFT MODELLER], a JAVA based GUI to MODELLER
 * [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://ssu.ac.ir/fileadmin/templates/fa/daneshkadaha/daneshkade_darosazi/group/shimi/apps/Modelface.exe Modelface], an interface to Modeller 9.10 and higher, Capable of making single point mutaion in a PDB structure, password=yazdpharmacy
 * [http://structuropedia.org 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 ===
-* [http://mozart.bio.neu.edu/friend/ Friend], an integrated multiple structure visualization and multiple sequence alignment application (see "extended capabilities")
-* [http://glinka.bio.neu.edu/StSNP/ Structure SNP], which compares structural nsSNP distributions in many proteins or protein complexes, and allows mapping onto protein structures by comparative modeling with Modeller
 * [http://www.fiserlab.org/servers/M4T M4T], Multiple Mapping Method with Multiple Templates: Comparative protein structure modeling by combining of multiple templates and optimizing sequence-to-structure alignments
 * [http://www.fiserlab.org/servers/mmm MMM], Multiple Mapping Method: a novel approach to the sequence-to-structure alignment problem in comparative protein structure modeling