Modeller Wiki

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== Links to other resources and people using Modeller ==
== 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!
💡 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 ===
=== Graphical and web interfaces ===
* [http://bioinf.modares.ac.ir/software/easymodel EasyModel], a user-friendly web-based interface based on MODELLER. It includes basic modeling, multiple template modeling, and loop refining.
* [http://www.bioinf.org.uk/software/mint/index.html MINT], a graphical interface to simple Modeller comparative modeling functions
* [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://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://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.
* [http://structuropedia.org Structuropedia], a simply yet powerful and versatile web interface with capabilities for modeling, transformation and rendering of proteins. Powered by a wide array of engines including Biopython, Blast, Clustal, JSmol, Modeller, [[RefSense]] and VMD.  


=== Usage of Modeller in other systems ===
=== 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/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
* [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
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=== Frameworks and other interfaces ===
=== Frameworks and other interfaces ===
* [http://biskit.pasteur.fr/ Biskit], a modular, object-oriented Python library for structural bioinformatics research.
* [http://biskit.pasteur.fr/ Biskit], a modular, object-oriented Python library for structural bioinformatics research.
 
* [https://github.com/philippjunk/homelette/ homelette], a unified and modular interface to homology modelling software.

Latest revision as of 05:14, 26 August 2023

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

  • EasyModel, a user-friendly web-based interface based on MODELLER. It includes basic modeling, multiple template modeling, and loop refining.
  • 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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