Modeller Wiki

Links: Difference between revisions

Page Discussion
modeller>andrasfiser
No edit summary
 
(42 intermediate revisions by 8 users not shown)
Line 1: Line 1:
__NOTOC__
__NOTOC__
== 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.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://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 ===
=== 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
* [http://www.fiserlab.org/servers/archpred ArchPred], template based loop structure prediction server that delivers a full comparative model with the predicted loop using Modeller
* [http://www.fiserlab.org/servers/archpred ArchPred], template based loop structure prediction server that delivers a full comparative model with the predicted loop using Modeller
* [http://salilab.org/Flex-EM/ Flex-EM], a method for protein structure fitting and refinement guided by cryoEM density.
=== 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.
Retrieved from "https://salilab.org/modeller/wiki-data/index.php?title=Links&oldid=808"