Links: Difference between revisions
modeller>KuntalBhusan No edit summary |
|||
| (39 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! | |||
=== 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://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 | ||
| Line 16: | Line 18: | ||
=== 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.