Other Sites of Interest:. Is a Python-based program package for the normal mode analysis of coarse grained elastic networks. The package includes the classic elastic network algorithm, the new bend-twist-stretch algorithm for arbitrary coarse networks, and various useful tools for analysis and animation of modes. Please send any inquiries, bug reports, etc. to modehunter at biomachina.org.
http://modehunter.biomachina.org/
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modehunter.biomachina.org | modehunter.biomachina.org Reviews
https://modehunter.biomachina.org
Other Sites of Interest:. Is a Python-based program package for the normal mode analysis of coarse grained elastic networks. The package includes the classic elastic network algorithm, the new bend-twist-stretch algorithm for arbitrary coarse networks, and various useful tools for analysis and animation of modes. Please send any inquiries, bug reports, etc. to modehunter at biomachina.org.
modehunter.biomachina.org
ModeHunter Program Package - References
http://modehunter.biomachina.org/fref.html
Joseph N. Stember and Willy Wriggers. Bend-Twist-Stretch Model for Coarse Elastic Network Simulation of Biomolecular Motion. J. Chem. Phys. 2009, 131:074112. [Abstract]. In addition, the following two earlier papers show applications of ENMs to multiscale structural data:. Pablo Chacón, Florence Tama and Willy Wriggers. Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions. 2003, Vol. 326, pp. 485-492. [Abstract]. Florence Tama, Willy Wriggers, and Charles L. Brooks III.
ModeHunter Program Package - User Guide
http://modehunter.biomachina.org/fguide.html
This guide is intended to be used as a reference manual. You can also get usage information by calling the Python programs below without any arguments. In addition, the tutorial. Gives examples of these utilities. More documentation is also available in the published articles. Oscillating Animation of Normal Modes. B-factor Calculation from Normal Modes. Bend-Twist-Stretch Elastic Rod Network Model. Carbon-Alpha Based Elastic Network Model. Extract Fine Modes from Coarse Modes by Interpolation. User-spec...
ModeHunter Download and E-mail Registration Form
http://modehunter.biomachina.org/freg1.html
ModeHunter Download and E-Mail Registration. Note: all personal information will be kept strictly confidential. Would you like receive important user infos by e-mail ( 2-3 times per year)? Please keep me posted. Any comments, e.g. about your lab or your project (optional)? Return to the front page.
ModeHunter Program Package - Tutorial
http://modehunter.biomachina.org/tutorial.html
This tutorial demonstrates the basic usage of ModeHunter tools using the default parameters. More documentation is available in the user guide. And in the published articles. Follow first the simple registration and download steps. You need to download the tutorial separately)! In addition to the Python programs, the ModeHunter Tutorial 1.2 directory contains also a number of additional data files and a directory:. 4AKE chain a ca.pdb. Adenylate kinase C-alpha atom representation. Return to the front page.
ModeHunter Program Package - History
http://modehunter.biomachina.org/fhis.html
Was initially developed in 2009 by Joseph Stember and Willy Wriggers at Weill Cornell Medical College. Updated information on our research can be found at the URL biomachina.org. The program history below describes changes that were implemented after version 1.0. Changes in Version 1.2 vs. Version 1.1:. Using cosine instead of sine in. To support single-frame output of modes for subsequent analysis with structural bioinformatics programs. Type selection parameter added for "arrows" or "needles" display in.
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links
http://www.papageorgiou.fr/links.html
Http:/ situs.biomachina.org/. Http:/ emotion.biomachina.org/. Http:/ modehunter.biomachina.org/. Http:/ sculptor.biomachina.org/. Http:/ www.cgl.ucsf.edu/chimera/. Https:/ sites.google.com/site/xsiebert/urox. Http:/ www.embl-hamburg.de/biosaxs/. Http:/ situs.biomachina.org/saxs/index.html. Http:/ www.esrf.eu/UsersAndScience/Experiments/StructMaterials/ID31/Applications/protein. Http:/ www.ccp14.ac.uk/. Http:/ www.ill.eu/instruments-support/instruments-groups/groups/dif/. UPPSALA A SOFTWARE FACTORY.
biomachina.org - old version
http://wriggers.biomachina.org/index_old.html
We are moving and we are hiring! Biomachina.org found a new home at Old Dominion University in Norfolk, Virginia. Will be the Frank Batten Professor of Mechanical and Aerospace Engineering. ODU has a long tradition in government and industrial applications of 3D modeling and visualization. We will complement the growing number of computational life sciences and biomedical engineering programs on campus. Popular multi-scale docking and modeling suite developed since 1998.
Situs Program Package
http://situs.biomachina.org/fflavors.html
The Situs package includes the distribution of Situs Flavors. Ie user modified and enhanced codes for a variety of purposes that are derived at least in part from earlier versions of Situs. These program packages come with their own documentation and licences (if applicable) and are provided "as is" without any specific support from the biomachina team. The available Flavors. Geometric feature tracking tools. By Willy Wriggers,. To accompany our paper on map and model assessment ( Wriggers and He, 2015.
biomachina.org - old version
http://www.biomachina.org/index_old.html
We are moving and we are hiring! Biomachina.org found a new home at Old Dominion University in Norfolk, Virginia. Will be the Frank Batten Professor of Mechanical and Aerospace Engineering. ODU has a long tradition in government and industrial applications of 3D modeling and visualization. We will complement the growing number of computational life sciences and biomedical engineering programs on campus. Popular multi-scale docking and modeling suite developed since 1998.
biomachina.org - old version
http://sensitus.biomachina.org/index_old.html
We are moving and we are hiring! Biomachina.org found a new home at Old Dominion University in Norfolk, Virginia. Will be the Frank Batten Professor of Mechanical and Aerospace Engineering. ODU has a long tradition in government and industrial applications of 3D modeling and visualization. We will complement the growing number of computational life sciences and biomedical engineering programs on campus. Popular multi-scale docking and modeling suite developed since 1998.
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modehunter.biomachina.org
Other Sites of Interest:. Is a Python-based program package for the normal mode analysis of coarse grained elastic networks. The package includes the classic elastic network algorithm, the new bend-twist-stretch algorithm for arbitrary coarse networks, and various useful tools for analysis and animation of modes. Please send any inquiries, bug reports, etc. to modehunter at biomachina.org.
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