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All Topics > Biocomputational Focus > Visualization |
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3 projects in result set.
Simbody: Multibody Physics API
- This project is a SimTK toolset providing general multibody dynamics capability, that is, the ability to solve Newton's 2nd law F=ma in any set of generalized coordinates subject to arbitrary constraints. (That's Isaac himself in the oval.) Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results.
Simbody uses an advanced Featherstone-style formulation of rigid body mechanics to provide results in Order(<em>n</em>) time for any set of <em>n</em> generalized coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait, robotics, avatars, and animation. Simbody can also be used in real time interactive applications for biosimulation as well as for virtual worlds and games.
This toolset was developed originally by Michael Sherman at the Simbios Center at Stanford, with major contributions from Peter Eastman and others. Simbody descends directly from the public domain NIH Internal Variable Dynamics Module (IVM) facility for molecular dynamics developed and kindly provided by Charles Schwieters. IVM is in turn based on the spatial operator algebra of Rodriguez and Jain from NASA's Jet Propulsion Laboratory (JPL), and Simbody has adopted that formulation.
<b>SOURCE CODE:</b> Simbody is distributed in source form. The source code is maintained at <a href="https://www.github.com/simbody">GitHub</a>. You can get a zip of the latest stable release <a href="https://github.com/simbody/simbody/releases">here</a>, then build it on your Windows, Mac OSX, or Linux machine (you will need CMake and a compiler).
You can also clone the git repository and build the latest development version <a href="https://github.com/simbody/simbody">here</a>; the repository URL is https://github.com/simbody/simbody.git. If you would like to contribute bug fixes, new code, documentation, examples, etc. to Simbody (and we hope you will!), please fork the repository on GitHub and send pull requests.
If you are new to git, you may want to start with GitHub's <a href="https://help.github.com/categories/54/articles">Bootcamp tutorial</a>. | |
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Registered: 2005-07-26 19:52 |
ViewCommonPaths Application
- The ViewCommonPaths program helps to simultaneously visualize a set of numeric sequences that have the same start and end elements by drawing them into a common directed acyclic graph (DAG). In particular, ViewCommonPaths helps to simultaneously visualize a set of allosteric communication paths with the same start and end residues. Given a set of allosteric paths (each a sequence of residues), ViewCommonPaths creates a DAG from the set of individual pathways and allows a quick visual analysis of these pathways and the relationships among the residues along these paths. | |
Activity Percentile: 30.68 Registered: 2008-09-16 04:02 |
ProDy: Protein Dynamics Analysis in Python
- ProDy is a free and open-source Python package for analyzing protein structural dynamics. It is designed and developed by Ahmet Bakan in Bahar lab at the University of Pittsburgh. New functional features are continually being added to ProDy. The following are the main features that have been successfully implemented to date:
The following are the main features that have been successfully implemented to date:
* Examination and analysis of structural variability observed in experiments:
- Efficient parsing of PDB files
- Powerful atoms selections and contact identification
- Matching, superposing, and comparing multiple structures/chains
- Principal component analysis (PCA) of X-ray structures
- PCA of NMR models
- PCA of mixed structural datasets from Blast search
* Prediction and analysis of protein dynamics using theory and simulation:
- Normal Mode Analysis using the Anisotropic network models (ANM)
- Gaussian network models (GNM) analysis
- Essential dynamics analysis (EDA) of MD snapshots
- Comparative analysis and visualization of dynamics | |
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Registered: 2010-12-28 19:53 |