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All Topics > Biocomputational Focus > Visualization |
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10 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 |
Computational Analysis of Kinase Selectivity using Structural Knowledge
- Here, we present a knowledge-based approach to profile kinase selectivity based on the similarity between drug binding microenvironments. To allow large-scale kinase site similarity profiling, we have created a kinome structure database consisting of 5000 inhibitor-binding pockets from 187 unique human kinase crystal structures. | |
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Registered: 2017-04-18 20:03 |
PDBManip: PDB (Protein Data Bank) Editor and Manipulator Utility
- PDBManip is a free program for editing and manipulating PDB (Protein Data Bank) files. It has a graphical user interface and it is provided as an executable file for running on Windows® operating systems. There is a bunch of free programs on the internet for the same purpose. While all those programs offer only a few predefined tasks, PDBManip uses AngelScript language which is very similar to C/C++ language, to allow the users to write their own scripts to define editing tasks, although PDBManip contains many useful example scripts. I know that the text-manipulation script languages such as Awk and Perl are available, and many users, uses these to do their works. However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. In this way, proficiency in computer programming, that is a must in using Awk or Perl, is not a barrier. | |
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Registered: 2016-08-06 06:48 |
HTMD - High Throughput Molecular Dynamics
- In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analyzing simulations, computing Markov state models, kinetic rates, affinities and pathways.
See more information on <a href="https://www.htmd.org/">https://www.htmd.org</a>.
HTMD Forum: <a href="https://forum.htmd.org/">https://forum.htmd.org</a>
We are also on Github: <a href="https://github.com/Acellera/htmd">https://github.com/Acellera/htmd</a>
Report issues on: <a href="https://github.com/Acellera/htmd/issues">https://github.com/Acellera/htmd/issues</a> | |
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Registered: 2016-05-13 07:45 |
Neurogene: Elucidating apoptotic pathways in brain tumor models
- Genomics has brought many important discoveries and changes into science and medicine. The central dogma of molecular biology where "DNA makes RNA and RNA makes protein" is well established (yet controversial). Watson and Crick had originally proposed a double stranded model of DNA. This served as a useful foundation for further understanding and research. Throughout the years more investigations demonstrated that human evolution was far more complex than originally believed. There was originally a great deal of migration around the world causing some hereditary lineages to become isolated and others to become more robust.
The life cycle of a cell usually begins with division and continues with replication. However, errors in mitosis can cause a cell to undergo apoptosis or form into a tumor. Differentiating between the two final pathways may be critical in helping to guide cells towards a less destructive pathway for the host organism. The critical component has to do with the environment the cell is in. The cell receives information from the outside environment and adapts according to received stimuli.
This project has been conceived to leverage a team based approach for elucidating the underlying apoptotic pathways responsible for tumor lysis and cell death. Combining the current understanding of molecular dynamics, genomics, and contrast imaging agents to discover novel therapeutic targets and further the current understanding of tumor biology within the genomic era. | |
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Registered: 2010-03-17 09:26 |
SMART: Single Molecule Analysis Research Tool
- We provide a standardized approach for analyzing single molecule data in the software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data. | |
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Activity Percentile: 0.00 Registered: 2011-12-19 00:53 |
FEATURE-Viz: A Web-Based Visualization System for Comparing
Pocket Similarity
- The PocketFEATURE algorithm seeks similar microenvironments within two binding sites, and assesses overall binding site similarity by the presence of multiple shared microenvironments.
Both the original perl implementation (http://simtk.org/home/pocketfeature) and the newer python implementation (http://simtk.org/home/pocketfeature2) produce text-based alignment results, with some small differences between implementations. FEATURE-Viz provides a web-based interface to visualize and manipulate alignments. | |
Activity Percentile: 0.00 Registered: 2015-04-15 19:50 |
C++ and Python code, distributed computing and OpenMM interfaces for simulations
- please cite: "Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon" (PLOS One 2013)
for any code related to protein-DNA modeling and
"Free Energy Monte Carlo Simulations on a Distributed Network" (Lecture Notes in Computer Science Journal for PARA 2010)
http://link.springer.com/chapter/10.1007%2F978-3-642-28145-7_1
for parallel client-server code, users of additional code should cite this web site. Code is provided as-is with no warranty and examples are provided to illustrate the usage of these modeling techniques with some sample systems. Code is the intellectual property of Luke Czapla, developer and biophysicist. Examples are provided in C/C++ and Python. | |
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Activity Percentile: 0.00 Registered: 2014-02-01 22:32 |
MSMExplorer: A Visualization Application for Markov State Models for Folding
- A java-based visualization application for Markov State Models for folding simulations. The programs is designed as a gui interface for viewing and interacting with MSMs constructed by MSMBuilder.
SOURCE CODE NOTICE:
for up-to-date source code access please visit:
http://github.com/brycecr/msmexplorer
Similarly, Up-to-date distributions can be downloaded from
https://github.com/brycecr/msmexplorer/downloads
but periodic major releases (considered "stable") will still be uploaded to simtk.
In the Documents section of this site, you'll find an illustrated Reference and Tutorial PDF and a short tutorial video. | |
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Activity Percentile: 0.00 Registered: 2010-06-15 00:10 |