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105 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6>
MMB (MacroMoleculeBuilder)
- MMB (a contraction of MacroMolecule Builder) was previously known as RNABuilder. The latter is available up to revision 2.2. We renamed the software since even some longtime users were unaware that the package now handles protein and DNA and protein as well as RNA. You can use MMB for morphing, homology modeling, folding (e.g. using base pairing contacts), redesigning complexes, fitting to low-resolution density maps, predicting local rearrangements upon mutation, and many other applications limited mostly by your imagination.
MMB was written by Samuel Coulbourn Flores at the Stanford Simbios Center. It is currently maintained by the same person, now as Dean of the Swedish National Graduate School in Medical Bioinformatics, based at Stockholm University, Sweden. | |
Registered: 2008-12-05 00:15 |
OpenMM
- OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It
provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.
<b>NEED HELP?</b> Check out the discussion forums under <a href="https://simtk.org/forums/viewforum.php?f=161">Public Forums</a> and the material from our workshops under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a>.
<b>GET STARTED QUICKLY:</b> Tutorials and sample scripts to run OpenMM are available in the <a href="http://wiki.simtk.org/openmm/VirtualRepository">OpenMM Code Repository</a>.
<b>SOURCE CODE:</b> The source code for OpenMM is available under <a href="https://simtk.org/project/xml/downloads.xml?group_id=161">Downloads</a> and also from the <a href="http://www.github.com/SimTk/openmm">Github Source Code Repository</a>.
<b>BENCHMARKS:</b> A collection of <a href="http://wiki.simtk.org/openmm/Benchmarks">benchmarks</a> is available to show the performance of OpenMM simulating a variety of molecular systems.
<b>CITING OPENMM:</b> Any work that uses OpenMM should cite the papers listed on the <a href="https://simtk.org/project/xml/publications.xml/?group_id=161">Publications</a> page. | |
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Registered: 2006-11-16 18:27 |
OpenMM Zephyr
- <b><i>OpenMM Zephyr has been deprecated. We invite you instead to explore the OpenMM Script Builder web application, which provides a similar functionality. </i></b>With pull-down menus and error checking, you can easily generate a script to run your simulation on OpenMM. Access the OpenMM Script Builder at http://builder.openmm.org. Read more about the OpenMM Script Builder and running scripts within OpenMM in Chapter 4 of the OpenMM Users' Guide at http://openmm.org.
OpenMM Zephyr is a molecular simulation application for studying molecular dynamics of proteins, RNA, and other molecules. Zephyr guides the user through a work flow for setting up and running a specialized version of the molecular dynamics application gromacs. This version of gromacs uses the OpenMM API for GPU-accelerated molecular simulations. | |
Registered: 2008-10-21 17:09 |
NAST (The Nucleic Acid Simulation Tool)
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August 2010 UPDATE
New Releases (1.0) of NAST and C2A are available!
Lots of exciting new features, detailed in the new manual NastTutorial.v4.pdf (under the "Downloads" button on the left).
C2A has been separated from NAST, please download and install separately from the C2A project page: simtk.org/home/c2a.
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Feb 2010 UPDATE 2 - If you are running C2A on a molecules that contains an "end" piece of length 1, please see the wiki for special instructions for fixing a bug that affects you
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Feb 2010 UPDATE 1 - Special instructions for running NAST with very large RNA molecules (>1000 nucleotides) are posted on the wiki
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Nov 09 UPDATE - NAST is now available on most unix/pc/mac platforms. Please read the instructions posted on the wiki for details.
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NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:
1. primary sequence
2. known or predicted secondary structure
3. known or predicted tertiary contacts (optional)
Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.
NAST uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate large numbers of plausible 3D structures that satisfy the constraints given on the secondary and tertiary structure. It then filter these structures based on agreement to the experimental data (if available). This results in a model of the molecule which satisfies all the known residue-resolution data.
TO USE NAST: Please read the README file under the downloads section. | |
Registered: 2005-09-29 16:51 |
3D RNA Modeling and Simulation Workshop, June 19, 2009
- The structure and dynamics of molecules is central to understanding biological function, and yet most experimentalists find existing structural modeling tools excessively limited in scope and difficult to use. In Simbios’ 3D RNA Modeling and Simulation Workshop, you will learn new tools that enable you to generate structures and dynamical trajectories based on your hypotheses, limited experimental information, and/or initial coordinates. The presented molecular modeling tools are designed to be easily applied by experimentalists to problems of current biological interest. | |
Activity Percentile: 82.11 Registered: 2009-07-08 20:17 |
Molecular Dynamics Workshop Series, June 24-26, 2009
- Simbios is excited to announce its Molecular Dynamics Workshop Series. The series consists of three workshops, showcasing software designed for individuals with different interests and experience with molecular dynamics (MD), from novices to experts.
<b>OpenMM Developers Workshop:</b> Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations. The workshop will highlight the explicit solvent capabilities that will be available in the next OpenMM release (in June) and include a special track focused on integration of OpenMM into AMBER.
<b>Introduction to Markov State Models and MSMBuilder:</b> For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software to automatically construct such models, as well as analyze and visualize them.
<b>Introduction to Molecular Dynamics and OpenMM Zephyr:</b> For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.
OpenMM and OpenMM Zephyr are accelerated only on specific NVIDIA and ATI GPU cards. | |
Activity Percentile: 78.86 Registered: 2009-05-27 17:19 |
Adun: high performance productivity molecular simulations code
- Objectives
Adun is a new extendible molecular simulation program that also includes data management and analysis capabilities. What follows is an overview of our main aims for the 1.0 version of our software. The current stable version is 0.81. For information on the specific features of each release see the Status section.
Description
The Adun molecular simulation application has been designed from the ground up to cater for a broad range of users and needs, from computational chemists to experimental biologists. Adun provides advanced algorithms and protocols for molecular simulation which can be accessed from an intuitive user interface but also from a more flexible programmatic level. It is built on the Adun framework which is a powerful library for creating and manipulating simulations. However it goes beyond just performing simulations by incorporating tools for analysis and management of simulation data aswell as providing mechanisms that allow the easy extension of its abilities. In many senses Adun is simply a structure that can incorporate any molecular simulation tools allowing it almost unlimited potential for growth.
Innovative Aspects
Data analysis features are extendible through plugins.
Control of a simulation can also be handled by plugins.
AdunKernel library provides a high level interface for creating, controlling and manipulating simulations
The basic libraries are scriptable.
Scripts can also run in the context of the running program e.g. Interact with live objects, automated common tasks etc.
Tightly integrated with a graphical user interface.
Data management features allows browsing, searching and grouping of various types of simulation data.
Data storage can be augmented through SQL databases allowing distributed data sharing.
Force Field independent – Adun is not coupled to any one force field and it can be extended to use any existing force field (aswell as new ones)
Advantages
Adun seeks to eliminate two of the barriers to productivity that exist with current simulation packages.
High Perfomance Productivity
The plugin & scripting capabilities coupled with the rigorous structure of the Adun framework allow for rapid implementation of new protocols and features. Moreover the implementation and distribution of these features is not tied to the main Adun distribution. New plugins and scripts can be uploaded by developers anywhere to the Adun website and thus users can benefit immediately from them.
Data management
Many current simulators leave managing their inputs and output to the user. However raw simulation data and subsequent data derived from it can have complex inter-relationships (between themselves and with the output of other simulations). Keeping track and accessing all this data is a time consuming and difficult task – a burden which Adun removes from the user. However Adun goes beyond data management as it can be augmented through the use of SQL databases. Not only does this provide more advanced storage solutions it also allows browsing and manipulation of Adun data residing in remote databases. This expands the amount of data available for analysis aswell as allowing collaboration through a single interface. | |
Activity Percentile: 76.02 Registered: 2009-07-20 20:27 |
Topological Methods for Exploring Low-density States in Folding Pathways
- In this paper, we develop a computational approach to explore the relatively low populated transition or intermediate states in biomolecular folding pathways based on a topological data analysis tool, Mapper. We applied Mapper to simulation data from large-scale distributed computing to provide structural evidence on multiple intermediate states of the unfolding and refolding of an RNA hairpin with a GCAA tetraloop. This project contains Mapper, the RNA conformations (in contact map format), and instructions to reproduce results from this paper.
<b> Motivation: </b> Characterization of transient intermediate or transition states is crucial for the description of biomolecular folding pathways, which is however difficult in both experiments and computer simulations. Such transient states are typically of low population in simulation samples. Even for simple systems such as RNA hairpins, recently there are mounting debates over the existence of multiple intermediate states.
<b> More about Mapper and the computational approach </b> The method is inspired by the classical Morse theory in mathematics which characterizes the topology of high dimensional shapes via some functional level sets. In this paper we exploit a conditional density filter which enables us to focus on the structures on pathways, followed by clustering analysis on its level sets, which helps separate low populated intermediates from high populated uninteresting structures.
The method is effective in dealing with high degree of heterogeneity in distribution, capturing structural features in multiple pathways, and being less sensitive to the distance metric than nonlinear dimensionality reduction or geometric embedding methods. The methodology described in this paper admits various implementations or extensions to incorporate more information and adapt to different settings, which thus provides a systematic tool to explore the low density intermediate states in complex biomolecular folding systems. | |
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Activity Percentile: 71.54 Registered: 2008-12-10 00:53 |
MSMBuilder
- MSMBuilder is an open source software package for automating the construction and analysis of Markov state models (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines.
MSMs are a powerful means of modeling the structure and dynamics of molecular systems, like proteins. An MSM is essentially a map of the conformational space a molecule explores. Such models consist of a set of states and a matrix of transition probabilities (or, equivalently, transition rates) between each pair of states. Intuitively, the states in an MSM can be thought of as corresponding to local minima in the free energy landscape that ultimately determines a molecule’s structure and dynamics.
MSMBuilder includes tools for
- Constructing an MSM from a set of computer simulations (typically molecular dynamics simulations in standard formats like xtc, dcd, and pdb)
- Validating statistical properties of MSMs
- Mimicking various experimental protocols to allow a quantitative comparison with experiments
- Driving efficient simulations via adaptive sampling (which decides where new simulations should be run to minimize statistical uncertainty in a model)
<p style="font-size:20px">For more information, including the latest releases, see our website at</p><p style="font-size:20px; text-align:center; font-weight:600;"><a href="http://msmbuilder.org">MSMBuilder.org</a></p> | |
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Registered: 2008-11-26 04:53 |
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 |
ProtoMol
- ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.
<b>Key Features of ProtoMol 3.0 (available Summer 2009):</b>
1) Interface to OpenMM, an MD library with NVIDIA and ATI general purpose GPU support. OpenMM supports AMBER force fields and Generalized-Born implicit solvent.
2)Python bindings offered as MDLab, which allow for prototyping of high level sampling protocols, new integrators, and new force calculations in Python.
3) Coarse grained normal mode analysis (CNMA), which provides a scalable O(N9/5) time and O(N3/2) memory diagonalization. CNMA approximates low frequency modes very well.
4) Normal Mode Langevin (NML) dynamics, which uses CNMA to periodically compute low frequency bases for propagation of dynamics, while fast modes are minimized to their equilibrium position. NML allows timesteps of 100 fs and more for even small proteins (> 30 residues) with real speedups that are about a third of the timestep used.
5) Full checkpointing support, which simplifies use in distributed computing platforms such as Condor or Folding@Home. | |
Activity Percentile: 66.67 Registered: 2009-05-28 17:47 |
Data repository for TIP3P-FB and TIP4P-FB water model parameterization.
- This is a data repository for the parameterization of the TIP3P-FB and TIP4P-FB rigid water models. | |
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Activity Percentile: 61.38 Registered: 2014-03-20 17:22 |
HiTRACE: High-Throughput Robust Analysis for Capillary Electrophoresis
- This project contains the HiTRACE software that allows users to accurately and automatically perform key quantitative analysis tasks involved in high-throughput capillary electrophoresis (CE) of nucleic acids. CE has become a workhorse technology underlying high-throughput experimental methods such as high-speed genome sequencing and large-scale footprinting for nucleic acid structural inference. Despite the wide availability of CE-based equipment, there remain challenges in leveraging the full power of CE for quantitative analysis of RNA and DNA structure. We developed HiTRACE in order to address this issue. See <a href="http://arxiv.org/abs/1104.4337">Preprint</a> for more information. | |
Activity Percentile: 60.98 Registered: 2010-11-10 08:11 |
LOOS: Lightweight Object Oriented Structure Library
- LOOS, the Lightweight Object Oriented Structure library, is a C++ library intended to aid the rapid development of new analysis tools for molecular simulation data. Although it is written in C++ for better performance, one of the goals of LOOS is to reproduce the feel of developing in a higher-level scripting language. | |
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Activity Percentile: 55.69 Registered: 2009-09-19 18:00 |
OpenMM Workshop February 2009
- Simbios is holding a two-day workshop on February 12 and 13 to introduce programmers and scientists to two important releases that will be made available mid January on Simtk.org by the Protein Folding group.
1) OpenMM, a high-performance, extensible library written in C++ for executing molecular dynamics (MD) simulations on high performance computer architectures, such as GPUs. Significant performance speed ups of over 100x were achived in some cases using OpenMM.*
Reference code for OpenMM was released in September 08. The January release includes a version of Gromacs that uses OpenMM and hence benefits from the speed-up afforded by executing portions of the code on recent versions of NVIDIA or ATI GPUs. The current release supports implicit solvent models, with explicit solvent models to be incorporated into the next release.
2) OpenMM Zephyr, an application that uses Gromacs with OpenMM, and is designed to allow MD novices run Molecular Dynamics simulations and visualize them with VMD.
At the workshop, you will hear from:
-Experts in molecular dynamics and
-Representatives from ATI and NVIDIA about their GPU architectures and future plans | |
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Registered: 2009-01-22 01:47 |
3D RNA Modeling & Simulation Workshop, UIC Chicago, March 2010
- The structure and dynamics of molecules is central to understanding biological function, and yet most experimentalists find existing structural modeling tools excessively limited in scope and difficult to use. In Simbios’ 3D RNA Modeling and Simulation Workshop, participants will learn new tools that enable them to generate structures and dynamical trajectories based on their hypotheses, limited experimental information, and/or initial coordinates. The presented molecular modeling tools were designed to be easily applied by experimentalists to problems of current biological interest.
<b> If you attended the workshop </b>please fill out the survey by going to https://simtk.org/docman/?group_id=489. | |
Registered: 2010-03-08 23:31 |
Contact Modeling with OpenSim: a User’s Approach
- This project presents step-by-step tutorials on how to integrate contact elements within a OpenSim model. Contact modeling is performed by editing two *.osim files. The first tutorial covers the classic model of a bouncing sphere on an even plane (two cases will be considered: pure elastic contact; and dissipative contact). The second tutorial considers multiple contact interactions between a sphere, an ellipsoid and a plane. Contact forces are described with the Hunt & Crossley and the Elastic Foundation models. No friction forces are applied. The main motivation of this project is to provide easy to follow tutorials for contact modeling in OpenSim, therefore, complementing the current documentation on this topic. Musculoskeletal modelers or computational researchers that wish to incorporate surface contact elements within a multibody model will find this project of their interest.
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Activity Percentile: 43.50 Registered: 2012-03-09 19:31 |
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: 36.59 Registered: 2011-12-19 00:53 |
FEATURE
- FEATURE is a suite of automated tools that examine biological structures and produce useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical/pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering). | |
Registered: 2005-05-18 16:39 |
AK-center: A fast geometric clustering method
- The study of this project considers the problem of clustering for conformation space. Clustering is a typical approach to study conformation space, which not only provides a concise representation of the free energy landscape but also is a necessary preprocessing step for building other more complicated representations such as Markov State Model. However most of current clustering methods often overlook an important property of conformation space, namely it is sampled according to Boltzmann distribution which is exponential to the free energy and thus large amounts of sampled conformations are concentrated at the free energy basins. Typically employed clustering algorithm such as K-means which measure the quality of clustering in terms of variance, tend to split
the densely sampled free energy basins into many small clusters and lump the low density regions into the clusters that have quite different structures.
In order to avoid over splitting the energy basin, in this paper, we consider the clustering from geometric point of view and measure the quality
of clusters in terms of their geometry property. We introduce a fast efficient clustering algorithm: approximating K-center clustering algorithm. This algorithm has two major advantages (1) It is fast, and can generate thousands of clusters from millions of conformations within several hours on a single PC, which is orders of magnitude faster than $K$-means clustering
algorithm. (2) The output clusters are about of the same radius and thus the population of each cluster represents its relative density determined by the underlying free energy landscape. Moreover, as it efficiently reduces the complexity of the system in a faithful way, it's proved to be very powerful in our experiments to combine it with more deliberate schemes which are otherwise not
applicable due to the massive nature of data. | |
Activity Percentile: 0.00 Registered: 2008-12-05 20:54 |
105 projects in result set. Displaying 20 per page. Projects sorted by alphabetical order.
<1> <2> <3> <4> <5> <6>