Open Source BSD Molecular Mechanics Software
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Molecular Mechanics Software for BSD
Browse free open source Molecular Mechanics software and projects for BSD below. Use the toggles on the left to filter open source Molecular Mechanics software by OS, license, language, programming language, and project status.
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MEMBPLUGIN
MEMBPLUGIN: studying membrane complexity in VMD
MEMBPLUGIN is a membrane analysis tool for molecular-dynamics simulations. It is a collection of visual and command-line tools that can be run within the Visual Molecular Dynamics (VMD) environment to analyze biomolecular simulations of lipid bilayers. -
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An open-source software to convert SDF files into TINKER XYZ files (and viceversa) with automatic assignment of MMFF94 atom types, bond types and charges
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level. -
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APL@Voro
APL@Voro a tool for model bilayer simulation analysis.
APL@Voro is a program designed to aid in the analysis of lipid bilayer simulations carried out by gromacs. It calculates the area per lipid and the membrane thickness even for mixed bilayers. Colored Voronoi diagrams and different types of plots are presented in an interactive environment. -
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AutoMap
AutoMap is a tool for structural biology and drug design.
AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes. -
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CAMPARI
Software for molecular simulations and trajectory analysis
We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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Iphigenie
A fast and versatile molecular dynamics program
The molecular mechanics (MM) program Iphigenie provides a broad range of molecular dynamics (MD) methods and technologies, including polarizable force fields (PMM), the HADES reaction field, and QM/(P)MM hybrid simulations. -
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MolTPC
MolTPC provides a solution for fully automatic tautomer enumeration.
Besides all their conformational degrees of freedom, drug-like molecules and natural products often also undergo tautomeric interconversions. Compared to the huge efforts made in experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare. The few freely available software packages limit their output to a subset of the possible configurational space by sometimes unwanted prior assumptions and complete neglection of ring-chain tautomerism. MolTPC provides an adjustable and fully automatic approach for this problem. The original publication can be found on http://onlinelibrary.wiley.com/doi/10.1002/jcc.23397/full. -
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OpenCDSurf
Compute CD cavity accessibility
An open-source software aimed at computing cavity accessibility in cyclodextrin derivatives -
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PyBrella
Python script to automate umbrella sampling with AMBER
PyBrella is a script designed to automate the umbrella sampling process, using the AMBER molecular dynamics package. -
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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QTASEP
Visualization application for various TASEP, ASEP and SSEP models.
Visualization of TASEP, ASEP, SSEP models with various update rules based on Zarja simulation library using QT GUI library. -
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Renumber Gromacs Top & Gro Files
Renumber Gromacs .top and .gro files
Renumber Gromacs .top and .gro files after removing atoms (e.g. hydrogens) for input into grompp -
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MDcore is an Open-Source library implementing the core functionality of a Molecular Dynamics engine. The engine is inherently multi-threaded and runs efficiently on multi-processor/multi-core shared-memory architectures.
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