Software

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Research work in BioSFLab relies on computer software, with strong preference towards the usage of free and open source software. The reasons for this preference are the limited use conditions, limited extensibility, and license cost of proprietary software.

Structure visualization, analysis, and editing

PyMOL

PyMOL (homepage, Wikipedia page) is free and open source molecular visualization system, maintained by Schrödinger. PyMOL is available as a package in both Debian and Fedora.

Specific uses

VMD

VMD (homepage, Wikipedia page) is a freely available molecular visualization system used for displaying and animation of biomolecular systems. VMD stands for Visual Molecular Dynamics, and it is maintained by [Theoretical and Computational Biophysics Group https://www-s.ks.uiuc.edu/] at University of Illinois at Urbana-Champaign. VMD is distributed with source code under VMD License, and it is not free and open source software. VMD is not available as a package neither in Debian nor in Fedora.

Specific uses

UCSF Chimera

UCSF Chimera (homepage, Wikipedia page) is a freely available visualization and analysis software. Chimera works with single molecules as well as supramolecular assemblies, sequence alignments, results of docking, and molecular dynamics trajectories. Chimera is distributed in a binary form under UCSF Chimera Non-Commercial Software License Agreement, and it is not free and open source software. Chimera is not available as a package in neither in Debian nor in Fedora.

Specific uses

wxMacMolPlt

wxMacMolPlt (homepage, Wikipedia page) is a free and open source graphical user interface for preparation and visualization of the input and output files for the GAMESS quantum chemistry package. wxMacMolPlt is not available as a package neither in Debian nor in Fedora.

MODELLER

MODELLER (homepage, Wikipedia page) is a proprietary software for modelling of tertiary structures of proteins. MODELLER is not available as a package neither in Debian nor in Fedora.

Avogadro

Avogadro (homepage, Wikipedia page) is a free and open source molecule editor. It is maintained by Kitware. Avogadro comes in two versions: orange Avogadro, and blue Avogadro 2. Avogadro (first version, the orange one) is available as a package in both Debian and Fedora.

ChemAxon Marvin Suite

ChemAxon Marvin Suite (homepage, Wikipedia page) is a freely available software for drawing and visualization of molecules. Marvin is distributed in binar form under ChemAxon EULA, and it is not free and open source software. Marvin is not available as a package neither in Debian nor in Fedora.

Cresset

Torch (homepage) is a proprietary software. Torch is not available as a package neither in Debian nor in Fedora.

Spark (homepage) is a proprietary software. Spark is not available as a package neither in Debian nor in Fedora.

Forge (homepage) is a proprietary software. Forge is not available as a package neither in Debian nor in Fedora.

Electrostatic calculation, docking and molecular simulation

APBS

APBS (homepage) is a free and open source software for computing the numerical solution of the Poisson-Boltzmann equation that describes electrostatic interactions between molecular solutes. APBS is available as a package in both Debian and Fedora.

PDB2PQR

PDB2PQR (homepage) is a free and open source software used for preparation of molecular structures for electrostatic calculation. PDB2PQR is available in Debian, but not in Fedora.

AutoDock and Vina

AutoDock (homepage, Wikipedia page) and AutoDock Vina (homepage) are free and open source protein-ligand docking software packages. AutoDock is available as a package in both Debian and Fedora. AudoDock Vina is available in Debian, but not in Fedora.

GROMACS

GROMACS (homepage, Wikipedia page) is a free and open source molecular dynamics package. It supports classical molecular mechanics and provides interface to a number of quantum mechanics software packages. GROMACS is available as a package in both Debian and Fedora.

Specific uses

NAMD

NAMD (homepage, Wikipedia page) is a freely available molecular dynamics package. NAMD is not available as a package neither in Debian nor in Fedora.

CP2K

CP2K (homepage, Wikipedia page) is a free and open source molecular dynamics package. It supports both quantum and classical molecular mechanics, and allows using both of them in the same simulation with QM/MM. CP2K is available as a package in both Debian and Fedora.

Specific uses

NWChem

NWChem (homepage, Wikipedia page) is a free and open source molecular dynamics package. NWChem is available as a package in both Debian and Fedora.

GAMESS (US)

GAMESS (US) (homepage, Wikipedia page) is a freely available quantum chemistry software. GAMESS (US) is not available as a package neither in Debian nor in Fedora.

Topology generation, file format conversion

AmberTools and acpype

AmberTools, a part of Amber molecular dynamics package (homepage, Wikipedia page), is a freely available set of tools for preparation and analysis of molecular dynamics simulations. Many of the tools are free and open source software. AmberTools is not available as a package neither in Debian nor in Fedora. However, there is an effort to package AmberTools for Fedora.

ACPYPE (homepage) is a free and open source software for generation of molecular topologies. It uses Antechamber and GAFF from AmberTools. ACPYPE is not available as a package neither in Debian nor in Fedora.

Open Babel

Open Babel (homepage, Wikipedia page) is free and open source software for conversion between different chemical file formats. It provides both command line and graphical user interfaces. Open Babel is available as a package in both Debian and Fedora.

Kinetics and quantitative molecular interactions

KinTek Explorer

KinTek Explorer (homepage) is a proprietary software for kinetic data analysis. KinTek Explorer is not available as a package neither in Debian nor in Fedora.

COPASI

COPASI (homepage, Wikipedia page) is a free and open source software for simulation and analysis of biochemical networks and their dynamics. COPASI is not available in Debian, but is in Fedora.

Tenua

Tenua (homepage, Wikipedia page) is a free and open source software for kinetics simulation. Tenua is not available as a package neither in Debian nor in Fedora.

Data processing and visualization

Maxima

Maxima (homepage, Wikipedia page) is a free and open source computer algebra system. Maxima is available as a package in both Debian and Fedora.

SciDAVis

SciDAVis (homepage, Wikipedia page) is a free and open source software. SciDAVis is available as a package in both Debian and Fedora.

LibreOffice

LibreOffice (homepage, Wikipedia page) is a free and open source software. LibreOffice is available as a package in both Debian and Fedora.

gnuplot

gnuplot (homepage, Wikipedia page) is a free and open source software. Gnuplot is available as a package in both Debian and Fedora.