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Open Source Software

Autodock A suite of automatic docking tools
Blast Blast finds regions of similarity between biological sequences
Gamess An ab initio quantum mechanics program for the computation of the properties of molecular systems using standard quantum chemical methods
Gromacs A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles
Modeler Homology or comparative modeling of protein three-dimensional structures
Molden A pre- and post processing program of molecular and electronic structure
MrBayes A software program which performs Bayesian inference of phylogeny
NAMD Parallel molecular dynamics code for large biomolecular systems
Quantum Expresso Programs for electronic structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using a Plane-Wave basis set
Siesta A software for performing electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
VMD A molecular graphics software

Autodock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.  A graphical user interface called AutoDockTools (ADT) was developed to helps set up ligands, docking sites and to analyze dockings results. AutoDock has applications in X-ray crystallography,  structure-based drug design, lead optimization, virtual screening (HTS), combinatorial library design, protein-protein docking, chemical mechanism studies.

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Blast

Blast finds regions of similarity between biological sequences

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Gamess

GAMESS is an ab initio quantum mechanics program, which provides many methods for computation of the properties of molecular systems using standard quantum chemical methods, many of them updated for parallel execution. For a detailed description, please look at the GAMESS home page or at the program description in $$GAMESS_DOCUMENTATION, which is available after executing "module load gamess ".

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Gromacs

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, and non-biological systems like polymers.  As a lot of algorithmic optimizations have been introduced in the code, GROMACS is claimed to have extremely high performance and runs 3-5 times faster than the other similar code. 

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Modeler

MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac.

 

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Molden

Molden is a pre- and post processing program of molecular and electronic structure. It is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density with the output from GAMESS  AUSSIAN and the Semi-Empirical packages Mopac/Ampac. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. Both Xwindows and OpenGL versions of Molden are also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. Molden also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface.

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MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem.

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NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR.

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Quantum Espresso

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

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Siesta

Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is an original method and a software implementation for performing electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. It uses a density functional theory code that predicts the physical properties of a collection of atoms. Properties that can be predicted using the code include Kohn-Sham band-structures, electron density, and Mulliken populations.

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VMD

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code

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