Molecular Simmulation

The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in computational structural biology to facilitate and standardize the development of molecular modeling, design and analysis tools.

QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.

The Nucleic Acid Modeling Tool(NAMOT) is a program to allow users to manipulate molecular models of nucleic acids based on a set of reduced co-ordinates developed at Los Alamos National Laboratory and the Max Planck Institute for Biophysical Chemistry.


Platforms: *nix

Brabosphere is a multiplatform application with two main uses: a 3D molecular visualisation tool and a graphical frontend for the quantum chemical program BRABO.


Platforms: *nix

Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.


Platforms: *nix

gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces.


Platforms: *nix

OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor harmonic oscillator approximation (RRHOA), with taking into account internal rotations and vibration anharmonicity. Such calculations often require individual approach for every molecule, and their...


Platforms: *nix

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.


Platforms: *nix

The brand new AbszOrb 3.0 is a game, it's a program, it's a screensaver - it's three mints in one. The new version of AbszOrb has been completely revamped. You can now texture orbs, arrange them in your universe, and fly freely throughout the whole universe or particle system. The new version...

CLC Protein Workbench is a scientific application for bioinformation, aimed at the advanced analysis of protein sequences. This program offers you a really wide range of analyses, all of them integrated in the same interface, which is very friendly and accessible to all users.The options and...


Platforms: Windows

Chemistry students and teachers shouldn+t miss this program. EniG. Chemistry Assistant is a specific calculator for chemical expressions. Maybe with this definition it isn+t clear enough what it does, but you+ll quickly see when you try it. You can precisely calculate the molecular weight of any...


Platforms: Windows

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...


Platforms: *nix

Biomolecule Toolkit project is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools. Whats New...


Platforms: *nix

Bioknoppix is a customized distribution of Knoppix Linux Live CD. With this distrubution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesnt touch the host...


Platforms: *nix

Libsball is a simple POSIX-based library for communicating with Spaceball 2003, 3000, 3003, and 4000 FLX six-degree-of-freedom motion control devices, via RS-232 serial ports on Unix-like systems. Spaceballs are excellent controllers for CAD/CAM, scientific visualization, and general 3-D VR...


Platforms: *nix

StrBio is a set of Java classes and libraries useful for development of software for computational structural biology research. They are licenced under the LGPL. he strbio.org classes are the basis for several published research projects, including the Pred2ary secondary structure prediction...


Platforms: *nix

cclib is a Python library for parsing and interpreting the results of computational chemistry packages. Among other data, cclib extracts coordinates, atomic orbital information, molecular orbital information, information on vibrational modes, and the results of a TD-DFT calculation. cclib...


Platforms: *nix

Phplabware project is a web-driven database management system. Phplabware runs on a server and is accessed through a web browser. Databases can be designed within a web-interface. Data-entry takes place in forms, which can be altered using phplabwares plugin mechanism. Search results can be...


Platforms: *nix

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries. SYNOPSIS use Bio::SAGE::Comparison; $sage = Bio::SAGE::Comparison->new(); This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE)...


Platforms: *nix

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data. SYNOPSIS use Bio::SAGE::DataProcessing; $sage = Bio::SAGE::DataProcessing->new(); # open sequence and quality files open( READS, "library.fasta" ); open( QUAL, "library.qual.fasta" ); #...


Platforms: *nix