Molecular Modelling

'FoldIt light' is a molecular modelling program to visualize and manipulate interactively protein structure files from the Brookhaven Protein Data Bank (PDB). It's an integrated environment allowing 3D manipulations as well as statistical analysis. Platforms: Mac

Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is more versatile than the one described by Milescu, et al. Biophys. J. 91:3135-3150 and can be used as a "blind" step detector or... Platforms: Matlab

ORMA (Oligonucleotide Retrieving for Molecular Applications) is a series of integrated scripts in Matlab, which performs an accurate search of all the positions able to specifically discriminate one species among homologous ones. ORMA also performs an accurate selection of high-quality... Platforms: Matlab

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt,... Platforms: Mac

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small... Platforms: Mac

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the... Platforms: Mac

Nanodesigner is a software platform for research on molecular nanotechnology. It has a plug-in architecture and will include tools for molecular visualization & modelling, design of complex new molecules, molecular dynamics,... Platforms: *nix

Art of Illusion is a free, open source 3D modelling and rendering studio. Many of its capabilities rival those found in commercial programs. Highlights include subdivision surface based modelling tools, skeleton based animation, and a graphical language for designing procedural textures and... Platforms: Windows, Mac, *nix, Java, BSD Solaris

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. This project offers a flexible rendering engine and a powerful plugin architecture. The main concept behind Avogadro... Platforms: *nix

Games::Othello is a Perl extension for modelling a game of Othello. SYNOPSIS use Games::Othello; my $game = Games::Othello->new(); while( !game->over ) { printf "It is presently %ss move", ($game->whos_move eq b) ? black, white; my @possible_moves = values $game->possible_moves(); if... Platforms: *nix

Alzabo is a Perl module with data modelling tool and RDBMS-OO mapper. SYNOPSIS Cannot be summarized here. What is Alzabo? Alzabo is a suite of modules with two core functions. Its first use is as a data modelling tool. Through either a schema creation GUI, a perl program, or reverse... Platforms: *nix

DbModeller project is a database schema modelling application for building physical database designs. This can connect to an existing database a pull down the schema or create from scratch. It currently allows modelling of tables and referential integrity constraints and generates SQL for the... Platforms: *nix

ASCEND is a flexible modelling environment for solving hard engineering and science problems. It offers: - an object-oriented model description language for describing your system, - an interactive user interface that allows you to solve your model and explore the effect of changing the model... Platforms: *nix

openModeller library is a spatial distribution modelling library, providing a uniform method for modelling distribution patterns using a variety of modelling algorithms. openModeller can be used via programatic interfaces, including SOAP and SWIG-python, as well as via a user friendly desktop... Platforms: *nix

Ayam is a free 3D modelling environment for the RenderMan interface, distributed under the BSD licence. This means that neither the author nor any contributors make money out of this software. We need your (yes your!) feedback to keep this project alive. If you use Ayam, please submit your... Platforms: *nix

Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers... Platforms: *nix

LAMMPS project is a Molecular Dynamics Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale... Platforms: *nix

Innesoft DeepMesh is a professional and reliable application designed for 3D modelling. It features support for over 20 model formats, skinned animation, a built-in uv mapper, lightmapper and hundreds of tools for building and editing character models, maps and environments. Ideal for game... Platforms: Windows

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is... Platforms: Windows

BALLView is our standalone molecular modeling and visualization application. Furthermore it is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS. It provides fast OpenGL-based visualization of... Platforms: Windows