Molecular Interaction
Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...
Platforms: Windows
License: Freeware | Download (466): Open3DGRID x64 Download |
Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...
Platforms: Linux
License: Freeware | Download (434): Open3DGRID for Linux Download |
Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...
Platforms: Mac
License: Freeware | Download (424): Open3DGRID for Mac OS X Download |
Open3DGRID is an application designed for high-throughput generation of molecular interaction fields or MIFs. Open3DGRID can generate steric potential, electron density and MM / QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA / CoMSIA...
Platforms: Windows
License: Freeware | Download (421): Open3DGRID Download |
Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary...
Platforms: Windows
License: Freeware | Size: 1.2 MB | Download (429): Open3DQSAR x64 Download |
Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary...
Platforms: Mac
License: Freeware | Size: 1.1 MB | Download (436): Open3DQSAR for Mac OS X Download |
Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary...
Platforms: Linux
License: Freeware | Size: 1.4 MB | Download (460): Open3DQSAR for Linux Download |
Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary...
Platforms: Windows
License: Freeware | Size: 1.01 MB | Download (488): Open3DQSAR Download |
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
License: Freeware | Size: 1.12 MB | Download (38): Molecular Dynamics Adiabatic Piston Model Download |
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
License: Freeware | Size: 829.44 KB | Download (49): Hidden Markov Models for Molecular Motors Download |
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
License: Freeware | Size: 286.72 KB | Download (47): ORMA (Oligonucleotide Retrieving for Molecular Applications) Download |
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
License: Freeware | Size: 1.3 MB | Download (36): Molecular Dynamics Model Download |
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
License: Freeware | Size: 1.3 MB | Download (38): Molecular Dynamics Demonstration Model Download |
Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of...
Platforms: Windows, Mac, Linux
License: Freeware | Size: 60.89 MB | Download (45): Gene-Environment iNteraction Simulator 2 Download |
PFMD performs a Molecular Dynamics simulation of some polarizable fluids at the liquid state by means of a dissociable potential. Supported molecules are H2O (water) and MX3, where M is a metal among Al, Fe, or Ga and X is a halogen among Cl, Br, or I.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 347.03 KB | Download (47): Polarizable Fluids Molecular Dynamics Download |
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!
Platforms: Windows, Mac, BSD, Solaris, Linux
License: Freeware | Size: 9.25 MB | Download (54): PyMOL Molecular Graphics System Download |
NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms...
Platforms: Matlab
License: Freeware | Size: 10 KB | Download (39): NanoVis: molecular visualizer Download |
Allows user interaction among a trusted community of users to foster a more direct and personal exchange of ideas.This module was created for a specific project of EKOS Communications. The intention of the module was to foster communication between users of a private website. The users and...
Platforms: PHP
License: Freeware | Size: 20.48 KB | Download (40): Interaction Centre Download |
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
License: Freeware | Size: 256 KB | Download (170): Avogadro Download |
Brcontrol is a set of patches to allow some interaction between a IDS and a firewall (currently snort and linux netfilter). It will help in the creation of aggresive honeypots or other advanced firewall and ids configurations. In can also work as bridge.. Get Brcontrol at SourceForge.net. Fast,...
Platforms: *nix
License: Freeware | Size: 15.36 KB | Download (93): Brcontrol Download |