Atoms Molecules Ions

A Java based molecular modeling program. Has support for generating movies by interpolating between given positions, interactive display and manipulation of atoms and bonds, and dynamic modeling of substance formation.

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.

A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)


Platforms: Windows, Mac, Linux

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

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

A collection of cheminformatics and machine-learning software written in C++ and Python. The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge...


Platforms: Windows, Mac, BSD, Linux

Gabedit is a Graphical User Interface to Gamess-US, Gaussian, Molcas, Molpro, MPQC and Q-Chem computational chemistry packages.Gabedit includes graphical facilities for generating keywords and options, molecule specifications and their input sections for even the most advanced calculation...


Platforms: *nix, C/C++, BSD

StoichTools comprises a set of Matlab functions for doing stoichiometric analysis. These functions parse standard chemical notation for a variety of stoichiometric calculations including finding molecular weights, balancing reactions for atom and charge conservation, finding independent...


Platforms: Matlab

This software has been realized by Bret Fortenberry at the CNS Technology Lab at Boston University (http://techlab.bu.edu/). A model to show the properties of EPSPs and IPSPs in the postsynaptic cell. The model allows a user to adjust the number of EPSP and IPSP inputs, the rise and fall times...


Platforms: Matlab

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid...


Platforms: Mac

This simulation allows students to compare the motion of free falling objects with and without the influence of air resistance. Air resistance is the result of collisions of the object's leading surface with air molecules. On Earth, objects falling through the air usually encounter some sort of...


Platforms: Mac

Fragmentation Analyzer is a tool for analyzing MS/MS fragmentation data. Currently nine different analysis types are supported: * Spectra Visualization - visualize the MS/MS spectra with fragment ion annotation, zooming and manual de-novo-sequencing. * Intensity Box Plots - analyze intensity...


Platforms: Mac

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

massXpert is about mass spectrometry. This is software that runs on MS-Windows, Apple-Mac-OS-X, GNU-Linux, and almost all variants of the UNIX system. With massXpert you actually have four programs in one : 1. With the XpertDef module you define brand new polymer chemistries (what are the...


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 PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and...


Platforms: Mac

The following dissertation outlines one possible answer to this question, including an example game-like problem and a Genetic Algorithm (GA) inspired solution. The Genetic Algorithm described acts upon a population of game playing computer agents. Each agent contains a set of expressible...


Platforms: Mac

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

ChemAzTech is an OpenSource (GPL licence) Web chemistry software connected to a MySQL database (L.A.M.P. software) which is storing molecules. You can manage a chemical laboratory database, with product's properties. Features MyChem + JChemPaint applet allow to the user to search by...


Platforms: *nix

Few days ago the new version of leeenux was released. Despite the fact I was really happy with the old version (2.0), I have decided to spend part of the belgian rainy easter testing the new version on my 701. With respect version 2.0, the main differences are: New kernel, new UNR menu,...


Platforms: *nix