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Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.
SDFCherry is a command-line program that searches for textual matches in molecular structure files of SDF format and outputs the structures that match. Optionally adds a data field to the matched structures, e.g., biological activity. Useful for QSAR.
NMkit is used in vibrational Normal Mode analysis. Using Gaussian Software's output, it determines the internal coordinate representations of normal modes, and performs other geometric manipulations in Internal Coordinate space.
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Wio-gpc is a commandline driven perl application designed for polymers molecular weight calculations based on chromatographic data. Results of GPC, SEC or GFC analysis can be converted to Mn, Mw and molecular weight distributions (MWD).
ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.
Goldify is a set of tools that allow automated addition of links into electronic documents. Its main purpose is to allow such addition of links into documents that wish to link to the IUPAC GoldBook (http://goldbook.iupac.org).
A family of programs for building coarse-grained models (eg. of macromolecules), manipulating them (geometrical transformations and more) and calculating their X-ray scattering patterns (1D and 2D too). Uses PVM for parallelization.
Project is closed, since useful alternatives exist. See http://toeholds.wordpress.com/2010/03/23/writing-chemistry-with-latex-33/ for an example. With write18 and openbabel, you probably can do whatever you want.
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Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
Commandline molar mass calculator that provides typo checking and options for printing elemental analysis and saving a record of previously calculated molar masses.
QMcBeaver is an object-oriented program to perform Quantum Monte Carlo calculations on atoms and molecules. It is designed to be easy to modify, allowing new ideas to be quickly implemented.
Open-source Cube Files Manipulator Program (OpenCubMan)is a tool for computational chemists interested in performing operations on files with volumetric data representing wavefunctions or electron densities (often called cube files).
The CheckCML project is a collection of modules for the production and checking of chemical experimental data represented as CML. The core CheckCML library provides classes for the checking process; tools such as OscarData allow for the production of CML
Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.