Molecular Science
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Avogadro Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.
1,553 weekly downloads -
Bowtie Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
1,532 weekly downloads -
picard A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
623 weekly downloads -
SASHIMI The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.
249 weekly downloads -
Gabedit Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, and Q-Chem computational chemistry packages.
194 weekly downloads -
APBS APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>.
126 weekly downloads -
Toxic Hazard Estimation A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation prediction -Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Structure Alerts for identification of Michael Acceptors -Structure Alerts for skin sensitisation -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.
162 weekly downloads -
RasTop RasTop is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules based on the popular Rasmol software. The program is aimed at the rapid visualization and analysis of molecules.
198 weekly downloads -
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
124 weekly downloads -
Ascalaph Designer Graphic molecular dynamic package.
95 weekly downloads -
GSim - tool for NMR spectroscopy GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
43 weekly downloads -
LAMMPS LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend.
62 weekly downloads -
SketchEl Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.
63 weekly downloads -
open enventory Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.
44 weekly downloads -
RDKit Open-Source Cheminformatics and Machine Learning
71 weekly downloads -
DNAStrider Mac upgraded to OSX, Lepard which do not support os9 anymore. This project is build to help DNA Strider user to get their data out and perform some basic DNA analyze function.
109 weekly downloads -
Open3DQSAR Open3DQSAR is a free, open-source tool written in C aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs).
59 weekly downloads -
PDB2PQR PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.
59 weekly downloads -
RasMol The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.
35 weekly downloads -
PyRx - Virtual Screening Tool Virtual Screening software for Computational Drug Discovery
95 weekly downloads -
STochastic Engine for Pathway Simulation Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
14 weekly downloads -
psicode An open-source quantum chemistry program package
77 weekly downloads -
Physics and Math Applets A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
27 weekly downloads -
RawGeno RawGeno Version 2.0-1 is released! RawGeno is an R CRAN library automating the scoring of AFLP electropherograms. The library includes a graphical user interface to simplify its use. Note that the 2.0-1 version is delivered as a source (*.tar.gz for Linux and Mac users) and as a binary file (*.zip, for Windows users). The installation procedure differs slightly according to your system; but this should remain simple. Have a look at the readme file when you download your new copy from https://sourceforge.net/projects/rawgeno/files/rawgeno/RawGeno%202.0-1/ Make also sure to have a look at https://sourceforge.net/projects/rawgeno/files/ where you can find a detailed manual, demo datasets and many demo scripts.
16 weekly downloads -
QMForge QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See the webpage for more info
20 weekly downloads
