Open Source Chemistry Software

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.

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 and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -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) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity 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.

Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.

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.

Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z

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.

ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details.

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 the open mzML/mzXML formats.

Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for rasterization, or used in page design software like Illustrator.

A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit 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 that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.

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.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

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.

GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html

Software and codes created in "Laboratorio de Química Computacional" of "Facultad de Ciencias y Tecnología" of "Universidad de Carabobo"

PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.

The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.

This space is not maintained anymore. If you want to get the latest updates on fpocket refer to https://github.com/Discngine/fpocket. Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schrödinger equation.

NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.

BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.