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.

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.

nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a board of reviewers. The project is supported by a scientific advisory board. nmrshiftdb2 is part of the NFDI4Chem initiative (https://nfdi4chem.de/) and will provide a component for a curated repository there. Please consult the documentation for more detailed information.

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.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas

⚠️ KherveFitting has moved. New releases will no longer be published here. Download the latest version from https://khervetools.com or directly from GitHub: https://github.com/KherveFitting/KherveFitting/releases/latest. This SourceForge page is kept for archival/older versions only. YouTube Channel: https://www.youtube.com/@xpsexamples-imperialcolleg6571

DWSIM is an open source, CAPE-OPEN compliant chemical process simulator for Windows, Linux and macOS systems. Written in VB.NET and C#, DWSIM features a comprehensive set of unit operations, advanced thermodynamic models, support for reacting systems, petroleum characterization tools and a fully-featured graphical interface. DWSIM Pro is a commercial sibling of DWSIM built on top of open-source software. It offers extended features, comes with private support, and is accessible in the cloud. Visit simulate365.com for details.

Stand-alone application and Python tools for interactive and/or batch processing analysis of X-Ray Fluorescence Spectra. Graphical user interface (GUI) and batch processing capabilities provided.

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling.

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.

GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program.

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.

ChemCrow is an AI-powered framework designed to assist in chemical research and discovery. It integrates AI models with chemical knowledge bases to provide intelligent recommendations for synthesis planning, reaction prediction, and material discovery. This tool helps automate and accelerate research in computational chemistry and drug development.

TARIS (Tree Analysis and Representation of Isopotential Surfaces) is a software package designed for molecular similarity purposes in the field of Computational Chemistry. Users are allowed to compare molecules through their MEP loading .cube files.

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OSRA is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD file format- a computer recognizable molecular structure You can find links to the binary executables here: https://sourceforge.net/p/osra/wiki/Download/

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.

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.

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.

MESMER is designed to analyze and simulate reactions in the gas phase that take place on a potential energy surface that is characterized by having one or more potential wells, and which are typically described by rate coefficients that depend on pressure (or concentration) as well as temperature. MESMER allows you to simulate systems over a wide range of pressures and temperatures, extract rate coefficients, analyze experimental data, fit model parameters and represent rate coefficients in formats that can be used directly in large scale simulations (e.g. Cantera or Chemkin).

JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app. It can be used in conjunction with the Java applet to provide an alternative to Java when the platform does not support that (iPhone/iPad) or does not support applets (Android). Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet platforms. JSmol can read all the files that Jmol reads. You can do all the scripting that Jmol does. You can create all the buttons and links and such that you are used to creating for Jmol. All of the rendering capability of the Jmol applet is there. JSmol has both a console and a popup menu. JSmol is integrated fully with JSME and JSpecView. A "lite" version of JSmol provides minimal functionality (balls and sticks only) for extremely small-bandwith apps. Released 1/12/2013

Object-oriented crystallographic library and program, for the analysis of Crystal structures from scattering experiments: optimized scattering computation, Graphical interface for structures and data, global optimization algorithms.

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