Difference between revisions of "Related Projects"

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m (OOPSE now OpenMD)
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* [http://www.nano-hive.org/ NanoHive-1 Nanospace Simulator] - Modular simulator for modeling nanometer scale physics and chemistry
 
* [http://www.nano-hive.org/ NanoHive-1 Nanospace Simulator] - Modular simulator for modeling nanometer scale physics and chemistry
 
* [http://openmd.net OpenMD] - Open source molecular dynamics engine
 
* [http://openmd.net OpenMD] - Open source molecular dynamics engine
 +
* [http://open3dalign.org/ Open3DALIGN] - Conformational search and unsupervised molecular alignment
 
* [http://www.open3dqsar.org/ Open3DQSAR] - High-throughput computation and chemometric analysis of molecular interaction fields
 
* [http://www.open3dqsar.org/ Open3DQSAR] - High-throughput computation and chemometric analysis of molecular interaction fields
 
* [http://cactus.nci.nih.gov/osra/ OSRA] - Optical Structure Recognition (graphics into [[SMILES]])
 
* [http://cactus.nci.nih.gov/osra/ OSRA] - Optical Structure Recognition (graphics into [[SMILES]])
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* [http://www.silicos.com Piramid] - Open source shape-based alignment using Gaussian volumes
 
* [http://www.silicos.com Piramid] - Open source shape-based alignment using Gaussian volumes
 
* [http://pyrx.scripps.edu/ PyRx] - Virtual Screening tool that includes Open Babel widget (watch [http://www.youtube.com/watch?v=niw6gHDLfO4 PyRx Screencast - Open Babel] to learn more).
 
* [http://pyrx.scripps.edu/ PyRx] - Virtual Screening tool that includes Open Babel widget (watch [http://www.youtube.com/watch?v=niw6gHDLfO4 PyRx Screencast - Open Babel] to learn more).
 +
* [http://sdf2xyz2sdf.sourceforge.net/ SDF2XYZ2SDF] - How to exploit TINKER power in cheminformatics projects
 
* [http://code.google.com/p/semanticwebopenbabel/ Semantic Web Open Babel] - Using Open Babel for a chemical Semantic Web
 
* [http://code.google.com/p/semanticwebopenbabel/ Semantic Web Open Babel] - Using Open Babel for a chemical Semantic Web
 
* [http://www.silicos.com/ Sieve] - Filtering molecule files based on calculated molecular properties, topologies and fragments
 
* [http://www.silicos.com/ Sieve] - Filtering molecule files based on calculated molecular properties, topologies and fragments

Revision as of 07:20, 23 June 2011

There are many projects which use Open Babel code internally, including several easy-to-use "front end" interfaces, as well as a variety of related open source chemistry projects.

Programs Using Open Babel

  • Avogadro - Flexible, cross-platform 3D molecular editor
  • ASE - Atomic Simulation Environment, a Python framework for building simulation codes, as well as pre- and post-processing tools.
  • Brabosphere - Brabosphere, a molecular visualization tool for the quantum mechanics package BRABO
  • CCP1GUI - Free, extensible molecular viewer and editor, including GUI for GAMESS-UK
  • ChemAzTech - Web/database solution. Manage your chemical database, with product's properties. Draw, edit molecules and interact with common chemical software.
  • Cheméo - Web search for high quality chemical properties
  • Chemtool - 2D molecular drawing tool using GTK toolkit
  • ChemSpotlight - Chemical indexing for Mac OS X
  • Chemical Structure Project - Open Source Chemical Structure Database
  • eMolecules - World-wide chemical search
  • fminer2 - Molecular subgraph mining
  • GChemPaint - 2D molecular drawing tool for GNOME environment
  • Ghemical - Molecular editor for GNOME environment
  • Gnome Chemistry Utils - GTK/Gnome based tools for chemistry software development
  • hBar Lab: Computer-aided Chemistry On Demand - First web application for performing molecular modeling calculations including quantum chemistry calculations online.
  • Kalzium - KDE Chemistry Education project
  • KMovisto - 3D molecular viewer for Linux
  • KNIME - Modular data processing (pipeline) environment
  • lazar - Lazy Structure-Activity Relationships (prediction of toxicity data)
  • Molekel - Advanced multiplatform 3D molecular viewer
  • molsketch - 2D molecular drawing tool for Qt/KDE environment (in development)
  • MyChem - MySQL extension for chemical databases
  • NanoEngineer-1 - Open source 3D molecular modeler for Windows, Mac and Linux.
  • NanoHive-1 Nanospace Simulator - Modular simulator for modeling nanometer scale physics and chemistry
  • OpenMD - Open source molecular dynamics engine
  • Open3DALIGN - Conformational search and unsupervised molecular alignment
  • Open3DQSAR - High-throughput computation and chemometric analysis of molecular interaction fields
  • OSRA - Optical Structure Recognition (graphics into SMILES)
  • pgchem::tigress - PostgreSQL database engine for molecules
  • Pharao - Open source pharmacophore generation and alignment
  • Piramid - Open source shape-based alignment using Gaussian volumes
  • PyRx - Virtual Screening tool that includes Open Babel widget (watch PyRx Screencast - Open Babel to learn more).
  • SDF2XYZ2SDF - How to exploit TINKER power in cheminformatics projects
  • Semantic Web Open Babel - Using Open Babel for a chemical Semantic Web
  • Sieve - Filtering molecule files based on calculated molecular properties, topologies and fragments
  • SMIREP - SMILES based structure-activity relationship rules
  • SPORCalc - Substrate Product Occurrence Ratio Calculator - Fingerprint Probabilistic Scoring of Sites of Metabolism
  • Stripper - Scaffold extraction tool following a number of published scaffold-extraction approaches, including Schuffenhauer, Oprea and Murcko
  • Toxtree - Estimate toxicity activity using decision trees
  • V-Sim Visualizes atomic structures such as crystals, grain boundaries, etc.
  • ViewMol - Molecular viewer and graphical front end for computational chemistry programs
  • WebBabel - WebBabel is a web application that uses OpenBabel to convert files from one format to another, or browse for files containing molecular structures.
  • XDrawChem - XWindows/Qt-based 2D molecular drawing tool
  • YASARA - Yet Another Scientific Artificial Reality Application
  • Zodiac - Cross-platform suite for Rational drug design

Front Ends

Related Open Chemistry Projects