Chemistry toolkits and utilities

  • ChemTreeMap - An Interactive Map of Biochemical Similarity in Molecular Datasets - standalone
  • molBLOCKS - Decomposing small molecule sets and uncovering enriched fragments - standalone
  • cApp - A practical Java tool for small-molecule compound appraisal (analyze collections, clustering…) - standalone
  • ClassyFire - A web-based application for automated structural classification of chemical entities (Computable Chemical Taxonomy) - online
  • AsteriX - A web-server that allows you to extract three dimensional coordinates of small molecules from two dimensional pictures, published in articles that are available in PDF format - online
  • UNICON - UNICON is a command-line tool to cope with common cheminformatics tasks (2016). The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles - standalone
  • QMForge - QMForge 2.3.1. A cross-platform, open-source program for interpreting and analyzing the results of QM calculations - standalone
  • ioChem-BD - An affordable solution to manage computational chemistry Big Data - standalone
  • DataWarrior - A very nice free tool for Chemistry Aware Data Visualization and Analysis (openmolecules.org). Numerous features from filtering compounds, to data analysis and computation of descriptors (eg, binned log P, log S, druglikeness score, rotatable bonds...automatic SAR, activity cliff, cluster compounds, find similar compounds...search fragments..look all your compounds, 2D, 3D, see physchem parameters...) (for Mac, Windows and Linux) - standalone
  • Link - The ChemicalToolBoX is a set of tools integrated into the Galaxy-workflow-management system to enable researchers easy-to-use, reproducible, and transparent access to cheminformatics libraries and drug discovery tools. It includes standard applications for similarity and substructure searches, clustering of compounds, prediction of properties and descriptors, filtering, and many other tools that range from drug-likeness classification to fragmentation and fragment-merging - standalone
  • Tripod - Several java tools for small compounds, Tripod, user-friendly chemical genomics browser developed by the informatics group at the NIH Chemical Genomics Center, automated R-group analysis, fragment activity profiler, library synthesizer, kinome viewer, molecular framework, pubchem search server, scaffold hopper, standardizer, tox21 chemical browser...Siphony, chemistry browser - standalone
  • HackaMol - An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales - standalone
  • CADD at NCI - Chemoinformatics Tools and User Services, chemical activity predictor, chemical identifier resolver, chemical structure lookup service, pseudorotation prosit tool for molecule in 3D, online SMILES translator, GIF image generator, VRML creator, optical structure recognition (OSRA)... - online tools for chemistry
  • Toolkit - The Chemistry Toolkit Rosetta is a wiki for sharing how to use different chemistry toolkits for the same set of common tasks - online information
  • ROCR - The ROCR is an R package for evaluating and visualizing classifier performance with only 3 commands - standalone
  • Chemkit -  Free open-source C++ library for molecular modelling, cheminformatics, and molecular visualization - standalone
  • ScrumPy -   Metabolic Modelling in Python - standalone
  • Chemical Identifier Resolver - This service works as a resolver for different chemical structure identifiers and allows one to convert a given structure identifier into another representation or structure identifier. It can help you identify and find the chemical structure if you have an identifier such as an InChIKey - online
  • UC Davis - Chemical Translation Service UC Davis - online
  • ChemSpot -  Recognition tool (standalone) - standalone
  • OPSIN - Open Parser for Systematic IUPAC nomenclature - online
  • Freiburg - Pharmaceutical Bioinformatics. Compounds In Literature (Pharmaceutical Bioinformatics) Search for compound name, InChI or SMILES - online
  • DAKOTA -  A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis - standalone
  • Link - ChemToolBox contains several internal databases that assist lab work - standalone
  • Link - PrecisionTree - standalone
  • Link - C4.5 - standalone
  • Link - C5.0 - standalone
  • Link - k Nearest Neighbor - standalone
  • Link - Neural network - standalone
  • Link - Neural network: JATOON - standalone
  • Link - SVM - standalone
  • Link - SVM - standalone
  • Link - Generates Kohonen's Self-Organizing Maps online - standalone
  • Link - learn about computer clusters - Training computer clusters
  • Condor - Condor: Tools to speed-up computations - standalone
  • OpenMolGrid - Tools to speed-up computations - Tools to speed-up computations
  • Rggobi - R package that provides an easy interface with GGobi - R interface -standalone
  • SLIMS - A laboratory information management system - Chemical data storage - database
  • Weka 3 - Data Mining Software in Java - Data Mining Software
  • SVMs - SVM light is an implementation of Support Vector Machines in C - Data Mining Software
  • RapidMiner -  Open-source system for data mining. It contains Brute force, Forward selection and Backward elimination algorithms for feature selection - Data Mining Software
  • Link - Feature Selection with Regularized Random Forest - standalone
  • Orange - Open source data visualization and analysis for novice and experts - Data Mining Software
  • TiMBL -  Open source software package implementing k-nearest neighbor classification - Data Mining Software
  • CDL - The Chemical Descriptors Library is a C++ library that provides functionality in the area of chemical informatics - Molecular Descriptors
  • Link - Open source clustering software - Clustering standalone
  • SUBSET - Clustering software - Clustering standalone
  • Aten - A tool for computational chemists, molecular dynamicists. It does: Build and edit atomic coordinates, Generate superstructures from crystal information  - Chemistry tools, standalone
  • Link - Many chemoinformatics tools - Prof Alexandre Varnek lab (ISIDA, fragmentor...etc) - Chemistry tools - toolkit - chemoinformatics, some are online, others are standalone
  • Link - Mol2 file format (2D or 3D) - Mol2 format (Chemistry)
  • Link - The Protein Data Bank, see section describing the PDB format - Macro-molecule 3D structures
  • OpenBabel / OpenBabel - File format conversion - Chemistry tools, can be online
  • Perlmol - Chemistry toolkit - Chemistry tools, standalone
  • TouchMol web - Next Generation Chemical/Biological Structure Drawing - online
  • GIF/PNG-creator - GIF/PNG-creator with SMILES input - Compound drawing, online
  • JOElib / JOElib - Computational chemistry package - Chemistry tools, standalone
  • Ghemical - Computational chemistry package - Chemistry tools, standalone
  • Chemaxon - Computer tools for chemistry, ADME-tox....Marvin is a suite of Java based chemistry software that have different forms: Marvin Applets, Marvin Beans, MarvinSketch - Chemistry tools, standalone
  • Link - Several java tools for small compounds, Tripod, user-friendly chemical genomics browser developed by the informatics group at the NIH Chemical Genomics Center, automated R-group analysis, fragment activity profiler, library synthesizer, kinome viewer, molecular framework, pubchem search server, scaffold hopper, standardizer, tox21 chemical browser... - online and standalone java tools
  • CDK - Chemistry development kit - Chemistry tools, standalone
  • Frowns - Chemistry toolkit - Chemistry tools, standalone
  • Link - A C++ toolbox for chemoinformatics - Chemistry tools, standalone
  • SketchEI - Chemical structure sketching tool - Compound drawing, standalone
  • Cactus - Online SMILES translator and structure generator - Compound drawing, online
  • RDKit - Cheminformatics and Machine Learning Software - Chemistry tools, standalone
  • Link - The SDF toolkit (in Perl) essentially for small molecules - Chemistry tools, standalone
  • Moloc - Roche Biostructural modeling package for small and large molecules. This package seems free but ? - Chemistry tools, standalone
  • MayaChem - MayaChemTools: A growing collection of Perl scripts to support day-to-day computational discovery needs... - Chemistry tools, standalone
  • Editor - A Java Chemical Structure Editor - Compound drawing, standalone
  • SDF format - Information about SDF format - SDF format
  • Vigyaan -  An electronic workbench for bioinformatics, computational biology and computational chemistry - Different modeling packages. standalone
  • MOPAC -  Molecular Orbital PACkage is a semiempirical quantum chemistry program - semiempirical quantum chemistry - ADME since pKa, standalone
  • Link - Walking the web of chemical informatics, package like Ruby CDK chemistry toolkit - Ruby CDK chemistry toolkit and many others
  • Link - An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP) - chemo- and bioinformatics
  • ChemFile -  ChemFileBrowser: A win32 free software for chemistry - some chemistry tools for windows
  • Bioinfo - Many tools from Andrew C.R. Martin's Bioinformatics group. From mutations to Profit for rmsd computations to sending jobs to cluster - many valuable tools for structural bioinformatics
  • Sourceforge - Chemistry and bioinformatics - sourceforge.net
  • Linux - Linux for Chemistry - in silico tools
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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira