[38;5;12m                                                                            [39m[38;2;255;187;0m[1m[4mAwesome Cheminformatics [0m[38;5;14m[1m[4m![0m[38;2;255;187;0m[1m[4mAwesome[0m[38;5;14m[1m[4m (https://awesome.re/badge.svg)[0m[38;2;255;187;0m[1m[4m (https://awesome.re)[0m

[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12mCheminformatics[39m[38;5;12m [39m[38;5;12m(also[39m[38;5;12m [39m[38;5;12mknown[39m[38;5;12m [39m[38;5;12mas[39m[38;5;12m [39m[38;5;12mchemoinformatics,[39m[38;5;12m [39m[38;5;12mchemioinformatics[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m[38;5;12minformatics)[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12muse[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mcomputer[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12minformational[39m[38;5;12m [39m[38;5;12mtechniques[39m[38;5;12m [39m[38;5;12mapplied[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mrange[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mproblems[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mfield[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mchemistry.—[39m[38;5;12m [39m[38;5;14m[1mWikipedia[0m[38;5;12m [39m
[38;5;11m[1m▐[0m[38;5;12m [39m[38;5;12m(https://en.wikipedia.org/wiki/Cheminformatics)[39m

[38;5;12mA curated list of awesome Cheminformatics software, resources, and libraries. Mostly command line based, and free or open-source. Please feel free to [39m[38;5;14m[1mcontribute[0m[38;5;12m (CONTRIBUTING.md) ![39m

[38;2;255;187;0m[4mContents[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mApplications[0m[38;5;12m (#applications)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVisualization[0m[38;5;12m (#app-visualization)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCommand Line Tools[0m[38;5;12m (#app-cmd)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDocking[0m[38;5;12m (#app-docking)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVirtual Machine[0m[38;5;12m (#app-virtual)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mLibraries[0m[38;5;12m (#libraries)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mGeneral Purpose[0m[38;5;12m (#lib-general)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVisualization[0m[38;5;12m (#lib-visualization)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCommand Line Tools[0m[38;5;12m (#lib-format)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDocking[0m[38;5;12m (#lib-dock)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolecular Descriptors[0m[38;5;12m (#lib-des)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMachine Learning[0m[38;5;12m (#lib-ml)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mWeb APIs[0m[38;5;12m (#lib-web)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDatabases[0m[38;5;12m (#lib-db)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOthers[0m[38;5;12m (#lib-others)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mJournals[0m[38;5;12m (#journals)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mResources[0m[38;5;12m (#resources)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCourses[0m[38;5;12m (#courses)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mBlogs[0m[38;5;12m (#blogs)[39m
[38;5;12m [39m[38;5;12m [39m[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mBooks[0m[38;5;12m (#books)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mSee Also[0m[38;5;12m (#see-also)[39m

[38;2;255;187;0m[4mApplications[0m


[38;2;255;187;0m[4mVisualization[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPyMOL[0m[38;5;12m (https://sourceforge.net/projects/pymol/) - Python-enhanced molecular graphics tool.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mJmol[0m[38;5;12m (http://jmol.sourceforge.net/) - Browser-based HTML5 viewer and stand-alone Java viewer for chemical structures in 3D.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mVMD[0m[38;5;12m (http://www.ks.uiuc.edu/Research/vmd/) - Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChimera[0m[38;5;12m (https://www.cgl.ucsf.edu/chimera/) - Highly extensible program for interactive molecular visualization and analysis. [39m[38;5;14m[1mSource[0m[38;5;12m (https://www.cgl.ucsf.edu/chimera/docs/sourcecode.html) is available.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChimeraX[0m[38;5;12m (https://www.cgl.ucsf.edu/chimerax/) - The next-generation molecular visualization program, following UCSF Chimera. Source is available [39m[38;5;14m[1mhere[0m[38;5;12m (https://www.cgl.ucsf.edu/chimerax/docs/devel/conventions.html).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDataWarrior[0m[38;5;12m (http://www.openmolecules.org/datawarrior/index.html) - A program for data Visualization and analysis which combines dynamic graphical views and interactive row filtering with chemical intelligence.[39m


[38;2;255;187;0m[4mCommand Line Tools[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOpen Babel[0m[38;5;12m (http://openbabel.org/wiki/Main_Page) - Chemical toolbox designed to speak the many languages of chemical data.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMayaChemTools[0m[38;5;12m (http://www.mayachemtools.org/index.html) - Collection of Perl and Python scripts, modules, and classes that support day-to-day computational discovery needs.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPackmol[0m[38;5;12m (http://m3g.iqm.unicamp.br/packmol/home.shtml) - Initial configurations for molecular dynamics simulations by packing optimization.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mBCL::Commons[0m[38;5;12m (http://meilerlab.org/index.php/bclcommons/show/b_apps_id/1)[39m


[38;2;255;187;0m[4mDocking[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAutoDock Vina[0m[38;5;12m (http://vina.scripps.edu/) - Molecular docking and virtual screening.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1msmina[0m[38;5;12m (https://sourceforge.net/projects/smina/) - Customized [39m[38;5;14m[1mAutoDock Vina[0m[38;5;12m (http://vina.scripps.edu/) to better support scoring function development and high-performance energy minimization.[39m


[38;2;255;187;0m[4mVirtual Machine[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mmyChEMBL[0m[38;5;12m (http://chembl.blogspot.com/2015/07/mychembl-20-has-landed.html) - A version of ChEMBL built using Open Source software (Ubuntu, PostgreSQL, RDKit)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1m3D e-Chem Virtual Machine[0m[38;5;12m (https://github.com/3D-e-Chem/3D-e-Chem-VM) - Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows[39m

[38;2;255;187;0m[4mLibraries[0m


[38;2;255;187;0m[4mGeneral Purpose[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/) - Collection of cheminformatics and machine-learning software written in C++ and Python.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mIndigo[0m[38;5;12m (https://github.com/epam/Indigo) - Universal molecular toolkit that can be used for molecular fingerprinting, substructure search, and molecular visualization written in C++ package, with Java, C#, and Python wrappers.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCDK (Chemistry Development Kit)[0m[38;5;12m (https://sourceforge.net/projects/cdk/) - Algorithms for structural chemo- and bioinformatics, implemented in Java.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemmineR[0m[38;5;12m (https://www.bioconductor.org/packages/release/bioc/vignettes/ChemmineR/inst/doc/ChemmineR.html) - Cheminformatics package for analyzing drug-like small molecule data in R.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemPy[0m[38;5;12m (https://github.com/bjodah/chempy) - A Python package useful for chemistry (mainly physical/inorganic/analytical chemistry)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolecularGraph.jl[0m[38;5;12m (https://github.com/mojaie/MolecularGraph.jl) - A graph-based molecule modeling and chemoinformatics analysis toolkit fully implemented in Julia[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mdatamol[0m[38;5;12m (https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCGRtools[0m[38;5;12m [39m[38;5;12m(https://github.com/cimm-kzn/CGRtools)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mToolkit[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mprocessing[39m[38;5;12m [39m[38;5;12mmolecules,[39m[38;5;12m [39m[38;5;12mreactions[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mcondensed[39m[38;5;12m [39m[38;5;12mgraphs[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mreactions.[39m[38;5;12m [39m[38;5;12mCan[39m[38;5;12m [39m[38;5;12mbe[39m[38;5;12m [39m[38;5;12mused[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m[38;5;12mstandardization,[39m[38;5;12m [39m[38;5;12mMCS[39m[38;5;12m [39m[38;5;12msearch,[39m[38;5;12m [39m[38;5;12mtautomers[39m[38;5;12m [39m[38;5;12mgeneration[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12mbackward[39m[38;5;12m [39m[38;5;12mcompatibility[39m[38;5;12m [39m[38;5;12mto[39m
[38;5;12mRDKit[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mNetworkX.[39m


[38;2;255;187;0m[4mFormat Checking[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChEMBL_Structure_Pipeline (formerly standardiser)[0m[38;5;12m (https://github.com/chembl/ChEMBL_Structure_Pipeline) - Tool designed to provide a simple way of standardising molecules as a prelude to e.g. molecular modelling exercises.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolVS[0m[38;5;12m (https://github.com/mcs07/MolVS) - Molecule validation and standardization based on [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mrd_filters[0m[38;5;12m (https://github.com/PatWalters/rd_filters) - A script to run structural alerts using the RDKit and ChEMBL[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mpdb-tools[0m[38;5;12m (https://github.com/haddocking/pdb-tools) - A swiss army knife for manipulating and editing PDB files.[39m


[38;2;255;187;0m[4mVisualization[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mKekule.js[0m[38;5;12m (http://partridgejiang.github.io/Kekule.js/) - Front-end JavaScript library for providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1m3Dmol.js[0m[38;5;12m (https://github.com/3dmol/3Dmol.js) - An object-oriented, webGL based JavaScript library for online molecular visualization.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mJChemPaint[0m[38;5;12m (https://github.com/JChemPaint/jchempaint) - Chemical 2D structure editor application/applet based on the [39m[38;5;14m[1mChemistry Development Kit[0m[38;5;12m (https://sourceforge.net/projects/cdk/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mrdeditor[0m[38;5;12m (https://github.com/EBjerrum/rdeditor) - Simple RDKit molecule editor GUI using PySide.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mnglviewer[0m[38;5;12m (http://nglviewer.org/nglview/latest/) - Interactive molecular graphics for Jupyter notebooks.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mRDKit.js[0m[38;5;12m (https://www.npmjs.com/package/@rdkit/rdkit) - Official JavaScript distribution of cheminformatics functionality from the RDKit - a C++ library for cheminformatics.[39m


[38;2;255;187;0m[4mMolecular Descriptors[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mmordred[0m[38;5;12m (https://github.com/mordred-descriptor/mordred) - Molecular descriptor calculator based on [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDescriptaStorus[0m[38;5;12m (https://github.com/bp-kelley/descriptastorus) - Descriptor computation(chemistry) and (optional) storage for machine learning.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mmol2vec[0m[38;5;12m (https://github.com/samoturk/mol2vec) - Vector representations of molecular substructures.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAlign-it[0m[38;5;12m (http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html#alignit-generating-pharmacophore-points) - Align molecules according their pharmacophores.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mRcpi[0m[38;5;12m (https://nanx.me/Rcpi/index.html) - R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions.[39m


[38;2;255;187;0m[4mMachine Learning[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDeepChem[0m[38;5;12m (https://github.com/deepchem/deepchem) - Deep learning library for Chemistry based on Tensorflow[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemprop[0m[38;5;12m (https://github.com/chemprop/chemprop) - Directed message passing neural networks for property prediction of molecules and reactions with uncertainty and interpretation.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemML[0m[38;5;12m (https://github.com/hachmannlab/chemml) - ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data. (based on Tensorflow)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1molorenchemengine[0m[38;5;12m (https://github.com/Oloren-AI/olorenchemengine) - Molecular property prediction with unified API for diverse models and respresentations,[39m
[38;5;12m  with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOpenChem[0m[38;5;12m (https://github.com/Mariewelt/OpenChem) - OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDGL-LifeSci[0m[38;5;12m (https://github.com/awslabs/dgl-lifesci) - DGL-LifeSci is a [39m[38;5;14m[1mDGL[0m[38;5;12m (https://www.dgl.ai/)-based package for various applications in life science with graph neural network.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mchainer-chemistry[0m[38;5;12m (https://github.com/pfnet-research/chainer-chemistry) - A Library for Deep Learning in Biology and Chemistry.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mpytorch-geometric[0m[38;5;12m (https://pytorch-geometric.readthedocs.io/en/latest/) - A PyTorch library provides implementation of many graph convolution algorithms.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mchemmodlab[0m[38;5;12m (https://github.com/jrash/ChemModLab) - A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models in R.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mSummit[0m[38;5;12m (https://github.com/sustainable-processes/summit) - A python package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).[39m


[38;2;255;187;0m[4mWeb APIs[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mwebchem[0m[38;5;12m (https://github.com/ropensci/webchem) - Chemical Information from the Web.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPubChemPy[0m[38;5;12m (http://pubchempy.readthedocs.io) - Python wrapper for the PubChem PUG REST API.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemSpiPy[0m[38;5;12m (http://chemspipy.readthedocs.org) - Python wrapper for the ChemSpider API.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCIRpy[0m[38;5;12m (http://cirpy.readthedocs.org/) - Python wrapper for the [39m[38;5;14m[1mNCI Chemical Identifier Resolver (CIR)[0m[38;5;12m (https://cactus.nci.nih.gov/chemical/structure).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mBeaker[0m[38;5;12m (https://github.com/chembl/chembl_beaker) - [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/) and [39m[38;5;14m[1mOSRA[0m[38;5;12m (https://cactus.nci.nih.gov/osra/) in the [39m[38;5;14m[1mBottle[0m[38;5;12m (http://bottlepy.org/docs/dev/) on [39m[38;5;14m[1mTornado[0m[38;5;12m (http://www.tornadoweb.org/en/stable/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mchemminetools[0m[38;5;12m (https://github.com/girke-lab/chemminetools) - Open source web framework for small molecule analysis based on Django.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mambit[0m[38;5;12m (http://ambit.sourceforge.net/) - offers chemoinformatics functionality via REST web services.[39m


[38;2;255;187;0m[4mDatabases[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mrazi[0m[38;5;12m (https://github.com/rvianello/razi) - Cheminformatic extension for the SQLAlchemy database.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemical Translation Service[0m[38;5;12m (https://bitbucket.org/fiehnlab/fiehnlab-cts/src/master/) - Source code of the [39m[38;5;14m[1mChemical Translation Service[0m[38;5;12m (https://cts.fiehnlab.ucdavis.edu/) web service.[39m


[38;2;255;187;0m[4mDocking[0m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mRosetta[0m[38;5;12m (https://www.rosettacommons.org/docs/latest/Home) - A comprehensive software suite for modeling macromolecular structures. Used larely for protein-protein docking.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDOCKSTRING[0m[38;5;12m (https://github.com/dockstring/dockstring) - Automates and standardizes ligand preparation for AutoDock Vina.[39m


[38;2;255;187;0m[4mMolecular Dynamics[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mGromacs[0m[38;5;12m (http://www.gromacs.org/) - Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOpenMM[0m[38;5;12m (http://openmm.org/) - High performance toolkit for molecular simulation including extensive language bindings for Python, C, C++, and even Fortran.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mNAMD[0m[38;5;12m (https://www.ks.uiuc.edu/Research/namd/) - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMDTraj[0m[38;5;12m (https://github.com/mdtraj/mdtraj) - Analysis of molecular dynamics trajectories.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mcclib[0m[38;5;12m (https://github.com/cclib/cclib) - Parsers and algorithms for computational chemistry logfiles.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mProDy[0m[38;5;12m (https://github.com/prody/ProDy) - A Python package for protein dynamics analysis [39m


[38;2;255;187;0m[4mOthers[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1meiR[0m[38;5;12m (https://github.com/girke-lab/eiR) - Accelerated similarity searching of small molecules[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOPSIN[0m[38;5;12m (https://github.com/dan2097/opsin) - Open Parser for Systematic IUPAC nomenclature[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCookiecutter for Computational Molecular Sciences[0m[38;5;12m (https://github.com/MolSSI/cookiecutter-cms) - Python-centric Cookiecutter for Molecular Computational Chemistry Packages by [39m[38;5;14m[1mMolSSL[0m[38;5;12m (https://molssi.org/)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAuto-QChem[0m[38;5;12m (https://github.com/PrincetonUniversity/auto-qchem) - an automated workflow for the generation and storage of DFT calculations for organic molecules.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mGypsum-DL[0m[38;5;12m (https://git.durrantlab.pitt.edu/jdurrant/gypsum_dl) - a program for converting 2D SMILES strings to 3D models.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mRDchiral[0m[38;5;12m (https://github.com/connorcoley/rdchiral) - Wrapper for RDKit's RunReactants to improve stereochemistry handling[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mconfgen[0m[38;5;12m (https://github.com/Et9797/confgen-webapp) - Webapp for generating conformers[39m
[38;5;12m [39m
[38;5;12m [39m
[38;2;255;187;0m[4mJournals[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mJournal of Cheminformatics[0m[38;5;12m (https://jcheminf.biomedcentral.com/)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mJournal of Chemical Information and Modeling (ACS Publications)[0m[38;5;12m (https://pubs.acs.org/journal/jcisd8)[39m

[38;2;255;187;0m[4mResources[0m

[38;2;255;187;0m[4mCourses[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mLearncheminformatics.com[0m[38;5;12m (http://learncheminformatics.com/) - "Cheminformatics: Navigating the world of chemical data" courese at Indiana University.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPython for chemoinformatics[0m[38;5;12m (https://github.com/Mishima-syk/py4chemoinformatics)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mTeachOpenCADD[0m[38;5;12m (https://github.com/volkamerlab/TeachOpenCADD) - A teaching platform for computer-aided drug design (CADD) using open source packages and data.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCheminformatics[0m[38;5;14m[1m [0m[38;5;14m[1mOLCC[0m[38;5;12m [39m[38;5;12m(https://chem.libretexts.org/Courses/Intercollegiate_Courses/Cheminformatics_OLCC_(2019))[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mCheminformatics[39m[38;5;12m [39m[38;5;12mcourse[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mCollaborative[39m[38;5;12m [39m[38;5;12mIntercollegiate[39m[38;5;12m [39m[38;5;12mOnline[39m[38;5;12m [39m[38;5;12mChemistry[39m[38;5;12m [39m[38;5;12mCourse[39m[38;5;12m [39m[38;5;12m(OLCC)[39m[38;5;12m [39m[38;5;12mcourse[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mUniversity[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m
[38;5;12mArkansas[39m[38;5;12m [39m[38;5;12mat[39m[38;5;12m [39m[38;5;12mLittle[39m[38;5;12m [39m[38;5;12mRock[39m[38;5;12m [39m[38;5;12mby[39m[38;5;12m [39m[38;5;12mRobert[39m[38;5;12m [39m[38;5;12mBelford[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mBigChem[0m[38;5;12m (http://bigchem.eu/alllectures) - All lectures of [39m[38;5;14m[1mBigChem[0m[38;5;12m (http://bigchem.eu/) (A Horizon 2020 MSC ITN EID project, which provides innovative education in large chemical data analysis.)[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolecular modeling course[0m[38;5;12m (https://dasher.wustl.edu/chem478/) - by Dr. [39m[38;5;14m[1mJay Ponder[0m[38;5;12m (https://dasher.wustl.edu/), a professor from WashU St.Louis.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mSimulation in Chemistry and Biochemistry[0m[38;5;12m (https://dasher.wustl.edu/chem430/) - by Dr. [39m[38;5;14m[1mJay Ponder[0m[38;5;12m (https://dasher.wustl.edu/), a professor from WashU St.Louis.[39m

[38;2;255;187;0m[4mBlogs[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mOpen Source Molecular Modeling[0m[38;5;12m (https://opensourcemolecularmodeling.github.io/README.html) - Updateable catalog of open source molecular modeling software.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPubChem Blog[0m[38;5;12m (https://pubchemblog.ncbi.nlm.nih.gov/) - News, updates and tutorials about [39m[38;5;14m[1mPubChem[0m[38;5;12m (https://pubchem.ncbi.nlm.nih.gov/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mThe ChEMBL-og blog[0m[38;5;12m (http://chembl.blogspot.tw/) - Stories and news from Computational Chemical Biology Group at [39m[38;5;14m[1mEMBL-EBI[0m[38;5;12m (https://www.ebi.ac.uk/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChEMBL blog[0m[38;5;12m (http://chembl.github.io/) - ChEMBL on GitHub.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mSteinBlog[0m[38;5;12m (http://www.steinbeck-molecular.de/steinblog/) - Blog of [39m[38;5;14m[1mChristoph Steinbeck[0m[38;5;12m (http://www.steinbeck-molecular.de/steinblog/index.php/about/), who is the head of cheminformatics and metabolism at the EMBL-EBI.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mPractical Cheminformatics[0m[38;5;12m (http://practicalcheminformatics.blogspot.com/) - Blog with in-depth examples of practical application of cheminformatics.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mSo[0m[38;5;14m[1m [0m[38;5;14m[1mmuch[0m[38;5;14m[1m [0m[38;5;14m[1mto[0m[38;5;14m[1m [0m[38;5;14m[1mdo,[0m[38;5;14m[1m [0m[38;5;14m[1mso[0m[38;5;14m[1m [0m[38;5;14m[1mlittle[0m[38;5;14m[1m [0m[38;5;14m[1mtime[0m[38;5;14m[1m [0m[38;5;14m[1m-[0m[38;5;14m[1m [0m[38;5;14m[1mTrying[0m[38;5;14m[1m [0m[38;5;14m[1mto[0m[38;5;14m[1m [0m[38;5;14m[1msqueeze[0m[38;5;14m[1m [0m[38;5;14m[1msense[0m[38;5;14m[1m [0m[38;5;14m[1mout[0m[38;5;14m[1m [0m[38;5;14m[1mof[0m[38;5;14m[1m [0m[38;5;14m[1mchemical[0m[38;5;14m[1m [0m[38;5;14m[1mdata[0m[38;5;12m [39m[38;5;12m(http://blog.rguha.net/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mBolg[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;14m[1mRajarshi[0m[38;5;14m[1m [0m[38;5;14m[1mGuha[0m[38;5;12m [39m[38;5;12m(http://blog.rguha.net/?page_id=8),[39m[38;5;12m [39m[38;5;12mwho[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mresearch[39m[38;5;12m [39m[38;5;12mscientist[39m[38;5;12m [39m[38;5;12mat[39m[38;5;12m [39m[38;5;12mNIH[39m[38;5;12m [39m[38;5;12mCenter[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mAdvancing[39m[38;5;12m [39m[38;5;12mTranslational[39m[38;5;12m [39m
[38;5;12mScience.[39m
[38;5;12m  [39m[48;2;30;30;40m[38;5;13m[3m Some old blogs [0m[48;2;30;30;40m[38;5;14m[1m[3m1[0m[48;2;30;30;40m[38;5;13m[3m (https://rguha.wordpress.com/) [0m[48;2;30;30;40m[38;5;14m[1m[3m2[0m[48;2;30;30;40m[38;5;13m[3m (http://www.rguha.net/index.html).[0m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mNoel O'Blog[0m[38;5;12m (http://baoilleach.blogspot.tw/) - Blog of [39m[38;5;14m[1mNoel O'Boyle[0m[38;5;12m (https://www.redbrick.dcu.ie/~noel/), who is a Senior Software Engineer at NextMove Software.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mchem-bla-ics[0m[38;5;12m (http://chem-bla-ics.blogspot.tw/) - Blog of [39m[38;5;14m[1mEgon Willighagen[0m[38;5;12m (http://egonw.github.io/), who is an assistant professor at Maastricht University.[39m
[38;5;12m<!---[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mAsad's Blog[0m[38;5;12m (https://chembioinfo.com/) - Bolg of Syed Asad Rahman, who is a research scientist in the [39m[38;5;14m[1mThornton group[0m[38;5;12m (http://www.ebi.ac.uk/research/thornton) at EMBL-EBI.[39m
[38;5;12m-->[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1msteeveslab-blog[0m[38;5;12m (http://asteeves.github.io/) - Some examples using [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/).[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMacs in Chemistry[0m[38;5;12m (http://www.macinchem.org/) - Provide a resource for chemists using Apple Macintosh computers.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDrugDiscovery.NET[0m[38;5;12m (http://www.drugdiscovery.net/) - Blog of [39m[38;5;14m[1mAndreas Bender[0m[38;5;12m (http://www.andreasbender.de/), who is a Reader for Molecular Informatics at University of Cambridge.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mIs life worth living?[0m[38;5;12m (https://iwatobipen.wordpress.com/) - Some examples for cheminformatics libraries.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCheminformatics 2.0[0m[38;5;12m (https://cheminf20.org/) - Blog of [39m[38;5;14m[1mAlex M. Clark[0m[38;5;12m (https://twitter.com/aclarkxyz), a research scientist at Collaborative Drug Discovery.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mDepth-First[0m[38;5;12m (https://depth-first.com/) - Blog of [39m[38;5;14m[1mRichard L. Apodaca[0m[38;5;12m (https://depth-first.com/about/), a chemist living in La Jolla, California.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mCheminformania[0m[38;5;12m (https://www.cheminformania.com) - Blog of [39m[38;5;14m[1mPh.D, Esben Jannik Bjerrum[0m[38;5;12m (https://www.cheminformania.com/about/esben-jannik-bjerrum/), who is a Principle Scientist and a Machine Learning and AI specialists at AstraZeneca.[39m

[38;2;255;187;0m[4mBooks[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mComputational Approaches in Cheminformatics and Bioinformatics[0m
[38;5;12m (https://books.google.com/books/about/Computational_Approaches_in_Cheminformat.html?id=bLqV4rYQoYsC) -  Include insights from public (NIH), academic, and industrial sources at the same time.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mChemoinformatics for Drug Discovery[0m[38;5;12m (https://onlinelibrary.wiley.com/doi/book/10.1002/9781118742785) - Materials about how to use Chemoinformatics strategies to improve drug discovery results.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolecular Descriptors for Chemoinformatics[0m[38;5;12m (https://onlinelibrary.wiley.com/doi/book/10.1002/9783527628766) - More than 3300 descriptors and related terms for chemoinformatic analysis of chemical compound properties.[39m


[38;2;255;187;0m[4mSee Also[0m

[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mdeeplearning-biology[0m[38;5;12m (https://github.com/hussius/deeplearning-biology#chemoinformatics-and-drug-discovery-) - Chemoinformatics and drug discovery section in deeplearning-biology repo.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mawesome-python-chemistry[0m[38;5;12m (https://github.com/lmmentel/awesome-python-chemistry) - Another list focuses on Python stuff related to Chemistry.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mawesome-small-molecule-ml[0m[38;5;12m (https://github.com/benb111/awesome-small-molecule-ml) - A list of papers, data sets, and other resources for machine learning for small-molecule drug discovery.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mawesome-molecular-docking[0m[38;5;12m (https://github.com/yangnianzu0515/awesome-molecular-docking) - A curated list of molecular docking software, datasets, and other closely related resources.[39m
[48;5;12m[38;5;11m⟡[49m[39m[38;5;12m [39m[38;5;14m[1mMolSSI Molecular Software Database[0m[38;5;12m (https://molssi.org/software-search/)[39m
[38;5;12m＊[39m[38;5;14m[1mPages created by Tobias Kind, PhD[0m[38;5;12m (https://fiehnlab.ucdavis.edu/staff/kind/metabolomics)[39m

[38;2;255;187;0m[4mLicense[0m

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