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Chemistry toolkits & utilities

 

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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