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LiSIs An Online Scientific Workflow System for Virtual Screening (granatum) online
ChemDes An integrated web-based platform for molecular descriptor and fingerprint computation online
Gusar Gusar antitargets, rat toxicity... online
CoFFer A QSAR web service that predicts chemical compounds and provides fragments to aid interpreting predictions. 76 (Q)SAR models (ADMET, off targets, repositioning..) online
Model Molecular descriptor lab online
DWFS A wrapper feature selection tool based on a parallel genetic algorithm online
VIDEAN VIDEAN Visual and Interactive Descriptor Analysis online
BioTriangle A web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (molecular descriptors) online
CheS CheS-Mapper 2.0 for visual validation of (Q)SAR models Visual validation with CheS-Mapper enables analyzing (Q)SAR information in the data and indicates how this information is employed by the (Q)SAR model. It reveals, if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs standalone
BioPPSy An Open-Source Platform for QSAR/QSPR Analysis (ADMET) standalone
LiSIs An Online Scientific Workflow System for Virtual Screening online
OOMMPPAA A tool to aid directed synthesis by the combined analysis of activity and structural data. Optimising both potency and cell permeability and use OOMMPPAA to highlight nuanced and cross-series SAR standalone
eTOXlab An open source modeling framework for implementing predictive models in production environments standalone
Danish Danish (Q)SAR Database. A repository of estimates from over 70 (Q)SAR models for 166,072 chemicals database of models
ChemProp Chemical Properties Estimation Software System is not a single piece of software, but comprises several different modules. There is a professional version covering all features including batch processing in terms of QSAR runs for compound lists standalone
CODESSA COmprehensive DEscriptors for Structural and Statistical Analysis (QSAR) standalone
T.E.S.T QSAR from EPA standalone
QSARINS QSARINS is a user-friendly platform for QSAR modeling in agreement with the OECD Principles and for the analysis of the reliability of the obtained predicted data standalone
QSAR_Tools Numerous statistical tools for QSAR studies, applicability domain..etc standalone
SEABED Small molEcule Activity scanner weB servicE-baseD. SEABED goes beyond the basic docking and QSAR web-tools and implements extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants online
AZOrange High performance open source machine learning for QSAR modeling in a graphical programming environment Standalone
Ligand datasets Datasets in SDF format for training and testing software from Prof. Bajorath Training sets to download
DMax Chemistry Assistant QSAR / QSPR data mining software package DMax Chemistry Assistant Standalone tool
MolSig Stereo signature molecular descriptor Standalone
CORALSEA Freeware to build up quantitative structure - property / activity   relationships   (QSPR / QSAR).  Can be used with Windows XP and Windows Vista. ADMET prediction, Peptides... Standalone
WEBCDK CDK online computation of descriptors, check also Online tool
Mold2 Descriptors Generator Software Standalone
4D-FAP The 4D Flexible Atom-Pair Kernel represents a 4D similarity measure for molecular graphs (4D FAP) standalone
BioVenn A web application for the comparison and visualization of biological lists using area proportional Venn diagrams Online
BlueDesc Molecular Descriptor Calculator, A key step in classical quantitative structure-activity/property relationship (QSAR/QSPR) modeling is the encoding of a chemical compound into a vector of numerical descriptors. Although most of the available chemoinformatic software packages provide routines for the calculation of descriptors they are not easy to use in most cases. This simple command-line tool converts an MDL SD file into ARFF and LIBSVM format for machine learning and data mining purposes using CDK and JOELib2. Compounds in 3D Standalone
log S datasets Water solublity (logS) database (several others, logBB, P-gp, Caco-2, oral...) Datasets
log P dataset Large, chemically diverse dataset of logP measurements for benchmarking studies, 707 validated logP values ranging from 0.30 to 7.50, molecules in SMILES, Eur J Pharm Sci. 2013 48 (Martel S, Gillerat F, Carosati E, Maiarelli D, Tetko IV, Mannhold R, Carrupt PA) log P dataset, go to the journal site
Drug and Lead dataset Emanuele Perola data: Analysis of the Binding Efficiencies of Drugs and Their Leads in Successful Drug Discovery Programs, J Med Chem 2010, Supporting Info, leads and corresponding drugs in SDF Dataset, check the article
Strip-it It is a tool to extract molecular scaffolds according predefined rules based on definitions as described by Murcko, Pollock and Schuffenhauer Standalone resources for QSAR & modeling professionals
TMACC Interpretable correlation descriptors for quantitative structure-activity relationships. The topological maximum cross correlation (TMACC) descriptors are alignment independent 2D descriptors for the derivation of QSARs Standalone
QSAR datasets Links to cheminformatics programs and QSAR datasets. These include, diversity and similarity searches. Many compounds designed for specific targets (e.g., coagulation factor Xa...), AMES, toxicity.... Many datasets Compound searching - Datasets - Database
SOMFA A graphical tool for structure-activity studies on Windows. SOMFA is a technique for 3D QSAR designed by Peter Winn and Daniel Robinson. The method is simple and avoids statistical selection procedures such as PLS. All tests so far show it to be as good as other QSAR methods, and better than many. The SOMFA code and executable may be downloaded  (on Windows only, the reported server seems down and I thus point to the publication)
E-DRAGON E-DRAGON is the electronic remote version of the well known software DRAGON, which is an application for the calculation of molecular descriptors developed by the Milano Chemometrics and QSAR Research Group of Prof. R. Todeschini. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and high-throughput screening of molecule databases Compute molecular properties online
OECD QSAR QSAR training. What is the (Q)SAR Application Toolbox? The Toolbox is a software application intended to be used by governments, chemical industry and other stakeholders in filling gaps in (eco)toxicity data needed for assessing the hazards of chemicals. (protein binding, DNA binding, liver metabolism, skin tox, eye tox, mutagenicity...)      Standalone
OCHEM Online database with modeling environment. Many data sets available, like for ADMET QSAR modeling, you can submit your experimental data, or you use other users' data to build predictive QSAR models for physical-chemical or biological properties (Tetko IV et al), contains ToxAlerts Standalone and online
Software list Software list from the QSAR and Modelling society, datasets Information datasets
QSAR Toolbox OECD QSAR Toolbox - ADME/tox  standalone
Open3dqsar An open-source software aimed at high-throughput chemometric analysis of molecular interaction fields standalone
McQSAR Generates QSAR equations using the genetic function approximation paradigm Standalone
PaDEL-Descriptor Calculate molecular descriptors and fingerprints. The software currently calculates 863 descriptors (729 1D, 2D descriptors and 134 3D descriptors) and 10 types of fingerprints Standalone
SMIREP A system for predicting the structural activity of chemical compounds Standalone
3-D QSAR 3-D QSAR models database for Virtual Screening Online tools and datasets
MOLE db Molecular Descriptors DataBase is a free on-line database comprised of 1124 molecular descriptors calculated for 234773 molecules database online
ChemDB portal Datasets: Experimentally annotated subsets Datasets for some targets including ADMET and also for organs
MolInfo Calculates descriptors for a Molecule (ChemDB portal) Online
Pattern Match Counter Counts Functional Groups (sub-structures) in molecules Online
VCCLAB PLS Partial Least Squares Regression Online
Basic QSAR tools Several software packages to download standalone
DTClab Basic QSAR tools Several software packages to download, for instance: To ensure that the compounds of the test set are representative of the training set (i.e. whether the test set structures are within the applicability domain or not). That tool is based on distance scores calculated by the Euclidean distance norm. Another tool is too observe structural diversity in selected dataset, in terms of distance scores... standalone