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URLs Ligand based virtual screening Comments
PubChem 3D Searches ligands in 3D using a starting query and shows the structures superimposed online
Pharmacophore Pharmacophore-Map-Pick: A Method to Generate Pharmacophore Models for All Human GPCRs. A total of 2386 pharmacophore models for 819 different GPCRs (99 % coverage (819/825) online
eSynth The tool can successfully reconstruct chemically feasible molecules from molecular fragments (A graph-based approach to construct target-focused libraries for virtual screening) standalone
LiSiCA LiSiCA PyMOL plugin (ligand-based screening), windows linux standalone
SwissSimilarity A web tool for low to ultra high-throughput ligand-based virtual screening online
Pharmit Online virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization online
USR-VS Server for large-scale prospective virtual screening using ultrafast shape recognition techniques online
Cancerin Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI-60 cancer cell lines. This server provides various facilities that includes; virtual screening of anticancer molecules, analog based drug design, and similarity with known anticancer molecules online
PoLi A virtual screening pipeline based on template pocket and ligand similarity online
MLViS A Web Tool for Machine Learning-Based Virtual Screening in Early-Phase of Drug Discovery and Development. The tool can classify molecules as drug-like and nondrug-like based on various machine learning methods, including discriminant, tree-based, kernel-based, ensemble and other algorithms online
3DAPfp and 3DXfp Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp should provide useful assistance to drug discovery projects online
GPURFSCREEN A GPU based virtual screening tool using random forest classifier (A ligand based virtual screening tool) standalone
mRAise An alternative algorithmic approach to ligand-based virtual screening standalone
LiSiCA A Software for Ligand-based Virtual Screening standalone
LiSIs An Online Scientific Workflow System for Virtual Screening (granatum) online
LiSIs An Online Scientific Workflow System for Virtual Screening online
UFSRAT Ultra-fast Shape Recognition with Atom Types, an efficient algorithm that considers both the 3D distribution (shape) and electrostatics of atoms to score and retrieve molecules capable of making similar interactions to those of the supplied query online
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
LIGSIFT An open-source tool for ligand structural alignment and virtual screening. Uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient virtual screening based on the statistical significance of the score standalone
Active Search Toolbox The active search method for iterative virtual screening. A method is introduced for sequential similarity searching for active compounds (2015). Active Search Toolbox for MATLAB standalone
Scaffolds Drug-Unique scaffolds: A list of 221 drug-unique scaffolds that represented approved drugs but were not detected in currently available bioactive compounds is provided (2014) dataset
Analog The program AnalogExplorer, i.e., a new method for graphical analysis of analog series and associated structure-activity relationship information standalone
LBVS An online platform for ligand-based virtual screening using publicly accessible databases (2014) online
ACPC A ligand-based virtual screening tool using AutoCorrelation of Partial Charges standalone
iDrug A web-accessible and interactive drug discovery and design platform. Computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building/editing, converting, displaying, and analyzing online
Link ChemMapper: Ligand-based virtual screening using the USR (Ultrafast Shape Recognition) method or the 3D similarity method SHAFTS. Many collections are already available online (can be used to predict off-targets, see this section on the present website) online
MCSS A multi-fingerprint browser for the ZINC database. To confirm the activity of an initial small molecule hit compound from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser assists this process online
Align-it Pharmacophore-based (Pharao) tool to align molecules by representing pharmacophoric features as Gaussian 3D volumes (silicos-it) standalone
Shape-it Shape-based alignment tool (silicos-it) standalone
SABRE Ligand-based Structure-Based Virtual Screening Approach Using Consensus Molecular-Shape Pattern Recognition. An academic license of the SABRE program is available on request standalone
Link MassiveSAR: Small molecule structural similarity analysis and clustering. The program for analysis of high-throughput screening data and generally for analysis of data sets containing multiple chemical compounds. This software is most suitable for finding related chemical structures and for establishing structure-activity relationships (SAR) within experimentally generated molecule sets or libraries of small molecules standalone
Link eSimDock: A similarity-based approach to ligand docking and binding affinity prediction. Given the receptor structure, anchor ligand and a query compound, it employs machine learning and a set of physics-based as well as statistical potentials to predict the binding pose and estimate the corresponding binding affinity standalone
ViCi in-silico ligand-based drug design (ViCi uses a combination of mathematical descriptors of molecular size, shape and topology to describe small molecule structures) online
Scaffold Scaffold Hunter: Interactive exploration of chemical space Chemoinformatics - navigation in chemical space, standalone
Link Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognition of this natural peptide using both pharmacophore and shape similarity techniques (Swimming into peptidomimetic chemical, NAR 2011) Chemoinformatics - navigation in chemical space, online
LINK IC50-to-Ki converter online (may not work)
BioDataFit BioDataFit is a data fitting program specifically designed for biologists. It can be used to model dose-response, ligand-binding, enzyme kinetics, and growth inhibition. Emphasis is given to the four-parameter model or sigmoidal model, which is frequently used to calculate EC50 (IC50, DC50, or GI50) values in dose-response experiments such as drug screening and inhibition assays online
LINK IC50-to-Ki converter online (may not work)
LINK de novo drug design engine to create new molecules either from scratch (lead-hopping) or based on a user-defined scaffold on which R-groups have to be optimized (Douguet) online
Pharmer A pharmacophore search technology standalone
PAPER PAPER is a program to calculate optimal molecular overlays, based on the Gaussian model of molecular shape (as used, for example, in OpenEye ROCS). It accelerates large screening experiments by evaluating multiple overlays in parallel on NVIDIA GPUs standalone
CATSlight2 Chemically Advanced Template Search, you can use CATSlight2 for molecular similarity searching online
PhAST Pharmacophore Alignment Search Tool online
Drugster A comprehensive and fully integrated drug design, lead and structure optimization toolkit. Drugster is a fully interactive pipeline designed to break the command line barrier and introduce a new user-friendly environment to perform drug design, lead and structure optimization experiments through an efficient combination of the PDB2PQR, Ligbuilder, Gromacs and Dock suites. The platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process, by providing a seamless interface to all incorporated packages standalone
fmcsR Mismatch Tolerant Maximum Common Substructure Searching in R standalone
SimG An alignment based method for evaluating the similarity of small molecules and binding sites standalone
SHAFTS A Hybrid Approach for 3D Molecular Similarity Calculation. SHAFTS can also be used to identify the potential drug targets or explore multiple drug targets for the given bioactive compounds and even explore potential mechanisms for drugs side effects. SHAFTS has been integrated into ChemMapper Server standalone
LINK Open-source platform to benchmark fingerprints for ligand-based virtual screening (Riniker S, Landrum GA, Journal of Cheminformatics 2013, 5:26). datasets to test fingerprints zip files in the supplement section datasets
LINK OAK Open Access Archive - Novartis Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules A matrix of 170 million HTS-FP similarities between 18600 public compounds from ChEmbl data
LINK Open Source for Computer-Aided Drug Discovery several online tools
ChemMine An online service for analyzing and clustering small molecules, similarity search online
Molecule The Molecule Cloud - compact visualization of large collections of molecules (P Erlt and B Rhode). Works with Avalon Cheminformatics Toolkit standalone
Link avalontoolkit: for The Molecule Cloud standalone
LINK Visualizing the words that characterize a text, online online
Link MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13 online and standalone
MolClass A web portal to interrogate diverse small molecule screen datasets with different computational models, MolClass thus defines a likelihood value for each compound entry and creates an activity fingerprint across diverse sets of screens online and standalone
DB REPROVIS-DB: A Benchmark System for ligand-based virtual screening - Data sets datasets
S66 A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures database
JACOB JACOB (just a collection of benchmarks): a dynamic database for computational chemistry benchmarking database
Filter-it and related Software packages to filter collections and many others, pharmacophore, extract molecular scaffolds, align shape... standalone
e-Drug3D Offers a facility to explore FDA approved drugs online
Decoy DecoyFinder: A graphical tool which helps finding sets of decoy molecules for a given group of active ligands standalone
3DFS Search 3D databases for compounds matching a pharmacophore query. Compound searching online (password to get in)
LigMerge Program combining structures of known binders to generate similar but structurally distinct compounds that can be tested for binding. LigMerge is an automated algorithm for swapping chemical substituents in known ligands to generate new ligands (fragment) standalone
LigCSRre LigCSRre 3D Ligand-Based virtual screening methods (Ligand-based screening)  online
MoFa Molecular fragment miner (Compound searching) standalone
MoSS Molecular Substructure Miner. A program to find frequent molecular substructures and discriminative fragments in a database of molecule descriptions (Compound searching) standalone
ShaEP ShaEP aligns (superimposes) two rigid 3D molecular structure models and computes a similarity index for the overlay standalone
FTreesWeb Similarity search with Feature trees  online
FTreesWeb FTreesWeb and related similarity search - ligand-based screening
LINK Many tools for chemistry docking ROCS-like tools, etc ADME Tox Cytochrome P450 site of metabolism....etc. Simtk.org is the home of the software framework initiated and developed by Simbios, the National NIH Center for Biomedical Computing focusing on Physics-based Simulation of Biological Structures Chemoinformatics - Toolkit, need to register
Zodiac A Molecular Modelling suite for drug design. Its features include support for haptic devices and nintendo wiimote fully undoable command list, MMFF94 implementation, POVRAY output Chemoinformatics - Toolkit, standalone
LigBuilder Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket Compound searching, ligand-based, standalone
SurflexSim VLS based on the ligand structure ligand-based screening, standalone
Pharma PharmaGist: Predicting molecular interactions is a major goal in rational drug design Compound searching, ligand-based, Pharmacophore, online
SAAMCO Similarity of Amino Acid Motifs to Compounds finds small molecules resembling peptides based on their side chains, many tools for peptides peptidomimetic, standalone
Molprint2D A fast fragment-based similarity searching method  standalone
USRCAT Real-time ultrafast shape recognition with pharmacophoric constraints  standalone
AURAmol Allows a user to take a candidate 2D or 3D molecular shape and use it to search for similarly shaped molecules in large databases Compound searching online
LINK Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials. Similarity search, standalone
MIPSIM Molecular Interaction Potential SIMilarity Analysis. The old MEPSIM program has been completely rewritten in a more modular and sophisticated program called MIPSIM. Contact This email address is being protected from spambots. You need JavaScript enabled to view it. Similarity search, standalone
MEssEM A MOLECULAR QUANTUM SIMILARITY MEASURES SYSTEM OF PROGRAMS (Molecular Similarity: Methodological Development and Applications of Quantum Molecular Similarity Measures to Chemical Reactivity and analysis of Charge Density Distributions). Please contact Dr. Miquel Sola i Puig Similarity search, standalone
LINK New Human GPCR modeling and virtual screening database is constructed using FINDSITEX GPCR modeling screening online
Link pharmACOphore: The flexible superimposition of biologically active ligands is a crucial step in ligand-based drug design. Our new approach pharmACOphore for pairwise as well as multiple flexible alignment of ligands is based on ant colony optimization (ACO). An empirical scoring function is used, which describes ligand similarity by minimizing the distance of pharmacophoric features standalone
DEKOIS Demanding Evaluation Kits for Objective In silico Screening The datasets are derived from active sets that are available at the Directory of Useful Decoys datasets
MolShaCS A free and open source tool for ligand similarity identification based on Gaussian descriptors standalone
MoSS Molecular Substructure Miner fragmentation analysis of collections substructures, standalone
MOLpro Calculate or predict molecular properties other than 3D structure online - descriptors
SMIREP A system for predicting the structural activity of chemical compounds. For that it can be categorized as a SAR/QSAR tool. The advantages of SMIREP are that it is failry fast, due to a heuristic approach of identifying the main features of active versus inactive compounds find key substructures, standalone
ZINC ZINCPharmer: Pharmacophore search of the ZINC database ZINCPharmer online
Pharm PharmMapper: Ligand based Pharmacophore search online
AMMOS Automated Molecular Mechanics Optimization tool for in silico Screening Small molecule pre-processing and post-docking processing, flexibility - induced-fit, standalone, but also online at mobyle RPBS
Pharmer A pharmacophore search technology that can search millions of chemical structures in seconds standalone
Open3D Open3DALIGN: Open-source software for unsupervised molecular alignment standalone
FTFlex Accounting for binding site flexibility to improve fragment-based identification of druggable hot spots FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library online
LINK Drug Design tools Drug Design tools
LINK Datasets for FXa, ADMET.. download
Link GEMSTONE: Grid Enabled Molecular Science Through Online Networked Environments Tools to speed-up computations
ChemGPS ChemGPS-NP Web: A tool tuned for navigation in biologically relevant chemical space Chemical Space, Chemoinformatics, online
SARANEA A freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets, activity cliff. Bajorath et al. J. Chem. Inf. Model., 2010. Also several compound collections for hERG, proteases... Chemoinformatics, standalone
Link ScaffoldTreeGenerator : navigation in chemical space standalone
ROCR An R package for evaluating and visualizing classifier performance Analyzing results of virtual screenings: ROC curves, standalone
LINK tutorials about ROC curve .
LINK tutorials about ROC curve .
LINK tutorials about ROC curve .
CoLiBRI Chemometric analysis of ligand receptor complementarity. Need to contact the authors, J Chem Inf Model 2006, 46, 844-851 Fast reduction of the compound collection
Link ValLigURL: Ligand Validator at Uppsala University online
Link I-interpret: Uses standard geometry information about small ligands, like a ligand present in a PDB file and performs automatic atom/bond-type assignment. It can takes several compounds at a time and propose protonation state. See Zhao, Cheng and Wang, J Chem inf Model in press 2007. Title: automatic perception of organic molecules based on essential structural information online
LINK McMaster Canada, HTS-VLS competition, does not seem to work April 17 2013 HTS-VLS competition, datasets. Check the publication
MLSCN The Molecular Libraries Screening Centers Network consists of 10 centers with a diverse set of screening platform technologies that include ultraHTS, cell based imaging, and flow cytometry.. NIH USA project on screening
LINK jCompoundMapper: An Open Source Java Library and Command-Line Tool for Chemical Fingerprints standalone
Alice Artificial intelligence foundation Artificial Intelligence, standalone, borderline with this topic
SoftDB A simple software database with a web interface designed to serve the needs of a particular field of research, in this case, structural biology. Since the scope of application is much more limited than similar systems such as freshmeat.net, the database and interface are relatively small, and can be run on almost any web server through the use of a few Perl scripts and a MySQL back-end database. data flows (often referred to as pipelines), standalone