Ligand-based virtual screening

 

  • PubChem 3D - Searches ligands in 3D using a starting query and shows the structures superimposed - online
  • HybridSim-VS - Combines 2D fingerprint and 3D shape-based similarity - online
  • PUMA - Platform for Unified Molecular Analysis. PUMA computes molecular properties of pharmaceutical relevance, Murcko scaffolds, and diversity analysis - 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
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