Structure-based virtual screening - Docking

 

  • OpenGrowth - Open-growth aims to create de novo ligands by connecting small organic fragments in the active site of proteins. Molecule growth is biased to produce structures that statistically resemble drugs in an input training database. Consequently, the produced molecules have superior synthetic accessibility and pharmacokinetic properties compared with randomly grown molecules - standalone
  • CrossDocker - A tool for performing cross-docking using Autodock Vina. written in Python language and is available as executable binary for Windows operating system - standalone
  • Octopus - Virtual high-throughput screening of a pool of compounds against a set of molecular targets (linux) - standalone
  • DockingApp - A user friendly interface for facilitated docking simulations with AutoDock Vina - standalone
  • PL-PatchSurfer2 - The authors note: performs better in general than AutoDock Vina and DOCK6, and particularly outperforms the two methods when apo form or template-based models of targets are used. ROCS, an LBVS method, showed comparable performance to PL-PatchSurfer2 on DUD, but PL-PatchSurfer2 consistently showed a higher value than ROCS on all the metrics when applied to the WOMBAT dataset, which has more diverse active - standalone
  • DOCK - DOCKovalent for covalent docking of large libraries for the discovery of chemical probes (UCSF) - online
  • ACFIS - Server for fragment-based drug discovery - online
  • Screening Explorer - This tool is designed to analyze the performances of virtual screening scoring functions. Interactive charts allow to calculate partial metrics on the fly and read metrics simultaneously on different charts. Simple consensus methods are also included - online
  • SPOT-Ligand - Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity (has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency) - online
  • BUDE - Bristol University Docking Engine (BUDE): A general purpose molecular docking program written in C++, OpenMP and OpenCL that uses GPU acceleration - standalone
  • Galaxy7TM - Flexible GPCR–ligand docking by structure refinement - online
  • systemsDock - A web server for network pharmacology-based prediction and analysis - online
  • Alloscore - A tool for predicting allosteric ligand-protein interactions - online
  • Exemplar - Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions (2015) - online
  • AutoDockFR - Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility - standalone
  • PoLi - A virtual screening pipeline based on template pocket and ligand similarity (2015) - online
  • MTi - MTiAutoDock@mobyle2 online small compound docking (2015) - online
  • Panther - Ultrafast protein structure-based virtual screening with Panther - standalone
  • FlexAID - Revisiting docking on non native-complex structures (flexible receptor, 2015). Probabilistic docking program that optimizes the ligand-protein complex by minimizing the complementarity function using genetic-algorithms (GA) as search procedure with utilities to prepare the targets...etc, and includes pocket analysis tools. FlexAID and its accessory software (GetCleft and Process_Ligand) as well as the NRGsuite are free and open-source and are licensed under the GNU General Public License 3.0. All software is compatible under Windows, MacOS X and Linux. The sources and pre-compiled bundles are available - standalone
  • GeauxDock - GeauxDock: A novel approach for mixed-resolution ligand docking using a descriptor-based force field (GPU Accelerated Molecular Docking, builds on the ideas of ligand homology modeling) - standalone
  • DOLINA - Docking Based on a Local Induced-Fit Algorithm. Dolina along with documentation and an application example is available for academic institutions upon request for Linux and MacOS X platforms - standalone
  • ODDT - Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software (docking with Vina) to ease the process of developing CADD pipelines - standalone
  • QVina - Fast, accurate, and reliable molecular docking with QuickVina 2. The C++ source code - standalone
  • cholmine - Determinants and Prediction of Cholesterol and Cholate Binding Across Nonhomologous Protein Structures - online with registration
  • LINK - MpSDockzn: The executable program of MpSDockzn can be provided upon request, and the knowledge-based zinc metalloprotein-specific scoring function of MpSDockZn is available. An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy - standalone
  • MTi - MTiOpenScreen@mobyle2 online small compound docking-screening (2015) - online
  • LINK - DockThor: The service is a free receptor-ligand docking server - online
  • LINK - DrugDiscovery@TACC provides a graphical interface for conducting a screen for identifying small molecules that bind to your target protein. Autodock/Vina, compound collections (from 45,000 to 600,000), it requires password - online
  • Lidaeus - It is a very fast parallel virtual screening program, currently capable of docking 4 million compounds in less than 15 hours - online with registration
  • LINK - Charmming: CHARMM online for simulation(CHARMM INterface and Graphics), Fragment-based docking: Development of the CHARMMing Web user interface as a platform for Computer-Aided Drug Design, computation of binding energy...ProPKa etc - online with registration
  • LINK - FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm (request to the authors) - standalone
  • PSOVina - The hybrid particle swarm optimization algorithm for protein-ligand docking (said to be much faster than Vina) - standalone
  • RAISE - Based on RApid Index-based Screening Engine (RAISE) approach, the authors propose CRAISE—a user-controllable structure-based VS method. This is a first step towards an integrated, synergetic VS platform combining structure and ligand-based techniques - standalone
  • LINK - GalaxySite: Ligand-binding-site prediction by using molecular docking - online
  • LINK - PharmDock combines pose sampling and ranking based on optimized protein-based pharmacophore models with local optimization using an empirical scoring function (with a plugin to interface with PyMOL) - standalone
  • LINK - Autodock: Accelerating Virtual High-Throughput Ligand Docking. A detailed tutorial, scripts, and source code for the MPI version of Autodock4 - standalone
  • LINK - FRODRUG: a virtual screening GPU accelerated approach for drug discovery - .
  • LINK - CrystalDock is a computer algorithm that aids the computational identification of molecular fragments predicted to bind a receptor pocket of interest - standalone
  • LINK - LigandRNA: Computational predictor of RNA-ligand interactions - online
  • e-LEA3D - e-Drug3D - Screen and dock small molecules into the structure of a target protein with PLANTS - online
  • DINC - A new webserver AutoDock-based protocol for docking large ligands (Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands) - online
  • DOCK6 - Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design (could also help docking in PPI) - standalone
  • LINK - GEMDOCK: Ligand docking - standalone
  • LINK - iGEMDOCK: A Graphical Environment for Recognizing Pharmacological Interactions and Virtual Screening - standalone
  • HomDock - HomDock is a combination of the ligand based GMA molecular alignment tool and the docking tool GlamDock - standalone
  • GANDI - Program for fragment-based de novo ligand design - standalone
  • RF-Score - Predicting protein–ligand binding affinity - standalone
  • iStar iDock - A Web Platform for Large-Scale Protein-Ligand Docking. idock a multithreaded virtual screening tool for flexible ligand docking - online
  • LINK - VAMMPIRE: A matched molecular pairs database for structure-based drug design and optimisation. The web interface provides valuable information for structure-based lead optimization, but but may also be used for studies engaged in fundamental understanding of protein-ligand interactions - online search of the database
  • 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
  • SABRE - Ligand/Structure-Based Virtual Screening Approach using consensus molecular-shape pattern recognition. An academic license of SABRE program is available on request - standalone
  • MoMA - MoMA-LigPath: A web server to simulate protein-ligand unbinding - online
  • Sliding - Sliding Box Docking: Stand-alone tool for managing docking-based virtual screening along the DNA helix axis - standalone
  • SimG - An alignment based method for evaluating the similarity of small molecules and binding sites - standalone
  • Covalent - CovalentDock Cloud - A web server for automated covalent docking - online
  • DST - Dempster Shafer Theory, A tool for the post data analysis of screened compounds derived from computer-aided docking scores - online
  • LINK - Open Source for Computer-Aided Drug Discovery (ligand and structure-based screening, ADMET...) - several online tools
  • LINK - AuPosSom: Automatic clustering of docking poses in virtual screening process using self-organizing map - online
  • S66 - A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures - database
  • Xscore - Scoring function - online
  • LINK - MiniMuDS: A new optimizer using knowledge-based potentials improves scoring of docking solutions (Dr Klebe s group) - standalone and online
  • e-Drug3D -  Offers a facility to explore FDA approved drugs by for instance docking with PLANTS - online
  • LINK -  DecoyFinder: A graphical tool which helps finding sets of decoy molecules for a given group of active ligands - standalone
  • RDock -  A very fast open source small molecule protein docking programme that was initially developed by Vernalis - standalone
  • Autogrow - Ligand design using fragment-based growing, docking, and evolutionary techniques - standalone
  • Simtk - It 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. Many tools for chemistry docking ROCS-like tools, etc ADME Tox Cytochrome P450 site of metabolism....etc.    - Chemoinformatics - Toolkit, need to register. standalone
  • 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
  • LINK -  FINDSITELHM: Homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction. It also provides a simple scoring function to rank the docked compounds - standalone
  • GPCR - New Human GPCR modeling and virtual screening database is constructed using FINDSITEX -  online
  • SEED -  Program for docking libraries of fragments with solvation energy evaluation; FFLD = Program for fragment-based flexible ligand docking; DAIM = Decomposition And Identification of Molecules; VLG = Virtual Library Generator -  standalone
  • GriDock -  The virtual screening front-end for AutoDock 4 -  standalone
  • LINK -  DockoMatic: Automated Ligand Creation and Docking. BMC Res Notes. 2010 Nov 8;3(1):289 -  standalone
  • LINK -  A free and open source application that unifies a suite of software programs within a user-friendly Graphical User Interface (GUI) to facilitate molecular docking experiments. DockoMatic 2.0; significant software advances include the ability to: (1) conduct high throughput Inverse Virtual Screening (IVS); (2) construct 3D homology models; and (3) customize the user interface - standalone
  • VSDocker - A tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters - standalone
  • BetaDock -  A molecular docking simulation software based on the theory of Beta-complex. The authors claim that BetaDock is superior to any contemporary docking software while it requires less human intervention - standalone
  • Q-dock -  (coming soon, Skolnick Research Group) - .
    • 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
    • Score - Score version 2 (Score calculator for molecular docking) - online
    • Ligscore - Online scoring (pose and rank) between a ligand in mol2 and a protein - online
    • LINK - MotifScore: Using interaction network and motif to perform non-energy-based docking - standalone
    • LINK -  BSP-SLIM: Low resolution small molecule docking on predicted structures - online
    • LINK - DockingServer offers a web-based, easy to use interface that handles all aspects of molecular docking from ligand and protein set-up - online in part commercial, need to register
    • EADock - Server, screening with EADock - Small molecule docking - screening, online
    • PyRx -  Virtual Screening software for Computational Drug Discovery (docking) - standalone
    • Vina - AutoDock Vina plugin for PyMol - standalone
    • LINK - The new Autodock/Vina plugin for PyMOL - standalone
    • LINK - AutoDock and AutoDock Vina: Check also at vina.scripps.edu - standalone
    • VinaMPI - Massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina. Free and open source. Provided by the University of Tennessee -  standalone
    • LINK - PARADOCKS: A Framework for Molecular Docking with Population-Based Metaheuristics. The source code is available -  standalone
    • LINK - Rosetta Ligand: Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously - standalone
    • LINK -  HADDOCK: High Ambiguity Driven biomolecular DOCKing is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. First developed from protein-protein docking, it can also be applied to protein-ligand docking - online and standalone
    • BDT - BDT (is an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock -  standalone
    • Dockres - Dockres (reads the log file of docking runs performed by Autodock - standalone
    • LINK - Information theory-based scoring. The tool could become available, check with Dr Richard Jackson - standalone
    • FRED - FRED small molecule docking. See the online demos to try many OpenEye applications - Small molecule docking, commercial
    • DOCK -  Small molecule docking - Small molecule docking standalone
    • LINK - MS-DOCK: Rigid docking based on DOCK - Small molecule docking, works with DOCK, standalone
    • ViewDock -  To analyze Dock data and tools for post-processing DOCK results, works with Chimera - Small molecule docking post-docking processing, standalone
    • Galaxy -  GalaxyDock: A protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand. Binary executible files (run on linux or MAC) and examples can be freely downloaded at the following LINK - Small molecule docking - structure_based_VLS, standalone
    • FITTED - FITTED and see also FORECASTER - Small molecule docking - structure_based_VLS, standalone
    • Surflex - Small molecule docking - Small molecule docking - structure_based_VLS, standalone
    • ISE-dock - Based on Autodock. Gorelik B, Goldblum A.  Proteins: 2008 71:1373-86. Contact the authors - Small molecule docking - structure_based_VLS, standalone
    • 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. Contact Dr Miteva
    • CDOCK -  A protein-ligand docking program similar to Autodock - Small molecule docking - structure-based screening, standalone
    • Plants -  Small molecule docking. There is also a tool to prepare small molecules called SPORES - Small molecule docking, standalone
    • LINK - SwissDock: A web service to ligand docking - Small molecule docking, full surface screening possible, structure-based screening, online
    • iScreen - Cloud-computing web server for virtual screening and de novo drug design  - Small molecule docking - structure-based screening online
    • LINK - 1-Click Docking - 1 free docking online
    • Sanjeevini -  Docking small molecules - online
    • LINK - DOCKBlaster: Online screening with DOCK - Small molecule docking - structure-based screening online
    • LINK - Docking@Home: A project which uses Internet-connected computers to perform scientific calculations that aid in the creation of new and improved medicines - Small molecule docking
    • DAPLDS - Dynamically Adaptive Protein-Ligand Docking System - .
    • 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
    • ParDOCK - An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes - standalone
    • BAPPL - Binding Affinity Prediction of Protein-Ligand -  online
    • Score - Allows to calculate some different docking scores of ligand-receptor complex that can be submitted as a whole file containing both interaction partners or as two separated files. The calculation phase is provided by VEGA - Small molecule scoring online
    • Bapplz - Binding Affinity Prediction of Protein-Ligand binding site with Zinc - Small molecule scoring, online
    • LINK - Drug Design tools - Drug Design tools
    • LINK - GlamDock: Receptor based molecular docking - Small molecule docking - structure-based ligand-based screening, standalone
    • PSI-DOCK - Small molecule docking. You may try via ftp via ftp2.ipc.pku.edu.cn then pub &software Small molecule docking standalone
    • GFscore -  A General Non-Linear Consensus Scoring Function for High-Throughput Docking - Scoring standalone
    • SCORE3 -  An empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure - Scoring standalone
    • DSX - DrugScore (now DSX): evaluate ligand-receptor interaction energy - Scoring, should be online
    • FOLDX -  Can compute binding energy - Scoring online
    • CLIBE -  Computed ligand binding energy, A database for facilitating the analysis of Drug Binding Competitveness - Help for scoring online
    • LINK - Scoring using molecular interaction fingerprints - package available upon request to Dr. D. Rognan or directely from the website, also online at RBPS mobyle - Scoring via molecular interaction fingerprints
    • HINT - Scroing - Scoring standalone
    • LINK - Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees - Scoring standalone
    • HBAT - Hydrogen Bond Analysis Tool is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph) - Post-docking analysis standalone
    • Xscore -  Tool to predict binding energy between ligand and receptor - Scoring standalone
    • LINK - The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms to users in industry and academia in the form of a C++ library - Help for docking
    • LINK -  GEMSTONE: Grid Enabled Molecular Science Through Online Networked Environments - standalone
    • BioDrug - BioDrugScreen: Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets. Structural Protein-Ligand Interactome (SPLINTER) - online
    • LINK - Kindock and Simdock Tool for comparative docking of protein kinase ligands and ligand transposition server -  online
    • Arguslab - A molecular modeling, graphics, and drug design program. Performs fast shape docking like FRED and has tools similar to AutoDock. Problems so far, it runs only on Windows - Molecular docking, standalone
    • LINK - The Ligand Explorer. Java Tools for interactive post-processing of docking studies -  standalone
    • LINK - Many computer tools for small (or large) molecules. Tools for docking and small molecules by Dr. Michel Petitjean - standalone
    • LIGPLOT -  Program for automatically plotting protein-ligand interactions - standalone
    • LIGPLOT - LIGPLOT+ the new version of ligplot -  standalone
    • PoseView -  Automatically creates two-dimensional diagrams of complexes -  online
    • LINK - ROCR is an R package www.r-project.org - Analyzing results of virtual screenings: ROC curves, standalone
    • LINK - tutorials about ROC curve - .
    • LINK - tutorials ROC curve - .
    • LINK - tutorial 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
    • PyPLIF - Python-based Protein-Ligand Interaction Fingerprinting - standalone
    • LINK - Pose and Rank : a web server for scoring protein-ligand complexes (Sali lab) - online
    • CaPTURE - The CaPTURE program can identify energetically significant cation-pi interactions within proteins - online
    • X-score - Scoring - online
    • LINK - Compute ligand-protein interaction energy after energy minimization performed by the package PLOP, protein local optimization program - standalone
    • VSDMIP - A platform for virtual screening (VS) of chemical libraries, integrated within a MySQL relational database. Virtual screening, structure-based screening. See also CRdock - pipelines, standalone
    • MM-ISMSA - A Scoring Function for Protein-Protein and Protein-Ligand Docking and Molecular Dynamics - standalone
    • CRDOCK - An ultrafast multipurpose protein-ligand docking tool. CRDOCK is now included within VSDMIP. CRDOCK is a protein-ligand docking program similar to Glide, DOCK or Autodock. It uses a hybrid scoring function based on GlideScore(tm) using a molecular mechanics energy function (AMBER-like) and the ChemScore function to score interactions. The docking program is particularly well suited to generate molecular models of ligand-receptor complexes for further use in COMBINE analysis. gCOMBINE : a graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes - standalone
    • pep - pepMMsMIMIC: 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) -  online
    • BAPPL-Z - Binding Affinity Prediction of Protein-Ligand complex containing Zinc - online
    • LINK - Predict DNA-Drug Interaction strength - online
    • 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
    • e-Drug3D - 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
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