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SB-screening & Protein-ligand interactions

See also screening utilities, binding pockets...

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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