Directory of computer-aided Drug Design tools

Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services.
This short list contains only the latest additions to the entire directory.
If you think that an interesting tool is missing in this list, please contact us.

Updated on 5/16/2013. Currently 742 links.

Last additions

• EPOS^BP. Calculates ensemble of Pockets on Protein Surfaces with BALLPass. Available for Linux x86. Provided by the Center for BioInformatics, university of Saarland.
  
• SVILP_ligand. General method for discovering the features of binding pockets that confer specificity for particular ligands. Provided by the Computational Bioinformatics Laboratory, Imperial College London.
  
• CLiBE. Database containing information about Computed Ligand-Receptor Interaction Energy and other attributes such as energy components; ligand classification, functions and properties. Ligand structure is also included. Provided by the BioInformatics and Drug Design group of the National University of Singapore.
  
• CHARMM-GUI. Provides (optimal, reasonable) CHARMM input files in a GUI fashion so that people can run the input on their machine, Helps people read and modify the input with their purposes, and provides also educational materials such as MM/MD lectures, as well as molecular animations. Provided by the University of Kansas.
  
• CHARMMing.org. CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results.
  
• ParamChem. Provides topology and parameters for small organic molecules from CGenFF, for use with CHARMM and GROMACS. provided by the University of Kentucky.
  
• Cavitator. Program developed to detect "pocket" or "cavity" in a protein structure, using a grid-based geometric analysis. Free and open source. Provided by the Center for the Study of Systems Biology, Atlanta.
  
• SiteEngine. Web service to predict regions that can potentially function as binding sites. The methods is based on recognition of geometrical and physico-chemical environments that are similar to known binding sites. Exists as a standalone program. Provided by the structural Bioinformatics group at Tel-Aviv University.
  
• PASSonline. (Prediction of Activity Spectra for Substances). Web service for evaluating the general biological potential of an organic drug-like molecule, based on the comparison of the user's compound to a database of 260,000 of drug-like biologically active compounds using the Multilevel Neighborhoods of Atoms (MNA) structure descriptors. Provided by the Orekhovich Institute of Biomedical Chemistry
  
• Target Hunter of Small Molecule. Web portal for predicting the therapeutic potential of small organic molecules based on chemogenomic database. Created and maintained by Prof. Xiang-Qun (Sean) Xie’s laboratory
  
• ElectroShape Polypharmacology server. Web service to estimate polypharmacology profiles and side effects of compounds based on the molecular similarity concept. Developed and maintained by Alvaro Cortes Cabrera.
  
• Pose & Rank. Web server for scoring protein-ligand complexes. Provided by the laboratory of Andrej Sali.
  
• 1-Click Scaffold Hop. Draw a reference structure to get new scaffolds using a ligand-based approach. Allows visualizing the similarity between the query and the identified scaffold. Provided by mcule.
  
• Property calculator. Create a physicochemical property profile for a compound. Provided by mcule.
  
• Toxicity checker. Webserver for searching substructures commonly found in toxic and promiscuous ligands. Based on more than 100 SMARTS toxic matching rules. Provided by mcule.
  
• FragmentStore. Fragment Store is a database, primarily designed for pharmacists, biochemists, and medical scientists but also researchers working in cognate disciplines like the fragment based drug design. It provides access to information about fragments of compounds with their properties (e.g. charge, hydrophobicity, binding site preferences). It allow the user to do statistical analysis of the fragments properties and binding site preferences. Moreover, the database supports to build an adequate fragment library for fragment based drug design. Provided by the Structural Bioinformatics Group of Charité Berlin.
  
• CDK Descriptor Calculator GUI. Free and open source GUI to CDK to calculate molecular descriptors.
  
• BlueDesc. Free and open source molecular descriptor calculator. Converts an MDL SD file into ARFF and LIBSVM format for machine learning and data mining purposes using CDK and JOELib2. Provided by the Tuebingen University.
  
• Molinspiration bioactivity score. Score a compound for its ability to be GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor, enzyme inhibitor. Based on Bayesian statistics to compare structures of representative ligands active on the particular target with structures of inactive molecules and to identify substructure features (which in turn determine physicochemical properties) typical for active molecules. Provided by Molinspiration.
  
• FINDSITE^COMB. Web service for large scale virtual ligand screening using a threading/structure-based FINDSITE-based approach. It offers the advantage that comparable results are obtained when predicted or experimental structures are used. The user can either provide a protein structure in PDB format or a protein sequence whose structure will first be predicted prior its use in virtual ligand screening. Freely available to all academic users and not-for-profit institutions. Provided by the Skolnick Research Group.
  
• OpenSMILES. Community sponsored open-standards version of the SMILES language for chemistry. OpenSMILES is part of the Blue Obelisk community.
  
• GLL. (GPCR Ligand Library). Database of 25145 ligands for 147 GPCRs. Associated with the GDD (GPCR Decoy Database). Provided by the Claudio N. Cavasotto Lab. of the Instituto de Biomedicina de Buenos Aires - Max Planck Society Partner (IBioBA-MPSP).
  
• GDD. (GPCR Decoy Database). For each ligand in GLL, 39 decoys were drawn from ZINC ensuring physical similarity of six properties (molecular weight, formal charge, hydrogen bond donors and acceptors, rotatable bonds and logP), but structural dissimilarity. Provided by the Claudio N. Cavasotto Lab. of the Instituto de Biomedicina de Buenos Aires - Max Planck Society Partner (IBioBA-MPSP).
  
• 1-Click Docking. Free online molecular docking solution. Solutions can be visualized online in 3D using the WebGL/Javascript based molecule viewer of GLmol. Provided by Mcule.
  
• Mcule docking. Commercial online solution to dock thousands to millions of potential ligands into target structures with the Vina docking tool. Reduced prices for academic. Provided ny Mcule.
  
• Mcule database. Commercial database of commercially available small molecules. Allows filtering by chemical supplier data (stock availability, price, delivery time, chemical suppliers, catalogs, minimum purity, etc.) and export the whole Mcule database including supplier and procurement related properties. Reduced prices for academic. Provided by Mcule.
  
• SimCYP for iPhone.. The SimCYP Population-based ADME Simulator is a platform for the prediction of drug-drug interactions and pharmacokinetic outcomes in clinical populations. For iPhone. Distributed by SimCYP.
  
• GalaxyDock. Protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand. Developed by the Computational Biology Lab, Department of Chemistry, Seoul National University.
  
• ChemSpider's InChI resolver. The InChI Resolver provides online access to a series of tools supporting the generation and look-up of InChIStrings and InChIKeys. Provided by ChemSpider.
  
• Protinfo ABCM. The Protinfo web server consists of a series of discrete modules that make predictions of, and provide information about, protein folding, structure, function, interaction, evolution, and design by applying computational methodologies developed by the Samudrala Computational Biology Research Group.
  
• Prime. Fully-integrated protein structure prediction program, providing graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction. Developed by Schrödinger.
  
• RaptorX web server. Protein structure prediction web server developed by Xu group, with a particular focus on the alignment of distantly-related proteins with sparse sequence profile and that of a single target to multiple templates. Currently, RaptorX consists of four major modules: single-template threading, alignment quality assessment, multiple-template threading and fragment-free approach to free modeling. Due to limited computational power, this server offers the first three modules for regular usage. Also exists as a standalone program.
  
• RaptorX. Protein structure prediction program developed by Xu group, with a particular focus on the alignment of distantly-related proteins with sparse sequence profile and that of a single target to multiple templates. Currently, RaptorX consists of four major modules: single-template threading, alignment quality assessment, multiple-template threading and fragment-free approach to free modeling. Also exists as a web service.
  
• SwissBioisostere. Freely available database containing information on millions of molecular replacements and their performance in biochemical assays. It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, and to give access to the details on particular molecular replacements. Users can provide a molecular fragment and get possible replacements, along with the biological assays in which they were observed. Users can also provide a given molecular replacement and get the corresponding information. The data were created through detection of matched molecular pairs and mining bioactivity data in the ChEMBL database. Developed and maintained by Merck Serono and the Swiss Institute of BioInformatics.