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 9/20/2013. Currently 781 links.

Last additions

  • HitPick. Web server that facilitates the analysis of chemical screenings by identifing hits and predicting their molecular targets. For target prediction, HitPick applies an approach that combines two 2D molecular similarity based methods: a simple 1-Nearest-Neighbour similarity searching and a machine learning method based on Laplacian-modified naive Bayesian models. provided by the Helmholtz Center Munich, germany.
  • Nucleos. Nucleos is a webserver for the identification of nucleotide-binding sites based on the concept of nucleotide modularity. Nucleos identifies binding sites for nucleotide modules (namely the nucleobase, the carbohydrate and the phosphate) and then combines them in order to build the complete binding sites for different types of nucleotides (e.g. ADP or FAD). Provided by the University of Roma 2, Italy.
  • LISE. Web server for ligand Binding Site Prediction Using Ligand Interacting and Binding Site-Enriched Protein Triangles. Exists as a standalone program. Provided by the Institute of Biomedical Sciences, Academia Sinica.
  • LISE. Program for ligand Binding Site Prediction Using Ligand Interacting and Binding Site-Enriched Protein Triangles. Exists as a web service. Provided by the Institute of Biomedical Sciences, Academia Sinica.
  • wwwPDBinder. Web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. Exists as a standalone program. Provided by the University of Roma 2, Italy.
  • PDBinder. Free program for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. Exists as a web server. Provided by the University of Roma 2, Italy.
  • eFindSite. Ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins identified by 10 threading/fold recognition methods. Exists as a web service. Provided by the Louisiana State University, Computational Systems Biology Group.
  • eFindSite. Web server for ligand binding site prediction and virtual screening algorithm that detects common ligand binding sites in a set of evolutionarily related proteins identified by 10 threading/fold recognition methods. Exists as standalone program. Provided by the Louisiana State University, Computational Systems Biology Group.
  • 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.
  • ChemMapper. Web server for target prediction for a query molecule. Based on 2D and 3D ligand similarity to existing ligands. Provided by the East China University of Science & Technology.
  • SHAFTS. (SHApe-FeaTure Similarity) is a program for 3D molecular similarity calculation and ligand-based virtual screening. SHAFTS adopts hybrid similarity metric combined with molecular shape and colored (labeled) chemistry groups annotated by pharmacophore features for 3D similarity calculation and ranking, which is designed to integrated the strength of pharmacophore matching and volumetric overlay approaches. Provided by the East China University of Science & Technology.
  • INDDEx. (Investigational Novel Drug Discovery by Example) logic-based machine-learning technique to learn from a training dataset of active and inactive molecules from a screening programme to generate quantitative logic-based rules. These rules are in the form of pairwise distances between fragments of substructure, which provide vital chemical insight into the stereochemical and structural requirements for biological activity. Provided by Equinox Pharma. Reduced rates are available for academic groups.
  • VAMMPIRE. (Virtually Aligned Matched Molecular Pairs Including Receptor Environment) matched molecular pairs database for structure-based drug design and optimisation. By building MMPs between PDBbind and ChEMBLdb ligands VAMMPIRE extrapolates the two-dimensional ChEMBLdb ligands to the assumed, three-dimensional binding mode and introduce the received binding information into the database. Provided by the Institute of Pharmaceutical Chemistry / Goethe University Frankfurt, Germany.
  • Aggregator Advisor. Free web service to suggest molecules that aggregate or may aggregate under biochemical assay conditions. The approach is based on the chemical similarity to known aggregators, and physical properties. Provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
  • SCIGRESS. Desktop/server molecular modeling software suite that can apply a wide range of computational models to all types of molecular systems, from small organic molecules, to whole proteins, including linear scaling semiempirical quantum methods for protein optimization and ligand docking. Developed and distributed by Fujitsu, Ltd.
  • MATCH server. The MATCH web server allows one to submit a molecule to generate both the topology and parameter file for a given small molecule. Molecule file formats: pdb, sdf, mol, mol2 are all accepted. Provided by the Brooks laboratory, University of Michigan.
  • NOC. Free molecular explorer for protein structure visualization, validation and analysis. Mainained by Dr. Nymeyer's Group, Inst. Mol. Biol., Florida State University.
  • OpenStructure. Open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics. Provided by the Swiss Institute of Bioinformatics and the Biozentrum, University of Basel.
  • SMARTSeditor. Graphic editing tool for generic chemical patterns. Based on the SMARTS language, chemical patterns can be created and edited interactively, similar to molecule editing in a chemical structure editor. The visualization of patterns is based on the visualization concept of the SMARTSviewer.Freely available for linux systems with 32 and 64 bit, windows 32bit systems and MacOS. Developed by the University of Hamburg.
  • PharmBench. The aim of PharmBench is to provide a community benchmark dataset for the evaluation of molecular alignment and pharmacophore elucidation approaches, and also a webservice to help users evaluate their own methods. The dataset consists of 81 targets, containing 960 ligands in total. The dataset is based on known pharmaceutically relevant co-crystallised protein ligand complexes, which were filtered to leave high-resolution structures containing drug-like small molecule ligands, for which electron density is also available. For each target the structures have been aligned using the receptor backbone atoms, and then the ligands extracted and prepared by fixing their atom types and adding hydrogen atoms. Provided by Moldiscovery.
  • Chemkit. Free open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.
  • Coot. Program for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Free and open-source.
  • Crystal Studio. Crystal Studio is a Windows XP/Vista/Windows 7 (32/64) software package for crystallography. It is a comprehensive tool for user-friendly creation, 3D graphical design, display and manipulation of crystal and macro-molecular structures, surface or interfaces and defects and for the simulation of X-Ray, neutron and electron diffraction patterns.
  • Friend. Integrated Front-End application for multiple structure visualization and multiple sequence alignment. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also available as an applet. Provided by the Ray and Stephanie Lane Center for Computational Biology.
  • Molekel. Free open-source multi-platform molecular visualization program, for Mac OSX, Windows and Linux. Provided by the Swiss National Supercomputing Centre: Lugano (Switzerland).
  • TouchMol Web. Tool for drawing chemical and biological structures online. Allows Copy/Paste to ChemDraw, ISIS/Draw, SciFinder and Word. Provides name-to-structure. Provided by Scilligence.
  • TouchMol Mobile App. Tool for drawing chemical and biological structures. Allows Copy/Paste to ChemDraw, ISIS/Draw, SciFinder and Word. Provides name-to-structure. For Windows 8 mobile devices. Provided by Scilligence.
  • TouchMol Deskop Application. Tool for drawing chemical and biological structures, optimized for Touch Operations. Allows Copy/Paste to ChemDraw, ISIS/Draw, SciFinder and Word. Provides name-to-structure. For Windows 8. Provided by Scilligence.
  • TouchMol for Office. Desktop tool for drawing chemical and biological structures, into the MS Office suite. Provided by Scilligence.
  • ModWeb. Server for Protein Structure Modeling based on the Modeller program. Maintained by Andrej Sali at the University of California, San Francisco.
  • ModEval. Model evaluation server for protein structure models. Maintained by Andrej Sali at the University of California, San Francisco.
  • ModLoop. Web server for automated modeling of loops in protein structures. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures. Maintained by Andrej Sali at the University of California, San Francisco.
  • ModPipe. Completely automated software pipeline that can calculate protein structure models for a large number of sequences with almost no manual intervention. In the simplest case, it takes as input a sequence identifier and a configuration file and produces one or more comparative models for that sequence. Free and open source software. Maintained by Andrej Sali at the University of California, San Francisco.
  • LigBase. Database of ligand binding proteins aligned to structural templates. The structural templates are taken from the PDB, 3D models of the aligned sequences are provided ModBase, and pairwise sequence alignments are provided by CE. Multiple Structural Alignments are built on the fly within LigBase from a series of pairwise alignments. Ligand diagrams are generated with the program Ligplot. Maintained by Andrej Sali at the University of California, San Francisco.
  • Chem3D for iPad. Chem3D for iPad enables scientists to view and manipulate 3D images of chemical and biochemical structures. Re-imagined for the iPad, the Chem3D app features a facile user interface to manipulate images using common touch, pinch and swipe gestures. Provided by PerkinElmer, Inc.
  • ChemDraw for iPad. iPad application to create, edit and share publication-quality chemical structures with just the touch of a finger, based on the world’s most popular chemical drawing software, ChemDraw. Provided by PerkinElmer, Inc.
  • ChemSpider Mobile. Allows searching the ChemSpider chemical database, provided by the Royal Society of Chemistry. Compounds can be searched by structure or by name, and browsed within the app. Results can be examined by jumping to the web page. Search structures are drawn using the powerful MMDS molecular diagram editor. For iPad. Provided by Molecular Materials Informatics, Inc.
  • SAR Table. Application designed for creating tables containing a series of related structures, their activity/property data, and associated text. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule. The table editor has many convenience features and data checking cues to make the data entry process as efficient as possible. For iPad. Provided by Molecular Materials Informatics, Inc.
  • StructureMate. Portable chemical dataset viewer for iPad, for browsing SAR reports, chemical catalogs, custom-made databases, and physical property references. Provided by Metamolecular, LLC.