Directory of computer-aided Drug Design tools

Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services. These tools are classified according to their application field, trying to cover the whole drug design pipeline. If you think that an interesting tool is missing in this list, please contact us

Updated on 4/5/2018. Currently 807 links. Show all links /Hide all links.

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In Silico Drug Design Pipeline

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Small Molecules Database Visualization Structure Based Screening Ligand Based Screening Structure Based Ligand Design Prepare Small Molecules Pharmacophore Based Ligand Design Molecular Modeling Homology Modeling Fragments Library Docking Affinity Estimation Affinity Database ADMET ADMETDatabases


Chemical databases

  • Approved Drugs. The Approved Drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. The detail view allows viewing of a 3D conformation as well as tautomers. Structures can be exported in a variety of ways, e.g. email, twitter, clipboard. For iPad and iPhone. Developed by Molecular Materials Informatics, 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.
  • SPRESImobile. iPod, iPhone and iPad application providing direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. Developed by InfoChem.
  • MORE. (MObile REagents). Mobile app, for iphone, ipad and android, which gives access to over 9 million molecules and 16 million chemical product variations offered by 56 different suppliers. Can search reagents by name, formula or by drawing a chemical structure. It is possible to limit the search to specific suppliers, bookmark the search results, and export small sdfiles. Allows converting a picture of a chemical structure taken from the iPhone camera into a structurally searchable molecule using OSRA (Optical Structure Recognition Application).
  • iKinase Universal. iPad/iPhone application providing sample structure activity data from Eidogen-Sertanty's Kinase Knowledgebase (KKB). Exists in a Pro version (iKinasePro).

Chemical structure representations

2D drawing

  • 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.
  • ChemDoodle Mobile. Free iPhone companion to ChemDoodle. ChemDoodle Mobile is a calculator for drawn organic structures. There are four main windows: Draw, Calculate, Spectra and Help. The Draw window shows a typical ChemDoodle sketcher, where you can draw and store your structures. The Calculate page calculates properties and the Spectra page simulates NMR spectra. All spectra are interactive. The Help page contains a thorough help guide. Provided by iChemLabs.
  • Chirys Draw. Application for drawing publication-quality molecular structures and reactions. Designed from the ground up for the iPad. Developed by Integrated Chemistry Design, Inc.
  • Chirys Sketch. Application for drawing publication-quality molecular structures and reactions, for iPhone and iPod Touch. Developed by Integrated Chemistry Design, Inc.
  • Mobile Molecular DataSheet. Allows viewing and editing chemical structure diagrams on an iPhone, iPod or iPad. Molecules are organized in collections of datasheets. Individual molecules, or whole datasheets, can be shared via iTunes or sent by email, using the standard MDL MOL and SDfile formats, which allows the data to be integrated into any external workflow. 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.
  • Molprime+. Chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet. Can send structure data via email, open structures from email or web, create graphical images or Microsoft Word documents with embedded structure graphics, calculate properties based on structures and use structures to search Mobile Reagents and ChemSpider. 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.
  • Elemental. Chemistry sketch for iphone and ipad. Developed by Dotmatics Limited.
  • ChemJuice. Molecular drawing software for iPhone. Developed by IDBS.
  • ChemJuice Grande. Molecular drawing software for iPad. Developed by IDBS.
  • MolPad. Free chemical structure drawing application. It can draw structures from scratch or load them from ChemSpider and modify them. Structures can be emailed in Molfile format. For Android.
  • DCE ChemPad. Free application to draw chemical structures and calculate molecular weight, molecular formula and to send the molfile. It shows the capabilities of the Dendro Chemical Editor control for Android to build chemistry-aware mobile applications. For Android.

2D drawing online

  • OLN JSDraw. Javascript libary you can display and draw chemical structures in web pages, which works cross browser, including IE, Firefox, Safari, Opera and Chrome, crose platform, including Window, Mac, Linux, and even iPhone, Android and other mobile devices. Free for education. Provided by Scilligence.

3D viewers

  • GLmol. Free and open source 3D molecular viewer based on WebGL and Javascript. GLmol runs on newer versions of Firefox, Chrome, Safari or Opera. Internet Explorer is not supported. GLmol also runs on Sony Ericsson's Android devices which support WebGL and WebGL enabled safari in iOS.
  • iMolview. Application to browse and view in 3D protein and DNA structures from Protein Data Bank, and drug molecules from DrugBank For iPhone and iPad. Provided by Molsoft.
  • PyMOL on the iPad.. High-performance 3D molecular visualizer, designed from the ground up for the iPad. it can search and download data from the PDB, PubChem, Dropbox, or an own secure custom PyMOL enterprise server. Provided by Schrödinger.
  • RCSB PDB.. The RCSB Protein Data Bank (PDB) mobile app is the official mobile app of the RCSB PDB. It provides fast, on-the-go access to the RCSB PDB resources. The app enables the general public, researchers and scholars to search the Protein Data Bank and visualize protein structures using either a WiFi or cellular data connection.
  • Ball&Stick. High-quality molecular visualization app for the iPad, iPhone and iPod Touch. Provided by MolySym.
  • CueMol for iOS. Interactive macromolecular viewer for structural biologists. CueMol viewer allows the users to open and view the scene files made by the desktop version of CueMol, and the Protein Data Bank (PDB) format files, as well.
  • 3D Molecules Edit&Drill. Application designed to enable students and professionals to build, construct, modify and examine molecules in 3D. Allows the users to open and view molecules in SDF format files, for example, from NCBI's PubChem. Developed by Virtualnye Prostranstva LLC.
  • 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.
  • CMol. Interactive 3D molecular viewer designed specifically for the iPad, iPhone and iPod touch. CMol allows the user to open and view PDB files with complete control over the representations and colours used for individual chains, residues and atoms.
  • Molecules. Free application for iPhone and iPad, for viewing three-dimensional renderings of molecules and manipulating them using your fingers. You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. These structures can be viewed in both ball-and-stick and spacefilling visualization modes.
  • iMolecular Builder. The IMoleBuilder is an application that can view, edit and build molecules in 3D. For iPhone.
  • iPharosDreams. Molecular visualization app for iPad to perform in-silico drug discovery. Downloads protein structure files from Protein Data Bank, displays 3D molecules, touch, rotation, zoom in/out. Hierarchy structure of molecules is shown with a table that select components in a protein and related things. It can generate pharmacophores and analyze 3D protein-ligand interaction of biological macromolecules for in-silico drug discovery. Allows selecting a ligand from a protein and generate a binding site from the selected ligand. Can generate receptor based pharmacophores and get inspiration. Developed by EQUISnZAROO CO., LTD.
  • Jmol Molecular Visualization. Free Jmol for Android tablets.
  • NDKmol. Free molecular viewer for Android.
  • Molecule Viewer 3D. Opens most common 3D molecule file formats saved on a SD card or found in a library of 243 included molecules. For Android.
  • 3D Molecule View. 3D molecule viewer. For Android.
  • Atomdroid. Free computational chemistry tool. It can be used as a molecular viewer/builder and contains local optimization and Monte Carlo simulation features. For Android.
  • Atom 3D. Free application to visualize molecules and crystal structures in 3D using the touchscreen to rotate and zoom. Includes 19 sample structures. Supports XYZ files and some protein data bank (PDB) files. For Android.
  • PDBs. Free application for molecular graphics visualization from PDB files. For Android.
  • PDB View 3D. Application for molecular graphics visualization from PDB files. For Android.

File format Converters

  • MolEngine. .NET Cheminformatics Toolkit completely built on Microsoft .NET platform. By using Mono, MolEngine can run on other platform, such as Mac, Linux, iPad. Distributed by Scilligence.

Molecular Modeling


  • iHyperChem Free Version. Free Version of iHyperChem for iPad. Provided by HyperChem.
  • iSpartan. iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. Molecules are created by two-dimensional sketching and converted into a three-dimensional structure. Low-energy conformations can then be calculated and their geometries be queried. A database of 5,000 molecules (a subset of the Spartan Spectra and Properties Database, SSPD) can furthermore be accessed to obtain NMR and IR spectra, molecular orbitals, electrostatic potential maps, and other atomic and molecular properties. The database can be searched for substructures. Developed by Wavefunction, Inc.

Homology Modeling

Web services and databases

  • iProtein. iPad application providing access to the Eidogen-Sertanty's Target Informatics Platform (TIP).

ADME Toxicity


  • 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.