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 8/24/2016. Currently 721 links.

Last additions

  • pDynamo. pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions. Developed by the Institut de Biologie Structurale, Grenoble, France.
  • Pcetk. Pcetk (a pDynamo-based continuum electrostatic toolkit) is a Python module extending the pDynamo library with a Poisson-Boltzmann continuum electrostatic model that allows for protonation state calculations in proteins. The module links pDynamo to the external solver of the Poisson-Boltzmann equation, extended-MEAD, which is used for the calculation of electrostatic energy terms. The calculation of protonation states and titration curves is done by using the module's own analytic or Monte Carlo routines or through an interface to the external sampling program, GMCT. Developed by the Institut de Biologie Structurale, Grenoble, France.
  • ProBiS-CHARMMing. Web server for detection of structurally similar binding sites, plus minimization of predicted protein-ligand complexes and their interaction energy calculation. Maintained by the National Institute of Health, USA.
  • ChemDes. is a free web-based platform for the calculation of molecular descriptors and fingerprints, which provides more than 3,679 molecular descriptors that are divided into 61 logical blocks.In addition, it provides 59 types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints, etc. Provided by the School of Pharmaceutical Sciences, Central South University, Hunan, China.
  • Smiles2Monomers. Smiles2Monomers is a software to infer monomeric structure of polymers from their atomic structure. The web server is available for peptide-like compounds in the second tab and provides an interface to upload a compound in the SMILES format to compute the monomeric structure in two different formats: text formats (the structure is downloadable in json and xml) or image format (the colored picture of the monomeric structure mapped on the atomic structure is directly available in the browser or downloadable into a zip file). Provided by the University of Lille, France.
  • ProBiS-CHARMMing. Web server for detection of structurally similar binding sites, plus minimization of predicted protein-ligand complexes and their interaction energy calculation. Maintained by the National Institute of Health, USA.
  • TopoTools. TopoTools is a VMD plugin for manipulating topology information. It is meant to be a complementary tool to psfgen, which is very much optimized for building topologies for biomolecules. It makes access to the topology related data stored in VMD easily. It also has a number of high-level tools that allow reading and writing of topology file formats that cannot be parsed by the molfile plugins, parsing of parameter and residue database files for generation of complete input files for MD codes like LAMMPS and HOOMD-blue, and replicating or combining multiple systems. Developed by the Temple University, Philadelphia, USA.
  • LipidBuilder. A web-server based on a VMD plug-in and CHARMM force field to create, store and share lipid libraries. LipidBuilder automatically generates the topology and template of a given lipid. The lipid topology is created by combining the selected head group, extracted from a built-in library of structures and the provided hydrocarbon chains. Four different classes of hydrocarbons have been parametrized in the CHARMM force field: saturated, unsaturated, branched and cyclopropane. Developed by the EPFL, Lausanne, Switzerland.
  • GPCR-Bench. GPCR-Bench provides a high quality GPCR docking benchmarking set: 25 PDB structures covering all NR structures as of January 2015, and active and decoy compounds in the spirit of DUD. Provided by Heptares Therapeutics Ltd., UK.
  • SwissSimilarity. Web tool for rapid ligand-based virtual screening of small to unprecedented ultralarge libraries of small molecules. Screenable compounds include drugs, bioactive and commercial molecules, as well as 205 million of virtual compounds readily synthesizable from commercially available synthetic reagents. Predictions can be carried out on-the-fly using six different screening approaches, including 2D molecular fingerprints as well as superpositional and fast nonsuperpositional 3D similarity methodologies. SwissSimilarity is part of a large initiative of the SIB Swiss Institute of Bioinformatics to provide online tools for computer-aided drug design, such as SwissDock, SwissBioisostere or SwissTargetPrediction with which it can interoperate, and is linked to other well-established online tools and databases. User interface and backend have been designed for simplicity and ease of use, to provide proficient virtual screening capabilities to specialists and nonexperts in the field. The SwissSimilarity website, developed by the Molecular Modeling Group of SIB Swiss Institute of Bioinformatics, is accessible free of charge or login.
  • SwissADME. A web tool that gives access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, druglikeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP, Bioavailability radar and Synthetic Accessibility score. Easy efficient input and interpretation are ensured thanks to the user-friendly interface through a login-free website. Sepcialists, but also nonexperts in chemoinformatics and computational chemistry can predict rapidly key parameters for a collecion of molecules to support their medicinal chemistry endeavors. Developed and maintained by the Molecular Modeling Group of the SIB Swiss Institute of Bioinformatics.
  • Metrabase. The Metabolism and Transport Database (Metrabase) is a cheminformatics and bioinformatics resource that provides structured data about the interactions between proteins and chemical compounds related to their metabolic fate and transport across biological membranes. The aim is to build a comprehensive resource providing high quality structural, physicochemical and biological data that entails minimal processing load for users. The data held in this database can be utilised to infer the relationships between transporters/enzymes and their ligands. The database also contains compounds that were experimentally found not to be substrates (as well as non-inhibitors and non-inducers), which makes it a valuable resource for building predictive models based on the characteristics of both the positive and the negative class. It contains 3438 compounds, 11649 interaction records, 1211 literature references. Developed and maintained by the University of Cambridge, UK.
  • ProPairs. A Data Set for Protein-Protein Docking that dentifies and presents protein docking complexes and their unbound structures. They can be used as benchmark sets to develop or to test docking algorithms. Hosted by Macromolecular Modelling Group, Freie Universität Berlin, Germany.
  • UCSF-FDA Transportal. The purpose of this database is to be a useful repository of information on transporters important in the drug discovery process as a part of the US Food and Drug Administration-led Critical Path Initiative. Information includes transporter expression, localization, substrates, inhibitors, and drug-drug interactions It contains 3438 compounds, 11649 interaction records, 1211 literature references. The FDA has partnered with the Giacomini lab at UCSF to create a transporter database of pharmacologically relevant transporters to support development of new pharmaceuticals. Information on important transporters, their localization, expression levels, substrates, and inhibitors have been curated from the literature and compiled into a single location to aid and inform drug developers, regulatory agencies and academic scientists about transporters important in drug action and disposition.. The database will also help drug developers in determining what experiments or analyses must be conducted to check for possible drug interactions through transporters as well as identify promising transporter candidates for the testing of possible genetic influences.
  • TSdb. The Transporter substrate database (TSdb) was developed to serve as a central repository of formated substrate information of transporters as well as their annotation. Most characteristic feature for our database is all the substrates are mapped to KEGG ligand compound database, thus it is easy to map all the substrate to the KEGG pathway. The database allows you to: (i) search and browse the transporter by their substrates and organisms; (ii) get an overview for all the transporter substrate in a pathway; (iii) crosslink the formated substrate to other compound or metabolic pathway; (iv) query the gene interaction relations for transporters and (v) discover the potential regulatory mechanisms among the transporter substrate and their inhibited metabolic enzymes. Developed by the Beijing Institute of Technology.
  • Zinc15 Database. A new version of ZINC database including 100+ million purchasable compounds in ready-to-dock, 3D formats, provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).
  • pkCSM. A novel approach to the prediction of pharmacokinetic properties, which relies on graph-based signatures. These encode distance patterns between atoms and are used to represent the small molecule and to train predictive models. They were successfully used across five main different pharmacokinetic properties classes to develop predictive regression and classification models. A web server to provide an integrated freely available platform to rapidly screen multiple pharmacokinetic properties was developed by the University of Cambridge, UK.
  • GLASS. GLASS (GPCR-Ligand Association) database is a manually curated repository for experimentally-validated GPCR-ligand interactions. Along with relevant GPCR and chemical information, GPCR-ligand association data are extracted and integrated into GLASS from literature and public databases. A list of currently-known GPCRs was compiled from UniProt and used to filter through the other chemical databases for ligand-association data (ChEMBL, BindingDB, IUPHAR, DrugBank, PDSP), GPCR diseases association (TTD), GPCR experimental structural data (PDB, BioLiP), and predicted models of GPCRs (GPCRRD). Subsequently, information from the extracted databases were unified to the same format and checked to ensure that all entries are only GPCR-related. Thus, the user would not find any entries on receptor tyrosine kinases or any other protein that is not a GPCR. All relevant ligand chemical data (PubChem) and GPCR data (UniProt) were extracted accordingly for each GPCR-ligand entry. Each molecule with a unique InChI key was considered a unique ligand entry in the database. Developed and maintained by the Zhang Lab at the University of Michigan, USA.
  • Knodle. KNOwledge-Driven Ligand Extractor is a software library for the recognition of atomic types, their hybridization states and bond orders in the structures of small molecules. Its prediction model is based on nonlinear Support Vector Machines. The process of bond and atom properties perception is divided into several steps. At the beginning, only information about the coordinates and elements for each atom is available: (i) Connectivity is recognized; (ii) A search of rings is performed to find the Smallest Set of Smallest Rings (SSSR); (iii) Atomic hybridizations are predicted by the corresponding SVM model; (iv) Bond orders are predicted by the corresponding SVM model; (v) Aromatic cycles are found and (vi) Atomic types are set in obedience to the functional groups. Some bonds are reassigned during this stage. Linux and MacOS version are free of charge. Maintained by the Nano-D team, Inria/CNRS Grenoble, France.
  • Siena. SIENA is a software pipeline enabling the fully automated construction of protein structure ensembles from the PDB. Starting with a single query structure, all binding sites with high sequence similarity are extracted from the PDB, aligned, and superimposed. SIENA is able to deal with complicated cases like binding sites at protein domain interfaces or within homo-multimeric proteins. Standalone and web-based tools developed and maintained by the University of Hamburg, Germany.
  • LEADS-PEP. A benchmark dataset for assessing peptide docking performance. The set includes 53 protein-peptide complexes with peptide ranging from 3 to 12 residues. Several well-known small molecule docking program were tested. Provided by the Fraunhofer Institute for Molecular Biology and Applied Ecology, Germany.
  • AutoT&T2. The Automatic Tailoring and Transplanting (AutoT&T) method is developed as a versatile computational tool for lead optimization as well as lead discovery in molecular-targeted drug design. This method detects suitable fragments on reference molecules, e.g. outputs of a virtual screening job in prior, and then transplants them onto the given lead compound to generate new ligand molecules. Then, binding affinities, synthetic feasibilities and drug-likeness properties are evaluated to select the promising candidates for further consideration. Standalone software and demo web version
  • VFFDT. It consists in a user-friendly Visual Force Field Derivation Toolkit (VFFDT) to derive the force field parameters via simply clicking on the bond or angle in the 3D viewer, and we have further extended our previous program to support the Hessian matrix output from a variety of quantum mechanics (QM) packages, including Gaussian 03/09, ORCA 3.0, QChem, GAMESS-US, and MOPAC 2009/2012. In this toolkit, a universal VFFDT XYZ file format containing the raw Hessian matrix is available for all of the QM packages, and an instant force field parametrization protocol based on a semiempirical quantum mechanics (SQM) method is introduced. The new function that can automatically obtain the relevant parameters for zinc, copper, iron, etc., which can be exported in AMBER Frcmod format, has been added. Furthermore, our VFFDT program can read and write files in AMBER Prepc, AMBER Frcmod, and AMBER Mol2 format and can also be used to customize, view, copy, and paste the force field parameters in the context of the 3D viewer, which provides utilities complementary to ANTECHAMBER, MCPB, and MCPB.py in the AmberTools.Proposed by the School of Pharmaceutical Sciences, Wenzhou Medical University
  • SCUBIDOO. a freely accessible database concept that currently holds 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions. This large data set was reduced to three representative and computationally tractable samples denoted as S, M, and L, containing 9994, 99 977, and 999 794 products, respectively. These small sets are useful as starting points for ligand identification and optimization projects. Proposed by the University of University of Marburg, Germany.
  • PockDrug. A methodology tehat predicts pocket druggability, efficient on both; estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure using several thresholds) and estimated pockets not guided by the ligand proximity (based on amino atoms that form the surface of potential binding cavities).. Developed and maintained by the University Paris-Diderot, France.
  • LiSiCA. LiSiCA (Ligand Similarity using Clique Algorithm) is a ligand-based virtual screening software that searches for 2D and 3D similarities between a reference compound and a database of target compounds which should be represented in a Mol2 format. The similarities are expressed using the Tanimoto coefficients and the target compounds are ranked accordingly. A PyMol plu-in is freely available, too. Developed by the University of Ljubljana, Slovenia.
  • POSIT. POSIT uses the information from bound ligands to improve pose prediction. Using a combination of approaches, including structure generation, shape alignment and flexible fitting, a ligand of interest is compared to bound ligands and its similarity to such both guides the nature of the applied algorithm and produces an estimate. Both 2D and 3D similarity measures are used in this reliability index. Provided by OpenEye scientific software.
  • ChemCom. a computer application which facilitates searching and comparing chemical libraries. ChemCom aims to expedite the current, time consuming processes of comparing large, chemical databases. As such, this application can be used to speedup many processes including drug research and discovery. A free java web application is also available. Developed by the University of Kansas, USA.
  • FlexAID. A small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. Precompiled Linux, MacOS and Windows versions are made available by the University of Sherbrooke, Canada.
  • IsoMIF. IsoMIF identifies binding site molecular interaction field similarities between proteins. The IsoMIF Finder Interface allows you to identify binding site molecular interaction field (MIF) similarities between a query structure and a database of pre-calculated MIFs or you own custom PDB entries. Developed by the University of Sherbrooke, Canada.
  • VAMMPIRE-LORD. LORD (Lead Optimization by Rational Design) is a prediction tool based on the VAMMPIRE database (of matched molecular pairs) and using a atom-pair descriptor to represent the substitution environment. It operates on the principle that molecular transformations cause similar effects in similar substitution environments and is therefore able to extrapolate the knowledge of a given substitution effect to any similar system. LORD was implemented as an easy-to-use web server that guides the user step-by-step through the optimization process of a defined lead compound.
  • Computer-Aided Drug-Design Platform using PyMOL. a simple Java tool for visual exploration of three-dimensional (3D) virtual screening data. The VSviewer3D brings together the ability to explore numerical data, such as calculated properties and virtual screening scores, structure depiction, interactive topological and 3D similarity searching, and 3D visualization. By doing so the user is better able to quickly identify outliers, assess tractability of large numbers of compounds, visualize hits of interest, annotate hits, and mix and match interesting scaffolds. We demonstrate the utility of the VSviewer3D by describing a use case in a docking based virtual screen. Developed by Data2Discovery Consulting Inc., USA.
  • ChemDoodle. A software suite for drawing chemical structure diagrams, including the ability to calculate NMR spectra, generate IUPAC names and line notations for structures, manipulate structures imported from the Internet, interpret and interconvert files generated by other chemical drawing software programs, illustrate glassware and equipment setups, and draw TLC plates. Distributed by iChemLabs LLC.
  • bSiteFinder. Algorithm involving Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering built on the largest database of cocrystals with stringent quality control. Free web service and code provided by the department of Bioinformatics, Tongji University, Shanghai, China.
  • Chemozart. Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. Provided by the Department of Chemistry, Shahid Beheshti University, Tehran, Iran
  • DASPfind. DASPfind is a tool that aims to predict new Drug-Target interactions from a network that encodes information about the known Drug-Target interactions, similarities between the drugs and similarities between targets. The algorithm for predicting new drug-target interactions is based on all simple paths of particular lengths on such network. The main idea in our method is to utilize the similarity information within the sub networks and combine it with information from the topology of the heterogeneous network to predict and rank new interaction edges. Provided by King Abdullah University of Science and Technology.
  • AtomicChargeCalculator. ACC is a complex yet intuitive utility for the calculation, visualization and analysis of atomic charges for small drug­like molecules, as well as for large biomolecular complexes. Up to thousands molecules can be processed in one run. Empirical atomic charges that respond to changes in molecular conformation are calculated via an efficient implementation of the well established Electronegativity Equalization Method (EEM). ACC allows to use any of the EEM parameters sets published in literature. You may download your results, or visualize and analyze them directly in the web browser. Developed by the Masaryk University, Brno, Czech Republic.
  • Open Drug Discovery Toolkit. ODDT is a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. It reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. Provided by the Institute of Biochemistry and Biophysics PAS, Warsaw, Poland.
  • CheS-Mapper. CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds. The tool can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. CheS-Mapper embedds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment. It is an open-source Java application, based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R. Developed and proposed by the Universität Mainz, Germany.
  • iDrug. A versatile online tool for computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). By using iDrug, various molecular design processing tasks can be submitted and visualized simply in one browser without installing locally any standalone modeling softwares. iDrug is provided free of charge by the School of Pharmacy, East China University of Science & Technology.
  • ParaDockS. ParaDockS includes algorithms for protein-ligand docking and is organized that every newly developed scoring function can be immediately implemented. Furthermore, interaction-based classifier, trained on a target-specific knowledge base can be used in a post-docking filter step. An implementation and validation of target-biased scoring methods within the open-source docking framework is implemented. developed and provided free of charge by the University of Halle-Wittenberg, Germany.
  • PharmDock. A protein pharmacophore-based docking program. PharmDock and a PyMOL plugin are made freely available by the Purdue University, West Lafayette, USA.