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 7/18/2014. Currently 777 links.

Last additions

  • DataWarrior. Free Cheminformatics Program for Data Visualization and Analysis. DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Compounds can be clustered and diverse subsets can be picked. Calculated compound similarities can be used for multidimensional scaling methods, e.g. Kohonen nets. Physicochemical properties can be calculated, structure activity relationship tables can be created and activity cliffs be visualized.
  • sc-PDB-Frag. Database of protein-bound fragments to help selecting truely bioisosteric scaffolds. The database allows to (i) search fragment among PDB ligands or sketch it; (ii) define similarity rules to retrieve potential bioisosteres; (iii) score bioisosteres according to interaction pattern similarity; (iv) align bioisosteres to the reference scaffold; (v) Visualize the proposed alignment.
  • SwissTargetPrediction. Oonline tool to predict the targets of bioactive small molecules in human and other vertebrates. This is useful to understand the molecular mechanisms underlying a given phenotype or bioactivity, to rationalize possible side-effects or to predict off-targets of known molecules. Provided by the Molecular Modeling group of the Swiss Institute of BioInformatics.
  • ACPC. (AutoCorrelation of Partial Charges) Open source tool for ligand-based virtual screening using autocorrelation of partial charges. ACPC uses a rotation-translation invariant molecular descriptor.
  • DDDPlus. Models and simulates the in vitro dissolution of active pharmaceutical ingredients (API) and formulation excipients dosed as powders, tablets, capsules, and swellable or non-swellable polymer matrices under various experimental conditions. Distributed by Simulations Plus, Inc.
  • Chemicalize. Calculates or predict molecular properties, including logP, tautomers, PSA, pK, lipinski-like filters, etc. Provided by ChemAxon.
  • COSMOS. (COordinates of Small MOleculeS). High-throughput method to predict the 3D structure of small molecules from their 1D/2D representations. Also exists as a standalone program. Provided by the University of california, Irvine.
  • AquaSol. Predicts aqueous solubility of small molecules using UG-RNN ensembles. Provided by the University of california, Irvine.
  • Molinfo. Calculates or predict molecular properties other than 3D structure. Provided by the University of california, Irvine.
  • ChemProt. The ChemProt 2.0 server is a ressource of annotated and predicted chemical-protein interactions. The server is a compilation of over 1 100 000 unique chemicals with biological activity for more than 15000 proteins. ChemProt can assist in the in silico evaluation of small molecules (drugs, environmental chemicals and natural products) with the integration of molecular, cellular and disease-associated proteins complexes. Provided by the Technical University of Denmark, and the University Paris Diderot.
  • FLAP. (Fingerprints for Ligands and Proteins). Provides a common reference framework for comparing molecules, using GRID Molecular Interaction Fields (MIFs). The fingerprints are characterised by quadruplets of pharmacophoric features and can be used for ligand-ligand, ligand-receptor, and receptor-receptor comparison. In addition, the quadruplets can be used to align molecules, and a more detailed comparison of the GRID MIF overlap calculated. When the template is a ligand, this enables ligand-based virtual screening and alignment. When the template is a receptor site, this enables structure-based screening and pose prediction. Provided by Molecular Discovery.
  • istar. Free web platform for large-scale protein-ligand docking based on the idock software. The web site can be downloaded and installed independently from GitHub. Developed by the Chinese university of Hong Kong.
  • istar. Free web platform for large-scale protein-ligand docking based on the idock software. This link corresponds to the web site code that can be installed independently. Developed by the Chinese university of Hong Kong.
  • idock. Free and open source multithreaded virtual screening tool for flexible ligand docking for computational drug discovery. Developed by the Chinese university of Hong Kong.
  • iview. Interactive WebGL visualizer of protein-ligand complex. Developed by the Chinese university of Hong Kong.
  • rDock. Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. Free and open source.Developed by the University of Barcelona.
  • CABS-flex. Server for fast simulation of protein structure fluctuations. CABS-flex is a procedure for the simulation of structure flexibility of folded globular proteins. Using an input protein structure the CABS-flex outputs a set of protein models (reflecting the flexibility of the input structure, in all-atom PDB format) ready to use in structure-based studies of protein functions and interactions. Developed by the university of Warsaw.
  • ZINClick. ZINClick is a database of triazoles generated using existing alkynes and azides, synthesizable in no more than three synthetic steps from commercially available products. This resulted in a combinatorial database of over 16 million of 1,4-disubstituted-1,2,3-triazoles (Molecular Weight < 1000), each of which is easily synthesizable, but at the same time new and patentable. Provided by the Università degli Studi del Piemonte Orientale "A. Avogadro".
  • NRLiSt. (Nuclear Receptors Ligands and Structures Benchmarking DataBase). Non-commercial manually curated benchmarking database dedicated to the Nuclear Receptor(NR) ligands and structures pharmacological profiles. Provided by the Conservatoire National des Arts et Métiers - Paris.
  • DTome. (Drug-Target Interactome). Provides a computational framework to effectively construct a drug-target networks by integrating the drug-drug interactions, drug-target interactions, drug-gene associations and target/gene-protein interactions. DTome also provides the network analysis illustration using the available network analysis software. Provided by the Vanderbilt University.
  • SIDER. Contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. Provided by the European Molecular Biology Laboratory, Heidelberg, Germany.
  • DRAR-CPI. Server for predicting Drug Repositioning and Adverse Reaction via Chemical-Protein Interactome. Provided by the Fudan University.
  • SePreSA. (Server for the Prediction of Population Susceptible to Serious Adverse Drug Reaction). This server has a comprehensive collection of the structure models of nearly all the well known SADR targets. Once a drug molecule is submitted, the interaction strength of it to all SADR targets will be calculated. The server will also suggest the drug-protein binding pattern of the lowest estimated free energy, with AA residuals within 6.4Å of the drug molecule highlighted and visualized in customer's browser. Provided by the Fudan University.
  • Natural product likeness calculator. Calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. NP-likeness is a useful criterion to screen compound libraries and to design new lead compounds. Free and open source.
  • TorsionAnalyzer. Generate and analyse 3D conformers of small molecules. TorsionAnalyzer is based on an expert-derived collection of SMARTS patterns and rules (assigned peaks and tolerances). Rules result from statistical analysis of histograms derived from small molecule X-ray data extracted from the CSD. Rotatable bonds of molecules loaded into the TorsionAnalyzer are color-coded on the fly by means of a traffic light highlighting regular, borderline and unusual torsion angles. This allows the user to see at a glance if one or more torsion angles are out of the ordinary. Provided by BioSolveIT.
  • MPACK. (Modeling Package). Integrated protein modeling suite that currently handles comparative and ab initio modeling procedures. The objective of this suite is to systematically bring different steps (or programs) under one roof in order to facilitate rapid model generation with minimal user effort and to create a biological data-flow pipeline for large scale-scale modeling of protein sequences from genomic projects. Provided by the University of Texas.