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 4/5/2018. Currently 807
- PL-PatchSurfer2. Virtual screening program using local surface matching between ligand and protein pocket. Zernike descriptor allows to calculate complementarity of the shape and physicochemical complementarity of both partners. Developed and provided as binary executable by Perdue University, United States.
- LigParGen. Web-based service that provides OPLS-AA force field parameters for organic molecules or ligands. Beside PGR files, other ouput format includes parameters and topologies to be used with CHARMM, Gromacs, LAMMPS, CNS/X-PLOR, Q, DESMOND, BOSS, OpenMM and MCPRO. Molecules can be input in SMILES, MOL or PDB format with a maximum of 200 atoms. Provided also as a standalone program by the Department of Chemistry, University of Yale, United States.
- openMM. High performance toolkit for CPU/GPU-accelerated molecular dynamics simulation and setup. Can be used as a library or as an application with an intuitive Python interface. Developed, maintained and provided open-source by Standford University, United States.
- SILCS. The Site Identification by Ligand Competitive Saturation Method (SILCS) allows for location and estimation of affinities of chemical groups on a protein surface. It relies on MD of the macromolecular structure in an explicit solvent/small molecules environment, representative of chemical fragments of diverse properties (hydophobic, aromatic, with H-bonding capacity). Maps are so created indidcating favorable fragment-protein interactions, to be used for structure-based designed. Distributed by SilcsBio, LLC.
- TRAPP. TRAnsient Pockets in Proteins (TRAPP) is a web server for the analysis of transient binding pockets in proteins. Contrarily to many tools, it is not intended for ligand binding pocket identification per se, but rather to predict significant changes in the spatial and physicochemical properties of a given pocket that may arise due to the protein's flexibility (both backbone and side chains). Several capabilities of visualization and analysis have been developed and are provided by the Molecular and Cellular Modeling group at Heidelberg Institute for Theoretical Studies, Germany.
- BiKi. The BiKi Life Sciences suite involves several tools (e.g. accelerated binding/unbinding methods) for performing and analyzing MD specifically dedicated to medicinal chemists with the aim of simplifying drug discovery. Provided by BiKi Technologies, Italy.
- AlloDeco. Server that implements a novel model for allostery. It computes the thermodynamic coupling between functional sites in proteins and then determines the contribution of specific interactions to that coupling. First, a 3-dimensional protein structure (PDB file) is transformed into a Gaussian Network Model. The coupled motions of two sites are then decomposed using Canonical Correlation Analysis. Finally, the statistical mechanics-based thermodynamic coupling function formalism is applied to identify interactions that mediate the thermodynamic coupling between the canonical pairs of motions. Developed at Weill Cornell Medical College, New York, United States.
- FORECASTER. Standalone interface that contains applications to perform docking and more. It includes the FITTED docking program, the sites of metabolism prediction IMPACTS, and the accessory programs to work with the proteins and the ligands. It comes with a java-based graphical interface that integrated all the program into workflows. Provided by Molecular Forecaster Inc.
- IMPACTS. In-silico Metabolism Prediction by A ctivated Cytochromes and Transition States (IMPACTS) predicts site of metabolism on small molecules by CYP450. This program combines docking to metabolic enzymes, transition state modeling, and rule-based substrate reactivity prediction. It is included in the Forecaser suite and provided by Molecular Forecaster Inc.
- SuperDRUG2. Database of more than 4,600 active pharmaceutical ingredients. Annotations include drugs with regulatory details, chemical structures (2D and 3D), dosage, biological targets, physicochemical properties, external identifiers, side-effects and pharmacokinetic data. Different search mechanisms allow navigation through the chemical space of approved drugs. A 2D chemical structure search is provided in addition to a 3D superposition feature that superposes a drug with ligands already known to be found in the experimentally determined protein-ligand complexes. It has been added simulations of "physiologically-based" pharmacokinetics of drugs. The interaction check feature identifies potential drug-drug interactions and also provides alternative recommendations for elderly patients. Maintained by the University of Charité, Berlin, Germany.