Handles and searches large virtual combinatorial libraries. FTrees performs similarity searches in the generated Fragment Space. It stores the physicochemical properties of the substructure represented by a node in a property profile for that node. This tool is able to select that topology-preserving mapping belonging to the best matching overlay of two molecules both represented by their corresponding Feature Trees.
Superposes pairs of molecules and takes full flexibility of one of the structures into account. FlexS serves for superimposing pairs of ligands, one of which is treated as flexible (test ligand) and is placed onto the other ligand which is treated as a rigid structure (reference ligand). This tool allows users to (1) screen databases of considerable size and (2) to analyze a single superposition in detail.
Determines the interaction strength between two bound molecules of a given orientation. DockoMatic eases set-up, calculation, and result analysis for large numbers of docking jobs. It permits users to construct a library of mutated peptides for docking to a multi-subunit protein receptor without manually generating the mutated peptide structures. This tool is useful for drug repurposing.
Builds small 3D compounds. Frog can construct single or ensembles of low to medium energy 3D conformations starting from a 1D/2D or 3D given structure. It clarifies compound stereochemistry including chiral sites with a user-defined maximum number of generated conformers. This tool is useful for in silico studies, such as ligand-based or structure-based virtual screening; or lead compounds optimization.
Allows users to guide the Scaffold Hopping procedure during the drug discovery process. SHOP is a program that substitutes one part of a molecule with another one and retains their pharmacophoric interaction points. Moreover, this tool can maintain 3D interaction capabilities, consider the synthetic feasibility and the ADME profiles of the potential candidates.
Offers a platform dedicated to the screening of proteins for ligand docking. SLIDE investigates ligand candidates into the binding site of the target protein by using distance geometry. It can be used for: (i) matching interactions made by previously known ligands with a specific protein; (ii) docking using unbiaised or merged templates or ligand conformers; (iii) generating interaction tables for matchprint analysis.
Streamlines the steps of performing a virtual screening and analyzes results. Raccoon is a graphical user interface (GUI) that includes (i) automated server connection manager and installation of docking services, (ii) ligand library for upload and management of large ligand collections, (iii) receptor management from multiple targets and flexible residues, (iv) graphical management of jobs on computational resources, (v) automated retrieval and preprocessing of results to extract features of interest, and many others.
A web-oriented peptidomimetic compound virtual screening tool based on a multi-conformers three-dimensional (3D)-similarity search strategy. Key to the development of pepMMsMIMIC has been the creation of a library of 17 million conformers calculated from 3.9 million commercially available chemicals collected in the MMsINC(R) database.
Performs ligand-based screening using a 3D molecular similarity engine. wwLigCSRre provides an online versatile facility to assist the exploration of the chemical similarity of families of compounds. It also proposes some scaffold hopping from a query compound. This tool allows the user to screen several chemically diversified focused banks, such as Kinase-, CNS-, GPCR-, Ion-channel-, Antibacterial-, Anticancer- and Analgesicfocused libraries.
A USRbased webserver for large-scale prospective virtual screening. USR-VS performs large-scale ligand-based Virtual Screening (VS), which is oriented to the prospective validation of the obtained results. It provides interactive visualization of the similarity of the query molecule against the hit molecules as well as vendor information to purchase selected hits in order to be experimentally tested.
Provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores, molecular shape and energy minimization. Users can import, create and edit virtual screening queries in an interactive browser-based interface. Queries are specified in terms of a pharmacophore, a spatial arrangement of the essential features of an interaction, and molecular shape. Search results can be further ranked and filtered using energy minimization. In addition to a number of pre-built databases of popular compound libraries, users may submit their own compound libraries for screening. Pharmit uses state-of-the-art sub-linear algorithms to provide interactive screening of millions of compounds. Queries typically take a few seconds to a few minutes depending on their complexity. This allows users to iteratively refine their search during a single session. The easy access to large chemical datasets provided by Pharmit simplifies and accelerates structure-based drug design.
Aids the computational identification of small-molecule ligands. NNscore is based on a neural-network scoring function and provides a single estimate of the pKd. It attempts to simulate, albeit inadequately, the microscopic organization of the brain. The tool can be used to successfully characterize the binding affinities of protein-ligand complexes. It appears that its major strength is largely orthogonal to other kinds of functions based on force fields, linear regression, and statistical analyses.
A multi-objective genetic algorithm for the generation of conformer ensembles. Balloon creates 3D atomic coordinates from molecular connectivity via distance geometry and conformer ensembles. The input can be SMILES, SDF or MOL2 format. Output is SDF or MOL2. Flexibility of aliphatic rings and stereochemistry about double bonds and tetrahedral chiral atoms is handled.
Enables any user to estimate polypharmacology profiles and side effects of compounds based on the molecular similarity concept. ElectroShape is a method that compares the distance and charge distributions of a molecule from 4 different surrounding points, which allows its 3D similarity to other molecules to be assessed in a very fast and efficient way. In addition, the calculated molecular descriptors can be stored for further use, which speeds up subsequent searches. ElectroShape provides a significant addition to the family of ultra-fast ligand-based virtual screening methods, and its higher-dimensional shape recognition approach has great potential for extension and generalisation.
Provides a graphical user interface for the virtual screening (VS) of chemical libraries integrated within a relational database. VSDMIP implements a visual interface for managing the most common tasks in VS. The software allows users to execute both structure-based VS (SBVS) and ligand-based VS (LBVS) protocols, or any combination of the two, by means of a GUI implemented in the PyMOL molecular graphics program.
Provides biologically relevant molecular alignments of the ligands. mRAISE is a tool for ligand-based virtual screening based on the RApid Index-based Screening Engine (RAISE) technology. The triangle-descriptor abstraction of small molecules allows fast non-sequential screening of millions of compounds. Calculated alignments are scored using a Gaussian-type scoring function which scores the general shape overlap as well as the compatibility of physicochemical features of aligned molecules.
Enables automatic comparison of RMDS-based molecular docking performances of different docking/scoring methods. MMsDockBench is a platform that automates the procedure from the setup of docking benchmarks to virtual screening (VS) campaigns. The software can assist users in identifying the best docking/scoring combination to perform a docking-based VS campaign.
Automates docking jobs with AutoDock. DOVIS is a utility software and a Linux cluster-based application that can reliably screen millions of compounds against a receptor and automatically save the top percentage of high-scoring hits. It runs in parallel on hundreds of central processing units (CPUs) and docks large numbers (millions) of ligands to a target receptor. It also automatically partitions input ligands, prepares parameter files for AutoDock, launches parallel AutoDock runs, parses results, and saves a set of top-ranking docked ligands.
Generates computational models from user-defined small molecule datasets based on structural features identified in hit and non-hit molecules in different screens. Each new model is applied to all datasets in the database to classify compound specificity. MolClass thus defines a likelihood value for each compound entry and creates an activity fingerprint across diverse sets of screens. MolClass uses a variety of machine-learning methods to find molecular patterns and can therefore also assign a priori predictions of bioactivities for previously untested molecules.
Creates in silico simulated high throughput screening data sets for use in testing and selecting appropriate statistical techniques for quality determination and hit identification. NoiseMaker can be useful for broader comparisons of available hit identification methods. This simulation software offers two main features: (i) the ability to generate a random set of ‘true hits’ that conform to expected characteristics and (ii) the ability to apply user-specified noise to a list of true hits to model realistically messy screening results.