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An online interface for searching the purchasable compounds of the ZINC database using the Pharmer pharmacophore search technology. A pharmacophore describes the spatial arrangement of the essential features of an interaction. Compounds that match a well-defined pharmacophore serve as potential lead compounds for drug discovery. ZINCPharmer provides tools for constructing and refining pharmacophore hypotheses directly from molecular structure. A search of 176 million conformers of 18.3 million compounds typically takes less than a minute. The results can be immediately viewed, or the aligned structures may be downloaded for off-line analysis. ZINCPharmer enables the rapid and interactive search of purchasable chemical space.
A web server dedicated to small molecule docking and virtual screening. MTiOpenScreen includes two services, MTiAutoDock and MTiOpenScreen, allowing performing docking into a user-defined binding site or blind docking using AutoDock 4.2 and automated virtual screening with AutoDock Vina. MTiOpenScreen provides valuable starting collections for screening, two in-house prepared drug-like chemical libraries containing 150 000 PubChem compounds: the Diverse-lib containing diverse molecules and the iPPI-lib enriched in molecules likely to inhibit protein-protein interactions.
A first web server to perform computer-aided de novo drug design, to build focused combinatorial libraries of molecules and to perform virtual screenings. The de novo drug design tool creates new molecules by using a genetic algorithm to evolve a population of molecules which are gradually improved by competing for the ‘survival of the fittest’. The second tool assists the user in the design of a combinatorial library where a central core is connected to reactants coming, for example, from a supplier. The generated virtual library can be automatically evaluated by using the same scoring function as the one used in the de novo drug design step. It aims to prioritize the reactants.
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.
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.
Np-likeness / Natural product-likeness
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. This scoring system can be used as a filter for metabolites in Computer Assisted Structure Elucidation (CASE) or to select natural-product-like molecules from molecular libraries for the use as leads in drug discovery.
RADER / RApid DEcoy Retriever
Facilitates decoy based assessment of virtual screening. RADER adopts a database-management regime that supports rapid and large-scale retrieval of decoys, enables high portability of databases, and provides multifaceted options for designing initial query templates from a large number of active ligands and generating subtle decoy sets. It can format and utilize large databases for future work and to append additional databases to the existing one at any time; select unique and diverse compounds as queries from a large number of active ligands, and then generate subtle decoy sets. Therefore, RADER provides a fast, versatile, and user-friendly method to automatically create tailor-made decoy sets for any given sets of bioactives.
A fully automated docking system including self-assessment. DockBlaster is tested for pose-fidelity, the ability to reproduce experimentally observed poses within some tolerance limit, and enrichment, the ability to enrich actives from among a database of decoys, where a decoy is a member of the database that does not bind to the target. We have developed DOCK Blaster to help nonspecialists find new reagents for biology without the need for an expert. As for experts, DOCK Blaster does not produce compelling results for all targets. But for the nearly 20% of targets we tried where it does produce results deserving of further investigation, DOCK Blaster offers a way to automatically leverage structure for ligand discovery.
Facilitates the need for the design and virtual screening of novel potent small–molecule inhibitors of TNF. TNFPubChem is a ligand-based model developed for the prediction of small-molecule TNF inhibition. The interested user can make their own predictions using the user friendly graphical interface that allows multiple options for submitting a new structure. User can submit a structure by using one of the following ways: (i) draw a structure using the sketcher, (ii) submit a SMILES notation of a molecule, or (iii) upload an sdf file. In any case, more than one compound can also be submitted.
Screening Assistant
Stores and analyzes small to very large chemical libraries. Screening Assistant stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. The tool can analyze the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed High Throughput Screening (HTS) SMARTS filters.
SABRE / Shape-Approach-Based Routines Enhanced
Consists of a rational ligand/structure shape-based virtual screening approach. SABRE is a program that combines ligand shape-based similarity SABRE and the 3D shape of the receptor binding site. The program can be useful for the identification of active compounds that are similar to reference molecules and the prediction of activity against other targets. Its performance were assessed using he Database of Useful Decoys (DUD) and the filtered version (WOMBAT) of 10 DUD targets.
Allows analysis of traditional chinese medicine (TCM) data. TCMAnalyzer is a web service that assists scientists in answering questions about TCM regarding active ingredients, protein targets, therapeutic mechanisms, and key structural fragments responsible for the therapeutic activities. It allows (1) identification of the potential compounds responsible for the bioactivities for a TCM herb through scaffold-activity relation searches, (2) study of the molecular mechanism of actions for a TCM herb at systemic level, and of the potential targeted bioactive herbs.
Protein Preparation Wizard
Permits to change a raw Protein Data Bank (PDB) structure into all-atom. Protein Preparation Wizard ensures the accuracy of all downstream modeling simulations. It aims to improve protein and ligand preparation in order to produce better virtual screening enrichments. The tool proceeds to an H-bond network optimization and geometry minimization to prepare proteins. It is able to automatically add missing hydrogen atoms and correct metal ionization states to ensure proper formal charge and force field treatment.
SCARE / SCan Alanines and REfine algorithm
Docks a ligand to receptor structure by homology represented by a single conformer. SCARE is an induced fit docking algorithm based on 4 steps: it (i) produces multiple variants of receptor pocket, (ii) docks flexible ligand to each variant of the receptor pocket and record best scored poses, geometrically cluster them and select best scoring position, (iii) restrains ligand for each of unique ligand poses and (iv) re-scores all optimized ligand-receptor pairs and select top scoring pose.
AuPosSOM / Automatic analysis of poses using self-organizing maps
Evaluates docking results based on the clustering of compounds by the similarity of their contacts with the receptor. AuPosSOM represents a good alternative to the energy-based scoring functions for the evaluation of docking results. It can be used for pharmacophore characterization and for contact activity relationship (CAR) analysis. The tool has been used to proceed integrative computational protocol for the discovery of the inhibitors of the Helicobacter pylori nickel response regulator.
LiSIs / Life Sciences Informatics
Facilitates the discovery of cancer chemopreventive agents. LiSIs uses numerous methods like RDKit, R or AutoDock Vina. It can proceed a lot of operations such as molecular descriptor calculation, predictive model generation and docking experiments. The tool enables the consideration of multiple pharmaceutically important properties to Virtual Screening (VS) and other library design experiments. It permits to drug discovery researchers to use state-of-the-art computational techniques on an easy way.
A versatile web server for both pharmacophore- and similarity-based virtual screening and target identification to facilitate computational drug discovery. The interface is easy-to-use and can be accessed by user customized sessions to free them from installing standalone softwares. iDrug provides ready-to-access compounds and pharmacophore target databases for virtual screening and target identification. Various applications like binding site identification, structure-based pharmacophore derivation, conformational sampling, pharmacophore searching, and 3D similarity calculation are integrated as individual modules. iDrug enables interactive editing and refinement of pharmacophore hypothesis as well as flexible customization of the parameters. The featured job management system ensures the user privacy and project tracking through a session-based mechanism.
Offers a set of tools allowing medicinal chemists working on selective estrogen receptor modulators (SERMs) to perform a series of actions. FORECASTER supports medicinal chemistry and computational molecular design. It provides tools that can be employed for: virtual screening of small molecules binding to biomacromolecules; preparation of the protein and ligand files for docking; generation of combinatorial libraries of ligands or extraction of diverse or focused libraries from large molecular libraries.
Takes over the steps of the LiBERO framework. ALiBERO starts from single or multiple receptor structures and creates receptor ensembles, performs virtual screening (VS) docking and selects the combination of pockets. It consists of two main steps: (1) the generation of a large population of receptor conformers; (2) a flexible-ligand static-receptor small-scale VS docking is carried out on each of the conformers and the best performing “children” pockets are selected for the next generation.
GSA / GPU-accelerated structure similarity algorithm
Speeds the performance of structure similarity search for over two orders of magnitude faster. GSA is a GPU-accelerated structure similarity algorithm based on atom center fragment (ACF) approach. This method is particularly good for virtual screening on large datasets. Virtual progressive screening results exhibited that GSA is not biased on particular groups of compounds or biological targets. It also can be a general tool for chemoinformatics applications.
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LigandBox / LIGANDs Data Base Open and eXtensible
Contains purchasable chemical compounds for the purpose of drug development. LigandBox is a 3D chemical compound library available for efficient structure-based virtual screening with a maximum common substructure (MCS) search engine. It can contribute to toward the discovery of new active chemical compounds by virtual screening. This resource contains about one million unique compounds that are not registered in the ZINC and PubChem databases.
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