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Pathema
Provides a core resource for the bio-defense and infectious disease research community. Pathema is a web application that permits the access to genomic data integrated with analysis tools designed to aid researchers in identifying potential targets for novel therapeutics, vaccines, and diagnostics. The priority pathogens support includes five prokaryotes (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Clostridium botulinum and Clostridium perfringens) and one eukaryote (Entamoeba histolytica).
Rchempp
A web service that identifies structurally similar compounds (structural analogs) in large-scale molecule databases. The service allows compounds to be queried in the widely used ChEMBL, DrugBank and the Connectivity Map databases. Rchemcpp utilizes the best performing similarity functions, i.e. molecule kernels, as measures for structural similarity. Molecule kernels have proven superior performance over other similarity measures and are currently excelling at machine learning challenges.
OPLS3
Allows to predict protein-ligand binding affinities with a high accuracy over a wide rande of targets and ligands. OPLS was one on the first models in which parameters were extensively optimized to reproduce liquid state thermodynamic properties for a variety of small organic molecules. This tool is a new generation of models based on the Optimized Potentials for Liquid Simulations (OPLS) force field. It can demonstrate that the accuracy of protein-ligand binding affinity is systematically improved by improving of this force field.
eMolFrag
Extracts molecular fragments, classified as bricks and linkers, from small molecule datasets. eMolFrag uses the fragments in order to construct targeted libraries for virtual screening. It stores the connectivity information for the extracted building blocks to help generate new series of chemically feasible compounds. It is optimized to work with eSynth, a recently developed molecular synthesis algorithm. It can also be integrated into other cheminformatics toolkits utilizing chemical fragments.
PROBELIST
Provides a database of chemical tool compounds for targets from medicinal chemistry literature and patents. PROBELIST was developed to help researchers make the best use of these chemicals and to easily locate useful functional inhibitors for a given biological pathway. The data set was annotated in a target-centric way, with the KEGG pathways, gene ontology (GO) terms (molecular function (MF), biological process (BP), and cellular compartment (CC)), reactome pathways, Entrez gene IDs, and Uniprot IDs for each protein target.
TPACM4 / Transferrable Partial Atomic Charge Model - up to 4 bonds
Derives the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. TPACM4 helps speed up the binding energy predictions. The partial charges of the tool were tested by estimating hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. The tool overcomes the limitations of time complexity in deriving the partial atomic charges of a given molecule while retaining accuracy.
MORE / MObile REagents
Gives access to over 9.7 million molecules and 17.6 million product variations. MORE is searchable by name, CAS#, formula or by structure within a hitlist or by drawing a structural query. It offers functionalities to limit the search to specific suppliers and bookmark search results. The tool is able to convert a picture of a chemical structure taken from the iPhone camera into a structurally searchable molecule using Optical Structure Recognition Application (OSRA).
SARvision | SM
Allows structure activity relationship (SAR) visualization, mining, and organization of chemical data. SARvision | SM automatically analyzes a series of inhibitors for common scaffold structures, filters the result by properties as scaffold type, physicochemical data, etc. The software enables to understand chemical data and identify chemotypes responsible for activity. In addition, it can identify chemotypes automatically, organize scaffold in a hierarchical tree, visualize data with plots that relate to chemotypes and search libraries with multiple queries at once.
AtomNet
Designed to predict the bioactivity of small molecules for drug discovery applications. AtomNet is a structure-based deep convolutional neural network (CNN) which combines information about the ligand with information about the structure of the target. The locally-constrained deep convolutional architecture allows the system to model the complex, non-linear phenomenon of molecular binding by hierarchically composing proximate basic chemical features into more intricate ones. The algorithm can predict new active molecules even for targets with no previously known modulators.
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PubChem
Contains chemical structures and biological properties of molecules including small molecules and siRNA reagents. PubChem consists of three interconnected databases: Substance, BioAssay and Compound. The database also provides a suite of web-based bioactivity analysis tools allowing to download and search individual test results, compare biological activity data from multiple screenings, examine target selectivity or explore structure–activity relationships for compounds of interest.
ChEMBL
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A well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services, which exposes significantly more data from the underlying database and introduces new functionality.
DTP / Anti-cancer Agent Mechanism Database
Provides services and resources to the academic and private-sector research communities worldwide to facilitate the discovery and development of new cancer therapeutic agents. Services available directly from DTP: (i) NCI-60 human cancer cell line screen, (ii) Molecular Target Program, (iii) Materials for research — tumor cells, chemicals, natural products and biological samples. Anti-cancer Agent Mechanism Database DTP is a set of 122 compounds with anti-cancer activity and reasonably well known mechanism of action. The list of compounds was assembled as a training set for neural network analysis of drug mechanism of action.
DrugBank
Gathers detailed drug, drug-target, drug action and drug interaction information about drugs. DrugBank is a web resource that contains information about FDA-approved drugs as well as experimental drugs going through the FDA approval process. The database also includes pharmaco-omic data covering the influence of drugs on metabolite levels, gene expression levels and protein expression levels, as well as data on investigational drug clinical trials and drug repurposing trials, and thousands of up-to-date drug images of approved drugs.
ChEBI / Chemical Entities of Biological Interest
A database and ontology containing information about chemical entities of biological interest. ChEBI currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.
CTRP / Cancer Therapeutics Response Portal
Links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics. CTRP hosts an 'Informer Set' of 481 small-molecule probes and drugs that selectively target distinct nodes in cell circuitry and that collectively modulate a broad array of cell processes. The CTRP is a living resource for the biomedical research community that can be mined to develop insights into small-molecule mechanisms of action and novel therapeutic hypotheses, and to support future discovery of drugs matched to patients based on predictive biomarkers.
KEGG DRUG
Contains a comprehensive collection of approved drugs in Japan, USA and Europe unified based on chemical structures and/or chemical components. KEGG DRUG is a database which contains information about molecular networks, such as targets, metabolizing enzymes and drug–drug interactions. All the marketed drugs in Japan, the prescription drugs but also the over-the-counter (OTC) drugs, are represented in the database, including crude drugs and Traditional Chinese Medicine (TCM) drugs.
ChemProt
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A publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity from molecular to clinical levels. In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19,504 proteins. Within ChemProt, it is possible to navigate the chemogenomics space and to link chemically induced target perturbations to diseases and other biological outcomes. Such tools might be of interest for drug discovery, drug safety and also chemical risk assessment. ChemProt 3.0 supports predicting bioactivities on targets and off-targets for new compounds and can assist in the associations to phenotypes and side effects relationships.
NPC / NCGC Pharmaceutical Collection
A comprehensive, publically-accessible collection of approved and investigational drugs for high-throughput screening. NPC provides a valuable resource for both validating new models of disease and better understanding the molecular basis of disease pathology and intervention. It has already generated several useful probes for studying a diverse cross section of biology, including novel targets and pathways. NCGC provides access to its set of approved drugs and bioactives through the Therapeutics for Rare and Neglected Diseases (TRND) program and as part of the compound collection for the Tox21 initiative, a collaborative effort for toxicity screening among several government agencies.
ChemBank
A public, Web-based informatics environment. ChemBank stores and makes freely available data derived from small molecules and small-molecule screens and has resources for relating and studying these data. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays performed at the Broad Institute screening center. Web-based analysis tools are available within ChemBank to study the relationships between small molecules, cell measurements, and cell states.
SMPDB / Small Molecule Pathway DataBase
An interactive, visual database containing more than 618 small molecule pathways found in humans. More than 70% of these pathways (>433) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways.
NutriChem
Allows to explore the medicinal value of diet and elucidate the synergistic effects of natural bioactive compounds on disease phenotypes. NutriChem is a database that contains food-compound pairs between some plant-based foods and phytochemicals, as well as the food-disease associations between some plant-based foods and diseases. It was generated by text mining of 21 million MEDLINE abstracts. The incorporation of confidence scores based on the availability of support from literature or patient records may serve as future update of NutriChem.
SuperDrug
Offers information of pharmaceutical ingredients. SuperDRUG provides annotated drugs with regulatory details, chemical structures (2D and 3D), dosage, biological targets, physicochemical properties, external identifiers, side-effects and pharmacokinetic data. It enables a comparison of 2D- and 3D-similarity between drugs of different indication classes elucidating structural reasons for adverse effects that might be neglected by exclusive consideration of their 2D-resemblence.
BARD / BioAssay Research Database
A public database and suite of tools developed to provide access to bioassay data produced by the NIH Molecular Libraries Program (MLP). Data from 631 MLP projects were migrated to a new structured vocabulary designed to capture bioassay data in a formalized manner, with particular emphasis placed on the description of assay protocols. New data can be submitted to BARD with a user-friendly set of tools that assist in the creation of appropriately formatted datasets and assay definitions.
SureChEMBL
A publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining pipeline on a daily basis. SureChEMBL provides access to a previously unavailable, open and timely set of annotated compound-patent associations, complemented with sophisticated combined structure and keyword-based search capabilities against the compound repository and patent document corpus; given the wealth of knowledge hidden in patent documents, analysis of SureChEMBL data has immediate applications in drug discovery, medicinal chemistry and other commercial areas of chemical science. The SureChEMBL database contains more than 17 million distinct compounds extracted from more than 14 million patent documents, spanning a time range from 1970 to present.
T3DB / Toxin-Toxin-Target DataBase
A resource that was specifically designed to capture information about the toxic exposome. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches.
Exposome Explorer
Provides biomarkers of exposure to environmental risk factors for diseases. Exposome-Explorer contains detailed information on the nature of biomarkers, populations and subjects in which biomarkers have been measured, samples analysed, methods used for biomarker analyses, concentrations in biospecimens, correlations with external exposure measurements, and biological reproducibility over time. This information can be used by epidemiologists and clinicians to compare the performance and field of application of various biomarkers and to identify the specific biomarkers or panels of biomarkers that are most useful for biomonitoring or disease etiology studies.
SwissSidechain
SwissSidechain is a structural and molecular mechanics database and curated platform of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins. Structural files (pdb, mol2, SMILES) for 230 sidechains can be found together with PyMOL and UCSF Chimera plugins to insert them into existing peptide or protein structures. Predicted rotamers as well as topologies and parameters to run molecular mechanics analysis are provided. This tool is provided and maintained by the Molecular modeling group at the Swiss Institute of Bioinformatics. This database is free for academic use.
WITHDRAWN
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A resource for withdrawn and discontinued drugs. WITHDRAWN not only contains information related to drug withdrawals and associated adverse drug reactions but also drug-target interactions and genetic variations of the protein targets. The drug-target interaction information is mapped to biological context by enriching the relevant pathways. The illustrated case study proves that, connecting links between drugs, targets and SNPs may explain the underlying mechanisms of toxicity. The knowledge presented in the database can improve the insights of drug-target interactions in toxicological context and provide the rationale for further off-target profiling and enhanced pharmacogenetics studies in different populations.
DrugCentral
Integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. DrugCentral includes content for active ingredients with pharmaceutical formulations, indexing drugs and drug label annotations, complementing similar resources available online. At the molecular level, DrugCentral bridges drug-target interactions with pharmacological action and indications. The integration with FDA drug labels enables text mining applications for drug adverse events and clinical trial information.
SuperSweet / Sweetening Agents Database
Compiles information on natural and artificial sweetening agents. SuperSweet includes sweetening agents’ properties such as 3D structure, origin, sweetness, approval, calories and provides hypotheses on their binding to the receptor. It contains more than 8000 carbohydrates, proteins, D-amino acids and artificial (synthesized) sweeteners, which were retrieved from the literature and different pre-existing data sources like Pubchem and the Protein Data Bank (PDB).
ASDB / Annotated Scaffold Database
Allows exploration of scaffolds or chemical probes for pharmaceutical innovations and chemical biology studies. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank, and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets, and medical indications. The database can be retrieved through text or structure query tools.
CCD / Chemical Component Dictionary
A chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described.
ChEpiMod
A free knowledgebase of chemical modulators with documented modulatory activity for epigenome reader domains. ChEpiMod organizes information about chemical modulators and their associated binding-affinity data, as well as available structures of epigenome readers from the Protein Data Bank. The data are gathered from the literature and patents. Entries are supplemented by annotation. The current version of ChEpiMod covers six epigenome reader domain families (Bromodomain, PHD finger, Chromodomain, MBT, PWWP and Tudor). The database can be used to browse existing chemical modulators and bioactivity data, as well as, all available structures of readers and their molecular interactions.
Psmir
Presents computationally predicted small molecule-miRNA associations through comparison of current gene expression profiles under miRNA perturbation and drug treatment. Psmir also provides detailed annotations of the predicted associations according to the known small molecule or miRNA information. The details contain the miRBase accession number of miRNA, the small molecule chemical structure, isomeric SMILES string, ATC code, various IDs (DrugBank ID, PubChem ID, PharmGKB ID) and whether the small molecule is FDA approved drug or not. Psmir served as a valuable resource for dissecting the biological significance in small molecules' effects on miRNA expression, which will facilitate developing novel potential therapeutic targets or treatments for human cancers.
S2RSLDB / sigma-2 Receptor Selective Ligands Database
Focuses on the sigma-2 (σ2) receptor selective ligands and contains more than 650 compounds. S2RSLDB is built with chemical structure information, radioligand binding affinity data, computed physicochemical properties, and experimental radioligand binding procedures. It offers a powerful search engine and allows the user to build complex queries, sort tabulated results, generate color coded 2D and 3D graphs and download the data for additional screening.
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