ChemMine tools
An online service for analyzing and clustering small molecules by structural similarities, physicochemical properties or custom data types.
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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).
Multi-Fingerprint Browser for ZINC
Enables to rapidly identify such close analogs among commercially available compounds in the ZINC database.
libefp
Consists in a Message Passing Interface/OpenMP (MPI/OpenMP) parallelization of the Effective Fragment Potential (EFP) method. libefp permits efficient utilization of multiple computer nodes and supercomputers. It allows multi-node parallel calculations that scale well up to several hundreds of compute cores. This tool can be used to describe large molecular systems by replacing chemically inert part of a system by a set of Effective Fragments.
MetiTree / Metabolite Identification Tree
Identifies metabolites from multi-stage mass spectrometry (MSn) data. MetiTree aims to assist in designation of chemical compounds by providing a set of tools for compute, visualize, compare and organize MSn information. It contains multiple features allowing users to access to a spectral tree viewer, a way for creating directories for gathering files according to projects and to query for similar MSn data stored in the library.
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.
pkCSM
Uses graph-based signatures to develop predictive models of central ADMET properties for drug development. pkCSM provides a platform for the analysis and optimization of pharmacokinetic and toxicity properties implemented in a web interface, and a valuable tool to help medicinal chemists find the balance between potency, safety, and pharmacokinetic properties. pkCSM achieved a performance as good as or better than similar methods currently available.
T-BioInfo
Combines statistical analysis modules into pipelines to deal with heterogenous big data. T-BioInfo is an application that can be used for: (1) next-generation sequencing (NGS) data (transcriptomics, genomics/epigenetics, and DNA/RNA); (2) mass-spectroscopy; (3) structural biology; and (4) data integration and modeling (virology, data association, and data mining).
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.
TB Mobile
Displays molecule structures and links to the bioinformatics data. TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The application is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts.
mcule
Offers a cost-effective way to identify and order new drug candidates has been recently launched. mcule provides a comprehensive, carefully curated database of molecules immediately available for virtual screening. It provides a convenient, online solution for managing compound databases and libraries as molecule collections. The user can keep track on all the previous compound selections and get back to start the compound ordering process whenever it is necessary.
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.
PPIMpred / Prediction of Protein-Protein Interaction Modulators
Allows high-throughput screening of small molecules for targeting specific protein– protein interactions (PPI). PPIMpred was trained on kernels of support vector machine (SVM) and machine learning techniques. It can be used to recognise lead in high-throughput screening of large chemical datasets. The tool permits to get the structural and chemical similarities with known chemical modulators or drug-like molecules.
eMolecules
Free chemical structure search engine with millions of public domain structures from vendors worldwide.
Approved Drugs
Contains over a thousand chemical structures and names of small molecule drugs approved by the US Food & Drug Administration (FDA). Approved Drugs offers a detail view that allows viewing of a 3D conformation as well as tautomers. Drugs can be browsed by structure or by names. The tool permits to filter results by structural features, and ranks it by similarity to a user-drawn structure.
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
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
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.
HAGR / Human Ageing Genomic Resources
Provides several online databases and tools relevant to the biology of ageing. HAGR is a web portal that hosts high-quality curated gene-centric information relevant to human ageing. All data sets are linked to each other, and each gene entry contains direct links to all other relevant entries in HAGR’s datasets. The database aims to organize the increasing amount of these information and make them accessible to the research community.
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.
mVOC / Microbial volatile organic compounds
Summarizes the volatilomes of bacteria and fungi. mVOC was constructed thanks to an automatic text mining procedure before being manually curated by experts. It provides a web browser that allows users to query for mass spectra peaks or for emitter and receiver of specific microbial volatile organic compounds (mVOCs). This database is searchable by compounds name, PubChem-ID, chemical formula or properties.
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.
ChemDB
Provides access to about 5M commercially available small molecules. ChemDB is a chemical database that contains data coming from the electronic catalogs of over 150 chemical vendors as well as a limited number of publicly available datasets. The database includes search tools in support of systems biology and drug discovery projects. Data can be searched by structural similarity, includes several, names and annotations and users can also search virtual chemical space.
PubChem Compound
Provides unique chemical structures that come from the Substance database and more than 60 million of Compound IDs (CIDs). PubChem Compound aggregates substance records from different data sources about the same molecule through a common ‘compound’ record. It provides features that allow users to see how their structures would be handled during the standardization process when they submit a structure.
PubChem Substance
Stores depositor-contributed information of chemical structures. PubChem Substance provides more than 157 million of Substance IDs (SIDs). It can contain information such as biological functions of glucose, or characteristics of a research grade sample of glucose. This tool stores different descriptions about the same molecule as separate records that are independent of each other. It allows users to submit descriptions following a standardization process.
ZINC
Provides commercially-available compounds for virtual screening. ZINC is composed of 3D molecules which have been assigned biologically relevant protonation states and are annotated with properties such as molecular weight, calculated LogP, and number of rotatable bonds. It is searchable through a query tool which incorporates a molecular drawing interface. The database enables investigators to attempt computational ligand discovery.
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.
SCRIPDB
A chemical structure database designed to make this metadata accessible. SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes.
PDBeChem
Dictionary of chemical components (ligands, small molecules and monomers) referred to in PDB entries and maintained by wwPDB. It provides comprehensive search facilities for finding a particular component, or determining components in structure entries. This database contains currently over 23.657 ligands.
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.
SuperPain
A database for pain stimulating and pain relieving compounds, which bind or potentially bind to ion channels, such as TRPV1, TRPM8, TRPA1, hERG, TREK1, P2X, ASIC or voltage-gated sodium channels. The database consists of about 8,700 ligands, which are characterized by experimentally measured binding affinities. Additionally, 100,000 putative ligands are included.
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.
SwissBioisostere
Contains information on molecular replacements and their performance in biochemical assays. The SwissBioisostere database is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, as well as to give interested scientists access to the details on particular molecular replacements.
SuperScent
Provides a dataset of volatile compounds collected from a variety of sources. SuperScent contains information about compounds chemical properties and commercial availability. The database is composed of more than 2000 compounds, 9000 synonyms and references to over 20 different suppliers. It permits users to retrieve information about scents or to get an overview of the known volatile organic compounds.
WITHDRAWN
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).
MMsINC
A database of non-redundant, richly annotated and biomedically relevant chemical structures.
Ligand Expo
Focuses on providing chemical and structural information for small molecules found as part of the structures deposited in the Protein Data Bank. Ligand Expo is an integrated data resource for finding information about small molecules bound to proteins and nucleic acids. Ligand Expo accepts keyword-based queries and also provides a graphical interface for performing chemical substructure searches.
DUD-E / Database of Useful Decoys : Enhanced
Designed to help benchmark molecular docking programs by providing challenging decoys.
PSMDB / Protein-Small Molecule DataBase
Gathers information about non-redundant protein-ligand complexe. PSMDB is an online repository allowing users to handle structural redundancy at both the protein and ligand levels. It contains highly similar ligands interacting with different proteins and different ligands. It preserves maximal information from structures containing bound ligands, and information contained in this database is regularly updated.
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.
Metab2MeSH
Uses a statistical approach to reliably and automatically annotate compounds with concepts defined in Medical Subject Headings, and the National Library of Medicine's controlled vocabulary for biomedical concepts. These annotations provide links from compounds to biomedical literature and complement existing resources such as PubChem and the Human Metabolome Database.
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.
RPdb
Gathers cellular reprogramming information. RPdb is an online repository that provides detailed information about experimentally verified genes and microRNAs, including gene descriptions and functional annotations. This database allows users to find genes, microRNAs (miRNAs) and novel reprogramming factors in a broad spectrum of cell reprogramming research.
PPDMs
A resource that maps small molecule bioactivities to protein domains from the Pfam-A collection of protein families. Small molecule bioactivities mapped to protein domains add important precision to approaches that use protein sequence searches alignments to assist applications in computational drug discovery and systems and chemical biology.
Ligandbook
Provides force-field parameters of small and drug-like molecules for all major all-atom force fields. Ligandbook aims to enable parameter re-use and simulation reproducibility by (1) facilitating the publication of force field parameters as open data; (2) acting as an archive for parameter sets that are supplied and maintained by the community; (3) making large, richly annotated parameter datasets easily available through human and machine accessible interfaces.
DrugAge
Aims to provide high-quality summary data on lifespan-extending drugs and compounds in model organisms. DrugAge contains 1316 entries featuring 418 different compounds from studies across 27 model organisms, including worms, flies, yeast and mice. The data contained in the database focus solely on assays performed in standard conditions. It integrates drug–gene interactions and cross-links to aging-related genes, allowing a deeper examination of lifespan extending drugs.
Phenol-Explorer
Provides data concerning polyphenols in foods, a major class of food bioactives. Phenol-Explorer is a resource that includes retention factors on the class of dietary bioactives. This resource allows the filtering of information according to various criteria. The data collated allow the most detailed analysis so far of how different domestic and industrial processes affect the polyphenol contents of foods.
InChI / IUPAC International Chemical Identifier
Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. InChI is a non-proprietary identifier for chemical substances that can be used in printed and electronic data sources thus enabling easier linking of diverse data compilations.
CSD / Cambridge Structural Database
Stores data for nearly 700 000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. The Cambridge Structural Database is a highly curated and comprehensive resource. It is the world’s repository for small-molecule organic and metal-organic crystal structures. This unique database of accurate 3D structures has become an essential resource to scientists around the world.
CompTox Chemistry Dashboard
Provides a platform allowing access to information related to chemical substances. CompTox Chemistry Dashboard is a repository applying both manual and algorithmic curation techniques for compiling data from various public datasets, such as the U.S. Environmental Protection Agency (EPA) Substance Registry Service or the PubChem database. It aims to assist users in evaluating the available data about a specific content or for data exploration.
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.
