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Small molecule tools

Software tools and databases for small molecule analysis.

PubChem
Dataset

PubChem

A public repository for information on chemical substances and their biological…

A public repository for information on chemical substances and their biological activities. Since launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National…

ChEBI
Dataset

ChEBI Chemical Entities of Biological Interest

A database and ontology containing information about chemical entities of…

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…

ChEMBL
Dataset

ChEMBL

A well-established resource in the fields of drug discovery and medicinal…

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…

DrugBank
Dataset

DrugBank

A comprehensive online database containing extensive biochemical and…

A comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms and their targets. Since it was first described in 2006, DrugBank has…

ChemProt
Dataset

ChemProt

A publicly available compilation of chemical-protein-disease annotation…

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…

DTP
Dataset

DTP Anti-cancer Agent Mechanism Database

Provides services and resources to the academic and private-sector research…

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…

PubChem…
Dataset

PubChem Substance

Stores depositor-contributed information of chemical structures. PubChem…

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…

PubChem…
Dataset

PubChem Compound

Provides unique chemical structures that come from the Substance database and…

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…

SMPDB
Dataset

SMPDB Small Molecule Pathway DataBase

An interactive, visual database containing more than 618 small molecule…

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…

ChemBank
Dataset

ChemBank

A public, Web-based informatics environment. ChemBank stores and makes freely…

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…

CTRP
Dataset

CTRP Cancer Therapeutics Response Portal

Links genetic, lineage, and other cellular features of cancer cell lines to…

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…

Pharos
Web
Desktop

Pharos

A multimodal web interface that presents the data from the Target Central…

A multimodal web interface that presents the data from the Target Central Resource Database (TCRD) which collates many heterogeneous gene and protein datasets. Pharos serves as entry point into the…

Ligandbook
Dataset

Ligandbook

Provides force-field parameters of small and drug-like molecules for all major…

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…

ZINC
Dataset

ZINC

Provides commercially-available compounds for virtual screening. ZINC is…

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…

eMolFrag
Desktop

eMolFrag

Extracts molecular fragments, classified as bricks and linkers, from small…

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…

ChemMine tools
Web

ChemMine tools

An online service for analyzing and clustering small molecules by structural…

An online service for analyzing and clustering small molecules by structural similarities, physicochemical properties or custom data types.

CSD
Dataset

CSD Cambridge Structural Database

Stores data for nearly 700 000 structures and is a comprehensive and fully…

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…

DrugCentral
Dataset

DrugCentral

Integrates structure, bioactivity, regulatory, pharmacologic actions and…

Integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. DrugCentral includes content…

DUD-E
Dataset

DUD-E Database of Useful Decoys : Enhanced

Designed to help benchmark molecular docking programs by providing challenging…

Designed to help benchmark molecular docking programs by providing challenging decoys.

Multi-Fingerpri…
Web

Multi-Fingerprint Browser for ZINC

Enables to rapidly identify such close analogs among commercially available…

Enables to rapidly identify such close analogs among commercially available compounds in the ZINC database.

Ligand Expo
Dataset

Ligand Expo

Focuses on providing chemical and structural information for small molecules…

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…

WITHDRAWN
Dataset

WITHDRAWN

A resource for withdrawn and discontinued drugs. WITHDRAWN not only contains…

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…

SureChEMBL
Dataset

SureChEMBL

A publicly available large-scale resource containing compounds extracted from…

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…

NutriChem
Dataset

NutriChem

Allows to explore the medicinal value of diet and elucidate the synergistic…

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…

pkCSM
Web

pkCSM

Uses graph-based signatures to develop predictive models of central ADMET…

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…

SuperDrug
Dataset

SuperDrug

The database contains approximately 2500 3D-structures of active ingredients of…

The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs.

ChemDB
Dataset

ChemDB

A chemical database containing nearly 5M commercially available small…

A chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and…

MMsINC
Dataset

MMsINC

A database of non-redundant, richly annotated and biomedically relevant…

A database of non-redundant, richly annotated and biomedically relevant chemical structures.

NPC
Dataset

NPC NCGC Pharmaceutical Collection

A comprehensive, publically-accessible collection of approved and…

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…

MUV
Dataset

MUV Maximum Unbiased Validation

Contains a collection of data sets of actives and corresponding decoy data sets…

Contains a collection of data sets of actives and corresponding decoy data sets that are unbiased with regard to both analogue bias and artificial enrichment. MUV is a collection of benchmark data…

BARD
Dataset

BARD BioAssay Research Database

A public database and suite of tools developed to provide access to bioassay…

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…

CFam
Dataset

CFam

It was developed to hierarchically cluster drugs, bioactive molecules, human…

It was developed to hierarchically cluster drugs, bioactive molecules, human metabolites, natural products, patented agents and other molecules into functional families, superfamilies and classes of…

T3DB
Dataset

T3DB Toxin-Toxin-Target DataBase

A resource that was specifically designed to capture information about the…

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…

cBinderDB
Dataset

cBinderDB

Provides information on covalent binding compound structures, chemotypes,…

Provides information on covalent binding compound structures, chemotypes, targets, covalent binding types, and other biological properties. cBinderDB is a covalent binder database. The covalent…

ASDB
Dataset

ASDB Annotated Scaffold Database

Provides a platform for scientists to explore novel scaffolds or chemical…

Provides a platform for scientists to explore novel scaffolds or chemical probes for pharmaceutical innovations and chemical biology studies. The scaffolds in ASDB were derived from public databases…

Metab2MeSH
Dataset

Metab2MeSH

Uses a statistical approach to reliably and automatically annotate compounds…

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…

EDKB
Dataset

EDKB Endocrine Disruptor Knowledge Base

Provides data across multiple assay types for chemicals across a broad…

Provides data across multiple assay types for chemicals across a broad structural diversity. EDKB contains more than 3200 records for over 1800 chemical compounds. It is composed of data from rat,…

SM-TF
Dataset

SM-TF Small Molecule-Transcription Factor

A structural database of small molecule-transcription factor complexes. The 3D…

A structural database of small molecule-transcription factor complexes. The 3D structures of the co-bound small molecule and the corresponding binding sites on transcription factors (TFs) are…

TPACM4
Web

TPACM4 Transferrable Partial Atomic Charge Model - up to 4 bonds

Derives the partial atomic charges of small molecules for use in…

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…

SuperPain
Dataset

SuperPain

A database for pain stimulating and pain relieving compounds, which bind or…

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…

S2RSLDB
Dataset

S2RSLDB sigma-2 Receptor Selective Ligands Database

Focuses on the sigma-2 (σ2) receptor selective ligands and contains more than…

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…

HIV-1…
Dataset

HIV-1 Integrase Inhibitor Database

Contains HIV-1 Integrase (IN) Inhibitors collected from peer-reviewed…

Contains HIV-1 Integrase (IN) Inhibitors collected from peer-reviewed scientific publications. HIV-1 Integrase Inhibitor Database is a manually built database which collects the basic data such as…

Rchempp
Desktop
Web

Rchempp

A web service that identifies structurally similar compounds (structural…

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…

PPDMs
Dataset

PPDMs

A resource that maps small molecule bioactivities to protein domains from the…

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…

CCD
Dataset

CCD Chemical Component Dictionary

A chemical reference data resource that describes all residue and small…

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…

SuperLigands
Dataset

SuperLigands

An encyclopedia that is dedicated to a ligand oriented view of the protein…

An encyclopedia that is dedicated to a ligand oriented view of the protein structural space.

VDS
Dataset

VDS Virtual Decoy Sets

Contains a small set of active ligands and a large set of nonbinding decoys.…

Contains a small set of active ligands and a large set of nonbinding decoys. VDS uses five physical descriptors: (i) molecular weight, (ii) number of rotational bonds, (iii) number of hydrogen bond…

CoCoCo
Dataset

CoCoCo Commercial Compound Collection

A suite of free and ready-to-use chemical databases to help setting up in…

A suite of free and ready-to-use chemical databases to help setting up in silico screening projects. CoCoCo collects molecular structural information of commercial compounds from various chemical…

EDCs DataBank
Dataset

EDCs DataBank

A database of endocrine disrupting chemicals (EDCs) with three-dimensional…

A database of endocrine disrupting chemicals (EDCs) with three-dimensional structures available for virtual screening. EDCs DataBank is suitable for virtual screening and other computational…

NRDBSM
Dataset

NRDBSM Non Redundant Database of Small Molecules

Aims at virtual high throughput screening of small molecules and their further…

Aims at virtual high throughput screening of small molecules and their further optimization into successful lead-like candidates. NRDBSM gives a special consideration to physicochemical properties…

ZINClick
Dataset

ZINClick

Is a database of triazoles generated using existing alkynes and azides,…

Is a database of triazoles generated using existing alkynes and azides, synthesizable in no more than three synthetic steps from commercially available products. ZINClick is freely available to…

ChemSpider
Dataset

ChemSpider

Provides access to chemical structures, properties, and associated information.…

Provides access to chemical structures, properties, and associated information. ChemSpider is a database which allows user to search by chemical name or by chemical structure. The database provides…

SCRIPDB
Dataset

SCRIPDB

A chemical structure database designed to make this metadata accessible.…

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…

KEGG DRUG
Dataset

KEGG DRUG

Contains a comprehensive collection of approved drugs in Japan, USA and Europe…

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…

SwissBioisoster…
Dataset

SwissBioisostere

Contains information on molecular replacements and their performance in…

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…

SwissSidechain
Dataset

SwissSidechain

SwissSidechain is a structural and molecular mechanics database and curated…

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…

PDBeChem
Dataset

PDBeChem

Dictionary of chemical components (ligands, small molecules and monomers)…

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…

Psmir
Dataset

Psmir

Presents computationally predicted small molecule-miRNA associations through…

Presents computationally predicted small molecule-miRNA associations through comparison of current gene expression profiles under miRNA perturbation and drug treatment. Psmir also provides detailed…

ChEpiMod
Dataset

ChEpiMod

A free knowledgebase of chemical modulators with documented modulatory activity…

A free knowledgebase of chemical modulators with documented modulatory activity for epigenome reader domains. ChEpiMod organizes information about chemical modulators and their associated…

OPLS3
Desktop

OPLS3

Allows to predict protein-ligand binding affinities with a high accuracy over a…

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…

mcule
Web

mcule

Offers a cost-effective way to identify and order new drug candidates has been…

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…

TB Mobile
Mobile

TB Mobile

Displays molecule structures and links to the bioinformatics data. 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…

CRDB
Dataset

CRDB Curcumin Resource Database

An integrated and curated repository of curcumin analogs and their molecular…

An integrated and curated repository of curcumin analogs and their molecular targets. CRDB also contains information of various international and national patents on curcumin and its analogs.…

EpiDBase
Dataset

EpiDBase

An interactive database of small molecule ligands of epigenetic protein…

An interactive database of small molecule ligands of epigenetic protein families by bringing together experimental, structural and chemoinformatic data in one place. Currently, EpiDBase encompasses…

PocketOptimizer
Desktop

PocketOptimizer

Predicts mutations in the binding pocket of proteins, which increase the…

Predicts mutations in the binding pocket of proteins, which increase the affinity of the protein to a given small molecule ligand. PocketOptimizer is a method for the computational design of…

HEMD
Dataset

HEMD Human Epigenetic Enzyme and Modulator Database

Provides a central resource for the display, search, and analysis of the…

Provides a central resource for the display, search, and analysis of the structure, function, and related annotation for human epigenetic enzymes and chemical modulators focused on epigenetic…

SWEETLEAD
Dataset

SWEETLEAD

Creates to provide an exhaustive and highly curated resource for chemical…

Creates to provide an exhaustive and highly curated resource for chemical structures of the world's approved medicines, drugs, and isolates from traditional medicinal herbs. This database has…

DrugPath
Dataset

DrugPath

Identifies and compares best-fit developmental drugs in industry for…

Identifies and compares best-fit developmental drugs in industry for preclinical testing in academic research laboratories. DrugPath is a free-of-charge, online resource that enhances the ability of…

CCCBDB
Dataset

CCCBDB Computational Chemistry Comparison and Benchmark DataBase

Provides experimental and computed (quantum mechanics) thermochemical data.…

Provides experimental and computed (quantum mechanics) thermochemical data. CCCBDB allows to compare experimental and computational ideal-gas thermochemical properties. The main purposes of this tool…

AtomNet
Algorithm

AtomNet

Designed to predict the bioactivity of small molecules for drug discovery…

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…

SARvision | SM
Desktop

SARvision | SM

Allows structure activity relationship (SAR) visualization, mining, and…

Allows structure activity relationship (SAR) visualization, mining, and organization of chemical data. SARvision | SM automatically analyzes a series of inhibitors for common scaffold structures,…

MORE
Desktop

MORE MObile REagents

Gives access to over 9.7 million molecules and 17.6 million product variations.…

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…

Approved Drugs
Mobile

Approved Drugs

Contains over a thousand chemical structures and names of small molecule 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…

TP-Search
Dataset

TP-Search Transporter Protein Search

A comprehensive database on drug transporters. TP-Search provides a research…

A comprehensive database on drug transporters. TP-Search provides a research tool for optimization of pharmacokinetic properties in terms of transporters during the early stage of drug development in…

InChI
Dataset

InChI IUPAC International Chemical Identifier

Since its public introduction in 2005 the IUPAC InChI chemical structure…

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…

CCD
Dataset

CCD Combined Chemical Dictionary

A chemical database containing over 500,000 substances which are formerly…

A chemical database containing over 500,000 substances which are formerly available from the following products: Dictionary of Analytical Reagents, Dictionary of Carbohydrates, Dictionary of…

DNP
Dataset

DNP Dictionary of Natural Products

A comprehensive and fully-edited database on natural products. It arose as a…

A comprehensive and fully-edited database on natural products. It arose as a daughter product of the well-known Dictionary of Organic Compounds (DOC) which, since its inception in the 1930s has,…

Phenol-Explorer
Dataset

Phenol-Explorer

A comprehensive web-based database on the content in foods of polyphenols, a…

A comprehensive web-based database on the content in foods of polyphenols, a major class of food bioactives that receive considerable attention due to their role in the prevention of diseases. The…

DailyMed
Dataset

DailyMed

Provides trustworthy information about marketed drugs. DailyMed is the official…

Provides trustworthy information about marketed drugs. DailyMed is the official provider of FDA label information (package inserts). This Web site provides a standard, comprehensive, up-to-date,…

CHEMnetBASE
Dataset

CHEMnetBASE

Contains a collection of chemistry databases edited by CRC Press. It also…

Contains a collection of chemistry databases edited by CRC Press. It also includes the electronic version of several basic reference works, which can be subscribed to individually or collectively. It…

BIAdb
Dataset

BIAdb

The Benzylisoquinoline Alkaloid Database (BIAdb) is an attempt to gather the…

The Benzylisoquinoline Alkaloid Database (BIAdb) is an attempt to gather the scattered information related to the BIA's. Many BIA's show therapeutic properties and can be considered as…

ChemIDplus
Dataset

ChemIDplus

This database allows users to search over 400,000 chemicals.

This database allows users to search over 400,000 chemicals.

eMolecules
Web

eMolecules

Free chemical structure search engine with millions of public domain structures…

Free chemical structure search engine with millions of public domain structures from vendors worldwide.

SPRESI
Dataset

SPRESI

Collects chemical structure and reaction. SPRESI provides access to over 5.8…

Collects chemical structure and reaction. SPRESI provides access to over 5.8 million structures, 4.5 million reactions and 33 million factual data entries extracted from 675,000 references and…

A A A
cmap
Web

cmap Connectivity Map

A reference collection of gene-expression profiles from cultured human cells…

A reference collection of gene-expression profiles from cultured human cells treated with bioactive small molecules, together with pattern-matching software to mine these data. CMAP resource can be…

EDULISS
Dataset

EDULISS EDinburgh University Ligand Selection System

Stores structural, physicochemical and pharmacophoric properties of small…

Stores structural, physicochemical and pharmacophoric properties of small molecules. The database comprises a collection of over 5 million commercially available compounds from different suppliers. A…

PDB-Ligand
Dataset

PDB-Ligand

A three-dimensional structure database of small molecular ligands that are…

A three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). PDB-Ligand is also a database tool that allows one to…

ASDCD
Dataset

ASDCD Antifungal Synergistic Drug Combination Database

A repository for the growing antifungal data and as a means of tracking…

A repository for the growing antifungal data and as a means of tracking scientific developments in this area. ASDCD would be specially designed for the input of synergistic antifungal drug…

CancerHSP
Dataset

CancerHSP Anticancer Herbs database of Systems Pharmacology

Records anticancer herbs related information through manual curation.…

Records anticancer herbs related information through manual curation. Currently, CancerHSP contains 2439 anticancer herbal medicines with 3575 anticancer ingredients. For each ingredient, the…

Luna
Dataset

Luna

A database of protein-ligand structural information derived from the Protein…

A database of protein-ligand structural information derived from the Protein Database.

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