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Small Molecules

Tools for dealing with the bioinformatics of small molecules

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Found 17 links

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ARISTOTool Content

http://www.ionspectra.org/aristo [open in a new window]

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Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules

Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry.20111
NAR Web Server Issue 2011
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tagsmass spectrometry small molecule libraries

ChemMine ToolsTool Content

http://chemmine.ucr.edu [open in a new window]

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Other Molecules > Small Molecules

ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
ChemMine tools: an online service for analyzing and clustering small molecules20116
NAR Web Server Issue 2011
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tagsalgorithms cluster analysis data mining drug discovery genomics pharmaceutical preparations small molecule libraries structure-activity relationship

DrugBankDatabase Content

http://redpoll.pharmacy.ualberta.ca/drugbank/index.html [open in a new window]

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Other Molecules > Small Molecules

DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 FDA approved small molecule and biotech drugs as well as >3200 experimental drugs. Additionally, >14,000 protein or drug target sequences are linked to these drug entries.

links directory index: 549
TitlePublication YearGoogle Scholar Citation Count
DrugBank: a comprehensive resource for in silico drug discovery and exploration2006549
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external linksLink on Wikipedia

eMoleculesDatabase Content

http://www.emolecules.com/index.htm [open in a new window]

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Other Molecules > Small Molecules

eMolecules is a search engine for chemical structures that allows for substructure searching.

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external linksLink on Wikipedia

FAF-DrugsTool Content

http://bioserv.rpbs.jussieu.fr/Help/FAFDrugs.html [open in a new window]

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Other Molecules > Small Molecules

Free ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.

links directory index: 39
TitlePublication YearGoogle Scholar Citation Count
FAF-Drugs: free ADME/tox filtering of compound collections200639
NAR Web Server Issue 2006
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tagsdrug design drug toxicity pharmaceutical preparations pharmacokinetics

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket [open in a new window]

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Other Molecules > Small Molecules
Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
fpocket: online tools for protein ensemble pocket detection and tracking201015
NAR Web Server Issue 2010
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FrogTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog [open in a new window]

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Other Molecules > Small Molecules

Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).

links directory index: 32
TitlePublication YearGoogle Scholar Citation Count
Frog: a FRee Online druG 3D conformation generator200732
NAR Web Server Issue 2007
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Frog2Tool Content

http://bioserv.rpbs.univ-paris-diderot.fr/Frog2 [open in a new window]

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Other Molecules > Compounds
Other Molecules > Small Molecules

Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by embedding new energy minimization and ring generation capacities.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Frog2: Efficient 3D conformation ensemble generator for small compounds20107
NAR Web Server Issue 2010
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tagsmolecular conformation molecular models pharmaceutical preparations stereoisomerism

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp [open in a new window]

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Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Biochemical Features

A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.

This content is being maintained by flebeda.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding200921
NAR Web Server Issue 2009
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

idTargetTool Content

http://idtarget.rcas.sinica.edu.tw [open in a new window]

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Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

idTarget is a web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. idTarget screens against protein structures in PDB.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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PepSiteTool Content

http://pepsite2.russelllab.org [open in a new window]

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Other Molecules > Small Molecules
Protein > 3-D Structure Prediction

PepSite webserver predicts binding of a given peptide onto a protein structure, enabling users to better understand the details of the interaction of interest.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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PharmMapperTool Content

http://59.78.96.61/pharmmapper [open in a new window]

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Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Networks & Interactions, Pathways and Enzymes

PharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a given molecule to interact with a target.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach201016
NAR Web Server Issue 2010
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tagsbinding sites drug design factual databases hormonal antineoplastic agents ligands pharmaceutical preparations proteins tamoxifen

PubChem BioAssay ServiceTool Content

http://pubchem.ncbi.nlm.nih.gov/assay/ [open in a new window]

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Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking
Protein > Networks & Interactions, Pathways and Enzymes

PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target selectivity examination.

links directory index: 171
TitlePublication YearGoogle Scholar Citation Count
PubChem: a public information system for analyzing bioactivities of small molecules2009171
NAR Web Server Issue 2009
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SIMCOMP/SUBCOMPTool Content

http://www.genome.jp/tools/simcomp/ [open in a new window]

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Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Networks & Interactions, Pathways and Enzymes

SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpretation of biological meanings of chemical structures.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses20104
NAR Web Server Issue 2010
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SwissDockTool Content

http://www.swissdock.ch [open in a new window]

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Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

SwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.

This content is being maintained by aurelieng.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
SwissDock, a protein-small molecule docking web service based on EADock DSS20115
NAR Web Server Issue 2011
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tagsdrug design ligands molecular models protein conformation protein engineering

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