> > Small Molecules

Small Molecules

Tools for dealing with the bioinformatics of small molecules

RSS FeedCompact ViewList as XMLList as JSON

Found 15 links

Displaying 15 links

ARISTOTool Content

http://www.ionspectra.org/aristo

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.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

ChemMine ToolsTool Content

http://chemmine.ucr.edu

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.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

DrugBankDatabase Content

http://redpoll.pharmacy.ualberta.ca/drugbank/index.html

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscomputational biology drug delivery systems drug design factual databases pharmaceutical preparations pharmacology proteins

eMoleculesDatabase Content

http://www.emolecules.com/index.htm

Other Molecules > Small Molecules

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

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

FAF-DrugsTool Content

http://bioserv.rpbs.jussieu.fr/Help/FAFDrugs.html

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.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdrug design drug toxicity pharmaceutical preparations pharmacokinetics

FpocketTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

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).

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsbinding sites hemoglobins ligands molecular dynamics simulation protein conformation protein structural homology

FrogTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/Frog

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).

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms chemical models chemistry computational biology computer simulation ligands molecular conformation molecular structure pharmaceutical chemistry pliability protein databases proteins quantitative structure-activity relationship x-ray crystallography

Frog2Tool Content

http://bioserv.rpbs.univ-paris-diderot.fr/Frog2

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.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmolecular conformation molecular models pharmaceutical preparations stereoisomerism

IC50-to-KiTool Content

http://botdb.abcc.ncifcrf.gov/toxin/kiConverter.jsp

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.

NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

PharmMapperTool Content

http://59.78.96.61/pharmmapper

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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/

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

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.

NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
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/

Other Molecules > Compounds
Other Molecules > Metabolites
Other Molecules > Small Molecules
Protein > Interactions, Pathways, 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.

NAR Web Server Issue 2010
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsfactual databases isomerism metabolic networks and pathways molecular structure

SwissDockTool Content

http://www.swissdock.ch

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.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

TarFisDockTool Content

http://www.dddc.ac.cn/tarfisdock/

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdrug design ligands protein databases proteins tamoxifen vitamin e

wwLigCSRreTool Content

http://bioserv.rpbs.univ-paris-diderot.fr/wwLigCSRre.html

Other Molecules > Compounds
Other Molecules > Small Molecules
Protein > 3-D Structure Comparison

The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer-, and analgesic-focused libraries or DrugBank database.

NAR Web Server Issue 2009
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagscyclin-dependent kinase 2 drug design factual databases igf type 1 receptor ligands molecular models protein kinase inhibitors small molecule libraries structure-activity relationship

Tags associated with subcategory 'Other Molecules/Small Molecules'

ligands drug design factual databases pharmaceutical preparations proteins molecular structure pharmacokinetics chemistry computational biology chemical models tamoxifen structure-activity relationship algorithms computer simulation protein databases x-ray crystallography pharmacology quantitative structure-activity relationship pliability molecular conformation vitamin e pharmaceutical chemistry small molecule libraries protein kinase inhibitors molecular dynamics simulation protein conformation protein structural homology hemoglobins drug delivery systems binding sites enzyme inhibitors cyclin-dependent kinase 2 drug toxicity stereoisomerism isomerism kinetics igf type 1 receptor molecular models inhibitory concentration 50 enzymes metabolic networks and pathways hormonal antineoplastic agents national library of medicine (u.s.) united states