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Compounds

Tools and resources for the analysis of compounds

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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
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ChemSynthesisDatabase Content

http://www.chemsynthesis.com/index.html

Other Molecules > Compounds

ChemSynthesis is a freely accessible database of chemicals. This website contains substances with their synthesis references and physical properties such as melting point, boiling point and density. Over 40,000 compounds are listed.

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DRAR-CPITool Content

http://cpi.bio-x.cn/drar/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.

NAR Web Server Issue 2011
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e-LEA3DTool Content

http://bioinfo.ipmc.cnrs.fr/lea.html

Other Molecules > Compounds

e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.

NAR Web Server Issue 2010
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tagsbenzoic acid computational biology drug design ligands pharmaceutical preparations retinoic acid receptors

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
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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
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tagsenzyme inhibitors enzymes inhibitory concentration 50 kinetics ligands

MetalDetectorTool Content

http://metaldetector.dsi.unifi.it/v2.0/

Other Molecules > Compounds
Protein > Sequence Features

MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.

NAR Web Server Issue 2011
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pepMMsMIMICTool Content

http://mms.dsfarm.unipd.it/pepMMsMIMIC

Other Molecules > Compounds
Protein > 3-D Structure Comparison

pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.

This content is being maintained by matteofloris.

NAR Web Server Issue 2011
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tagschemoinformatics peptidomimetics virtual screening

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
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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/

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
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tagsfactual databases molecular structure national library of medicine (u.s.) pharmaceutical preparations pharmacology structure-activity relationship united states

SePreSATool Content

http://SePreSA.Bio-X.cn/

Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program.

NAR Web Server Issue 2009
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tagsalgorithms binding sites drug toxicity genetic polymorphism humans molecular models pharmaceutical preparations protein conformation proteins

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
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tagsfactual databases isomerism metabolic networks and pathways molecular structure

SuperPredTool Content

http://bioinformatics.charite.de/superpred

Other Molecules > Compounds

The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. Such information can be useful in drug classification and target prediction.

This content is being maintained by robertpreissner.

NAR Web Server Issue 2008
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tagsbiological effect drug classification and target prediction drug design structure-activity relationship world health organization

UM-PPSTool Content

http://umbbd.msi.umn.edu/predict/

Model Organisms > Microbes
Other Molecules > Compounds
Protein > Interactions, Pathways, Enzymes

The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of these groups based on biotransformation rules. Multi-level predictions are made.

This content is being maintained by lynda.

NAR Web Server Issue 2008NAR Web Server Issue 2011
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tagsbiotransformation environmental pollutants factual databases

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
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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/Compounds'

pharmaceutical preparations factual databases ligands drug design molecular models structure-activity relationship binding sites molecular structure proteins igf type 1 receptor inhibitory concentration 50 kinetics enzymes algorithms protein kinase inhibitors humans protein conformation genetic polymorphism drug toxicity small molecule libraries world health organization united states pharmacology cyclin-dependent kinase 2 biotransformation environmental pollutants enzyme inhibitors molecular conformation chemoinformatics peptidomimetics virtual screening biological effect drug classification and target prediction hormonal antineoplastic agents tamoxifen national library of medicine (u.s.) metabolic networks and pathways isomerism stereoisomerism benzoic acid computational biology retinoic acid receptors