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Links tagged with 'pharmaceutical preparations'

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BioDrugScreenDatabase Content

http://www.biodrugscore.org

Other Molecules > Databases

BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets in BioDrugScreen originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, which we have created for the purpose of this effort. This makes the BioDrugScreen resource highly valuable in drug discovery.

NAR Database Issue 2010
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tagscomputational biology drug design genetic databases humans ligands nucleic acid databases pharmaceutical preparations preclinical drug evaluation protein binding proteome proteomics

ChEBIDatabase Content

http://www.ebi.ac.uk/chebi/

Other Molecules > Databases

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities.

NAR Database Issue 2010
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tagsagrochemicals animals biological products chemical dictionaries computational biology controlled vocabulary factual databases humans pharmaceutical preparations
setsEuropean Bioinformatics Institute (EBI)

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
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tagsalgorithms cluster analysis data mining drug discovery genomics pharmaceutical preparations small molecule libraries structure-activity relationship

ChemProtDatabase Content

http://www.cbs.dtu.dk/services/ChemProt/

Other Molecules > Databases

ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events.

NAR Database Issue 2011
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tagsdisease drug discovery factual databases genes humans pharmaceutical preparations protein interaction mapping proteins

DrugBank 3.0Database Content

http://www.drugbank.ca

Other Molecules > Databases

DrugBank is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, proteins, genes and organisms on which these drugs act. New data field additions include illustrated drug-action pathways, drug transporter data, drug metabolite data, pharmacogenomic data, adverse drug response data, ADMET data, pharmacokinetic data, computed property data and chemical classification data. DrugBank 3.0 also offers expanded database links, improved search tools for drug-drug and food-drug interaction, new resources for querying and viewing drug pathways and hundreds of new drug entries with detailed patent, pricing and manufacturer data.

NAR Database Issue 2011
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tagsfactual databases metabolomics pharmaceutical preparations pharmacogenetics pharmacological processes proteomics

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

EDULISSDatabase Content

http://eduliss.bch.ed.ac.uk/

Other Molecules > Databases

EDULISS (EDinburgh University Ligand Selection System) database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition is demonstrated by making use of small subgroups of the descriptors.

NAR Database Issue 2011
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tagscyclin-dependent kinases data mining enzyme inhibitors factual databases pharmaceutical preparations protein kinase inhibitors pyruvate kinase small molecule libraries

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
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tagsdrug design drug toxicity pharmaceutical preparations pharmacokinetics

FMMTool Content

http://FMM.mbc.nctu.edu.tw/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.

NAR Web Server Issue 2009
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tagsbacteria factual databases metabolic networks and pathways pharmaceutical preparations plants

FragmentStoreDatabase Content

http://bioinformatics.charite.de/fragment_store

Other Molecules > Databases

FragmentStore, a resource for the comparison of fragments found in metabolites, drugs or toxic compounds. Starting from 13,000 metabolites, 16,000 drugs and 2200 toxic compounds we generated 35,000 different building blocks (fragments), which are not only relevant to their biosynthesis and degradation but also provide important information regarding side-effects and toxicity. The FragmentStore provides a variety of search options such as 2D structure, molecular weight, rotatable bonds, etc. Various analysis tools have been implemented including the calculation of amino acid preferences of fragments' binding sites, classification of fragments based on the enzyme classification class of the enzyme(s) they bind to and small molecule library generation via a fragment-assembler tool.

This content is being maintained by robertpreissner.

NAR Database Issue 2011
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tagsbinding sites drug design drug toxicity factual databases metabolic networks and pathways pharmaceutical preparations

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

IUPHAR-DBDatabase Content

http://www.iuphar-db.org

Protein > Databases

The IUPHAR database is an online reference resource for classes of human drug targets and related proteins. As well as providing recommended nomenclature, the database integrates information on the chemical, genetic, functional and pathophysiological properties of receptors and ion channels, curated and peer-reviewed from the biomedical literature by a network of experts. The database now includes information from four superfamilies in human and rodent model organisms: G protein-coupled receptors, voltage- and ligand-gated ion channels and nuclear hormone receptors (NHRs). New data types for NHRs include details on co-regulators, DNA binding motifs, target genes and 3D structures. The interface provides tools for the visualization and exploration of ligand structure-activity relationships and the structural diversity of compounds active at each target.

NAR Database Issue 2011
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tagsanimals cytoplasmic and nuclear receptors g-protein-coupled receptors humans ion channels ligands pharmaceutical preparations protein databases

KEGGDatabase Content

http://www.genome.ad.jp/kegg

Model Organisms > Databases

The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmental factors at the molecular level, diagnostic markers and therapeutic drugs, which may reflect the underlying molecular system. The KEGG DRUG database contains chemical structures and/or chemical components of all drugs in Japan, including crude drugs and TCM (Traditional Chinese Medicine) formulas, and drugs in the USA and Europe. The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets.

NAR Database Issue 2010
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tagsalgorithms computational biology genetic databases human genome humans ligands nucleic acid databases pharmaceutical preparations protein databases protein interaction mapping systems biology tertiary protein structure

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MEDockTool Content

http://medock.csie.ntu.edu.tw/

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.

This content is being maintained by dirty.

NAR Web Server Issue 2005
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tagsalgorithms binding sites computer simulation dna drug design entropy ligands molecular models pharmaceutical preparations proteins