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Links tagged with 'drug design'

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Found 19 links

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ASDDatabase Content

http://mdl.shsmu.edu.cn/ASD/

Protein > Databases

AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.

NAR Database Issue 2011
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tagsallosteric regulation allosteric site drug design protein databases proteins

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

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

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

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

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

KinDOCKTool Content

http://abcis.cbs.cnrs.fr/kindock/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).

NAR Web Server Issue 2006
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tagsadenosine triphosphate binding sites drug design ligands protein conformation protein kinase inhibitors protein kinases

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

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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tagsbiomimetic materials chemoinformatics drug design molecular models peptides peptidomimetics protein conformation virtual screening

PharmaGistTool Content

http://bioinfo3d.cs.tau.ac.il/PharmaGist

Protein > Molecular Dynamics and Docking

PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with the receptor for outputs of candidate pharmacophores that can be used in rational drug design.

NAR Web Server Issue 2008
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tagsalgorithms drug design ligands molecular models pharmaceutical preparations

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

QuadruplexTool Content

http://www.quadruplex.org

DNA > Structure and Sequence Feature Detection

A website to serve the quadruplex community. Contains conference information, forums, database and parsers.

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tagsanimals antineoplastic agents drug design g-quadruplexes gene expression regulation gene therapy genetic promoter regions guanine humans ligands molecular models molecular structure neoplasms neoplastic gene expression regulation nucleic acid conformation telomere theoretical models

SfoldTool Content

http://sfold.wadsworth.org

DNA > Tools For the Bench
Expression > Gene Regulation
RNA > Structure Prediction, Visualization, and Design

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

NAR Web Server Issue 2004
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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

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

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
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tagsdrug design ligands molecular models protein conformation protein engineering