> Tag > Links tagged with 'factual databases'

Links tagged with 'factual databases'

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Found 132 links

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The BRENDA Tissue Ontology (BTO)Database Content

http://www.BTO.brenda-enzymes.org [open in a new window]

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Other Molecules > Databases

BTO, the BRENDA Tissue Ontology is a structured encyclopedia of tissue terms. BTO contains different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues.

This content is being maintained by Dietmar Schomburg.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources20115
NAR Database Issue 2011
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tagscell line cells controlled vocabulary dictionaries as topic enzymes factual databases systems integration

The Comparative Toxicogenomics DatabaseDatabase Content

http://ctd.mdibl.org [open in a new window]

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Other Molecules > Databases

The Comparative Toxicogenomics Database (CTD) is a curated database about the interaction of environmental chemicals with gene products, and their effects on human health. New features include statistical analyses and analytical tools, including GeneComps and ChemComps (to find comparable genes and chemicals that share toxicogenomic profiles), enriched Gene Ontology terms associated with chemicals, statistically ranked chemical-disease inferences, Venn diagram tools to discover overlapping and unique attributes of any set of chemicals, genes or disease, and enhanced gene pathway data content, among other features.

links directory index: 36
TitlePublication YearGoogle Scholar Citation Count
The Comparative Toxicogenomics Database: update 2011201136
NAR Database Issue 2011
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tagsdisease environmental exposure factual databases gene regulatory networks genes hazardous substances humans toxicogenetics

TIGR Gene IndicesTool Content

http://compbio.dfci.harvard.edu/tgi/ [open in a new window]

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Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Fish
Model Organisms > Fly
Model Organisms > General Resources
Model Organisms > Mouse and Rat
Model Organisms > Other Organisms
Model Organisms > Other Vertebrates
Model Organisms > Worm

An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.

links directory index: 703
TitlePublication YearGoogle Scholar Citation Count
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species2001408
The TIGR gene indices: reconstruction and representation of expressed gene sequences2000295
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tagsanimals base sequence database management systems dna expressed sequence tags factual databases genes human genome project humans molecular sequence data nucleic acid sequence homology sequence alignment species specificity

TMBETA-NETTool Content

http://psfs.cbrc.jp/tmbeta-net/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins200529
Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins200470
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acids bacterial outer membrane proteins cell membrane factual databases membrane proteins molecular models neural networks (computer) reproducibility of results secondary protein structure

TogoWSTool Content

http://togows.dbcls.jp/ [open in a new window]

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Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services20109
NAR Web Server Issue 2010
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tagscomputational biology factual databases systems integration

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/ [open in a new window]

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Protein > 2-D Structure Prediction
Protein > Localization and Targeting

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

links directory index: 984
TitlePublication YearGoogle Scholar Citation Count
TRAMPLE: the transmembrane protein labelling environment200510
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins2002160
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor2001101
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins199625
Topology prediction for helical transmembrane proteins at 86% accuracy1996688
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

tRNAscan-SETool Content

http://lowelab.ucsc.edu/tRNAscan-SE/ [open in a new window]

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RNA > Functional RNAs

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

links directory index: 2589
TitlePublication YearGoogle Scholar Citation Count
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs2005125
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence19972464
NAR Web Server Issue 2005
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tagsanimals bacterial rna evaluation studies as topic factual databases genome genomics introns rna small nucleolar rna transfer rna

TTDDatabase Content

http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp [open in a new window]

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Other Molecules > Databases

Therapeutic Target Database (TTD) has been developed to provide information about therapeutic targets and corresponding drugs. TTD includes information about successful, clinical trial and research targets, approved, clinical trial and experimental drugs linked to their primary targets, new ways to access data by drug mode of action, recursive search of related targets or drugs, similarity target and drug searching, customized and whole data download, and standardized target ID.

links directory index: 46
TitlePublication YearGoogle Scholar Citation Count
Update of TTD: Therapeutic Target Database201046
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsclinical trials as topic computational biology drug approval drug therapy factual databases genetic databases humans pharmaceutical chemistry pharmaceutical preparations protein databases united states united states food and drug administration

UM-PPSTool Content

http://umbbd.msi.umn.edu/predict/ [open in a new window]

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Model Organisms > Microbes
Other Molecules > Compounds
Protein > Networks & Interactions, Pathways and 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.

links directory index: 35
TitlePublication YearGoogle Scholar Citation Count
The University of Minnesota pathway prediction system: predicting metabolic logic200835
NAR Web Server Issue 2008NAR Web Server Issue 2011
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tagsbiotransformation environmental pollutants factual databases

WebFEATURETool Content

http://feature.stanford.edu/webfeature/ [open in a new window]

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Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
WebFEATURE: An interactive web tool for identifying and visualizing functional sites on macromolecular structures200364
Recognizing protein binding sites using statistical descriptions of their 3D environments199857
NAR Web Server Issue 2003
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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

WebLabTool Content

http://weblab.cbi.pku.edu.cn [open in a new window]

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Computer Related > Web Services

An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share data under an intuitive web interface. These tools can be further organized as customized workflows.

This content is being maintained by Yang Ding.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
WebLab: a data-centric, knowledge-sharing bioinformatic platform20099
NAR Web Server Issue 2009
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tagscomputational biology cooperative behavior factual databases

wwLigCSRreTool Content

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

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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.

This content is being maintained by tuffery.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
wwLigCSRre: a 3D ligand-based server for hit identification and optimization20094
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

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