> Tag > Links tagged with 'factual databases'

Links tagged with 'factual databases'

RSS Feed Compact View Sort by Links Directory Index
downloadList as XML List as JSON List as TSV List as CSV

Found 132 links

Displaying 15 links

Hide Resources (7)Hide Databases (53)Hide Tools (72)

SPACETool Content

http://ligin.weizmann.ac.il/space/ [open in a new window]

Share This Link
Protein > 3-D Structure Prediction

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

This content is being maintained by lpsobol.

links directory index: 692
TitlePublication YearGoogle Scholar Citation Count
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment200537
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins200456
MutaProt: a web interface for structural analysis of point mutations20019
Automated analysis of interatomic contacts in proteins1999457
Molecular docking using surface complementarity1996133
NAR Web Server Issue 2005
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms amino acids automation bacterial proteins binding sites biotin computational biology factual databases formycins hydrogen bonding ligands molecular conformation molecular models molecular structure nucleic acids point mutation protein binding protein conformation protein databases proteins ribonucleotides ricin site-directed mutagenesis solvents streptavidin thermodynamics water x-ray crystallography

SPIKEDatabase Content

http://www.cs.tau.ac.il/~spike/ [open in a new window]

Share This Link
Human Genome > Databases
Protein > Networks & Interactions, Pathways and Enzymes

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database for highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. Pathways are laid out as maps that reflect the curator's understanding and make the utilization of the pathways easy. The database currently focuses primarily on pathways describing DNA damage response, cell cycle, programmed cell death and hearing related pathways.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
SPIKE: a database of highly curated human signaling pathways20114
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsapoptosis cell cycle dna damage factual databases humans intercellular signaling peptides and proteins signal transduction

SSAHA2Tool Content

http://www.sanger.ac.uk/resources/software/ssaha2/ [open in a new window]

Share This Link
DNA > Mapping and Assembly
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Pairwise Sequence Alignments

SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.

links directory index: 490
TitlePublication YearGoogle Scholar Citation Count
SSAHA: a fast search method for large DNA databases2001490
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms base composition base sequence database management systems dna factual databases sensitivity and specificity sequence alignment

SStructViewTool Content

http://helix-web.stanford.edu/sstructview/home.html [open in a new window]

Share This Link
RNA > Structure Prediction, Visualization, and Design

RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.

links directory index: 18
TitlePublication YearGoogle Scholar Citation Count
RNA secondary structure as a reusable interface to biological information resources199718
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbase sequence factual databases molecular sequence data nucleic acid conformation rna

STITCHDatabase Content

http://stitch.embl.de [open in a new window]

Share This Link
Protein > Databases

STITCH database integrates the data for interactions between small molecules and proteins dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. Interactions are incorporated from BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses.

This content is being maintained by MKuhn.

links directory index: 178
TitlePublication YearGoogle Scholar Citation Count
STITCH 3: zooming in on protein-chemical interactions.201211
STITCH 2: an interaction network database for small molecules and proteins201064
STITCH: interaction networks of chemicals and proteins2008103
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals aspirin biochemical processes chemical models computational biology factual databases humans information storage and retrieval internet pharmaceutical preparations preclinical drug evaluation protein databases protein interaction mapping proteins software stereoisomerism user-computer interface

STRAPTool Content

http://www.bioinformatics.org/strap/ [open in a new window]

Share This Link
Protein > 3-D Structure Comparison
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done using one of several methods, including ClustalW, JAligner and T_coffee. STRAP is also able to incorporate structure information and interfaces with programs such as Pymol and Rasmol. There is also a tutorial included.

links directory index: 121
TitlePublication YearGoogle Scholar Citation Count
KISS for STRAP: user extensions for a protein alignment editor200316
STRAP: editor for STRuctural Alignments of Proteins2001105
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscysteine endopeptidases factual databases molecular models multienzyme complexes proteasome endopeptidase complex protein databases protein sequence analysis proteins sequence alignment

SuperimposeTool Content

http://bioinformatics.charite.de/superimpose [open in a new window]

Share This Link
Protein > 3-D Structure Comparison

Superimpose web server performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selection of algorithms and databases that best suit their needs.

links directory index: 16
TitlePublication YearGoogle Scholar Citation Count
Superimpose: a 3D structural superposition server200816
NAR Web Server Issue 2008
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms binding sites factual databases molecular conformation molecular models pharmaceutical preparations protein structural homology proteins

SuperSweetDatabase Content

http://bioinformatics.charite.de/sweet/ [open in a new window]

Share This Link
Other Molecules > Databases

SuperSweet is a collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Structural information and properties such as number of calories, therapeutic annotations and a sweetness-index are stored in SuperSweet. The database provides a modeled 3D structure of the sweet taste receptor and binding poses of the small sweet molecules. A user-friendly graphical interface allows similarity searching, visualization of docked sweeteners into the receptor etc. A sweetener classification tree and browsing features allow quick requests to be made to the database.

This content is being maintained by robertpreissner.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
SuperSweet--a resource on natural and artificial sweetening agents20113
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsamino acids binding sites carbohydrates factual databases g-protein-coupled receptors protein structural homology proteins sweetening agents

Swiss ModelTool Content

http://www.expasy.ch/swissmod/SWISS-MODEL.html [open in a new window]

Share This Link
Protein > 3-D Structure Prediction

Automated protein modelling server.

links directory index: 11411
TitlePublication YearGoogle Scholar Citation Count
The SWISS-MODEL Repository: new features and functionalities200681
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling20061560
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models2004229
SWISS-MODEL: An automated protein homology-modeling server20032847
Large scale protein modelling and model repository199726
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling19976668
NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Twitter Link on Wikipedia
tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence automation chemical models computational biology computer simulation factual databases genome humans molecular models molecular sequence data online systems protein conformation protein databases protein sequence analysis protein structural homology proteins reproducibility of results sequence alignment switzerland systems integration

SWISS-2DPAGEDatabase Content

http://us.expasy.org/ch2d/ [open in a new window]

Share This Link
Expression > Protein Expression
Protein > Protein Expression

This is a 2D gel electrophoresis database containing data for proteins identified on SDS-PAGE or 2D-PAGE reference maps.

links directory index: 103
TitlePublication YearGoogle Scholar Citation Count
The 1999 SWISS-2DPAGE database update2000103
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsanimals dictyostelium escherichia coli factual databases gel electrophoresis humans mice saccharomyces cerevisiae

SYFPEITHIDatabase Content

http://www.syfpeithi.de/ [open in a new window]

Share This Link
Protein > Databases

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. The database can be used to predict the immunogenicity of given peptide sequences.

links directory index: 1525
TitlePublication YearGoogle Scholar Citation Count
SYFPEITHI: database for MHC ligands and peptide motifs19991525
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid motifs amino acid sequence amino acid sequence homology animals factual databases humans immunogenicity prediciton ligands major histocompatibility complex molecular sequence data

Systems Biology Markup Language (SBML)Resource Content

http://www.sbml.org/ [open in a new window]

Share This Link
Computer Related > Bio-* Programming Tools

The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology.

links directory index: 1440
TitlePublication YearGoogle Scholar Citation Count
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models20031440
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Twitter Link on Wikipedia
tagsbiological models chemical models controlled vocabulary database management systems documentation factual databases gene expression regulation metabolism programming languages software design terminology as topic

T-COFFEETool Content

http://www.tcoffee.org/ [open in a new window]

Share This Link

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

links directory index: 4274
TitlePublication YearGoogle Scholar Citation Count
R-Coffee: a web server for accurately aligning noncoding RNA sequences200817
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods200768
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments200615
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee2006137
3DCoffee: combining protein sequences and structures within multiple sequence alignments2004222
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment2004121
Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments2003201
T-Coffee: A novel method for fast and accurate multiple sequence alignment20003173
COFFEE: an objective function for multiple sequence alignments1998183
NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Twitter Link on Wikipedia
tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence databases as topic dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans information storage and retrieval internet messenger rna molecular sequence data nucleic acid conformation phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment software untranslated rna user-computer interface

T3DBDatabase Content

http://www.t3db.org [open in a new window]

Share This Link
Other Molecules > Databases

The Toxin and Toxin-Target Database (T3DB) is a unique bioinformatics resource that compiles comprehensive information about common or ubiquitous toxins and their toxin-targets. Each T3DB record (ToxCard) contains over 80 data fields providing detailed information on chemical properties and descriptors, toxicity values, protein and gene sequences (for both targets and toxins), molecular and cellular interaction data, toxicological data, mechanistic information and references. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, government documents, textbooks and scientific journals. A key focus of the T3DB is on providing 'depth' over 'breadth' with detailed descriptions, mechanisms of action, and information on toxins and toxin-targets. Potential applications of the T3DB include clinical metabolomics, toxin target prediction, toxicity prediction and toxicology education.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
T3DB: a comprehensively annotated database of common toxins and their targets20107
NAR Database Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbiological toxins computational biology drug design drug toxicity factual databases humans pharmaceutical preparations pharmacology protein databases reproducibility of results

TDR TargetsDatabase Content

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

Share This Link
Human Genome > Health and Disease
Other Molecules > Databases

Tropical Disease Research (TDR) Database: Designed and developed to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data for genes collected from various sources, including literature curation. Information can be browsed and queried.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
TDR Targets: a chemogenomics resource for neglected diseases.20125
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsdrug discovery factual databases genomics helminth genome humans neglected diseases pharmaceutical preparations proteins

Associated Tag Cloud