> Tag > Links tagged with 'protein interaction mapping'

Links tagged with 'protein interaction mapping'

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

Found 85 links

Displaying 15 links

Hide Resources (1)Hide Databases (45)Hide Tools (39)

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/ [open in a new window]

Share This Link
Protein > 3-D Structural Features
Protein > Networks & Interactions, Pathways and Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

links directory index: 27
TitlePublication YearGoogle Scholar Citation Count
3D-partner: a web server to infer interacting partners and binding models200727
NAR Web Server Issue 2007
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

3didDatabase Content

http://3did.irbbarcelona.org/ [open in a new window]

Share This Link
Protein > 3-D Structure Retrieval/Viewing
Protein > Databases

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
3did: identification and classification of domain-based interactions of known three-dimensional structure201121
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsmolecular models peptides protein databases protein interaction domains and motifs protein interaction mapping

APIDTool Content

http://bioinfow.dep.usal.es/apid/ [open in a new window]

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

Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.

links directory index: 88
TitlePublication YearGoogle Scholar Citation Count
APID: Agile Protein Interaction DataAnalyzer200688
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagscomputational biology protein databases protein interaction mapping

AtPIDDatabase Content

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

Share This Link
Model Organisms > Databases
Protein > Databases

The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis20114
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsarabidopsis proteins molecular sequence annotation protein databases protein interaction mapping proteomics

Bacteriome.orgDatabase Content

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

Share This Link
Model Organisms > Microbes
Protein > Networks & Interactions, Pathways and Enzymes

A database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Tools are provided which allow the user to select and visualize functional, evolutionary and structural relationships between groups of interacting proteins and to focus on genes of interest.

links directory index: 24
TitlePublication YearGoogle Scholar Citation Count
Bacteriome.org--an integrated protein interaction database for E. coli200824
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsescherichia coli escherichia coli proteins protein databases protein interaction mapping proteomics systems integration
setsUniversity of Toronto

BIND - The Biomolecular Interaction Network DatabaseDatabase Content

http://bond.unleashedinformatics.com/Action [open in a new window]

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

Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.

links directory index: 932
TitlePublication YearGoogle Scholar Citation Count
BIND: the Biomolecular Interaction Network Database2003752
BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways2000180
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence animals dna factual databases humans macromolecular substances molecular biology protein databases protein interaction mapping proteins rna sequence alignment statistical models tertiary protein structure

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/ [open in a new window]

Share This Link
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

links directory index: 64
TitlePublication YearGoogle Scholar Citation Count
BiologicalNetworks: visualization and analysis tool for systems biology200664
PathSys: integrating molecular interaction graphs for systems biology.20060
NAR Web Server Issue 2006
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

BioMet ToolboxTool Content

http://www.sysbio.se/BioMet [open in a new window]

Share This Link
Expression > Networks
Expression > Transcript Expression Analysis
Other Molecules > Metabolites
Protein > Networks & Interactions, Pathways and Enzymes

The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rates and metabolic production rates. Files for model organisms are included.

This content is being maintained by marija.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
BioMet Toolbox: genome-wide analysis of metabolism201017
NAR Web Server Issue 2010
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms ethanol gene expression profiling gene expression regulation genome glucose metabolic networks and pathways protein interaction mapping transcription factors

BioProfiling.deTool Content

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

Share This Link
Expression > Gene Set Analysis

BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
BioProfiling.de: analytical web portal for high-throughput cell biology20113
NAR Web Server Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsaniline compounds animals drug discovery factual databases gene regulatory networks genes high-throughput screening assays humans mice nitriles protein interaction mapping protein kinase inhibitors proteins quinolines rats

BIOSMILETool Content

http://bws.iis.sinica.edu.tw/BWS/ [open in a new window]

Share This Link
Literature > Text Mining and Semantics

BIOSMILE is a web-based NCBI PubMed search tool. Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
BIOSMILE web search: a web application for annotating biomedical entities and relations20089
NAR Web Server Issue 2008
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsgenes protein interaction mapping pubmed

BioverseTool Content

http://bioverse.compbio.washington.edu/ [open in a new window]

Share This Link
DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

links directory index: 95
TitlePublication YearGoogle Scholar Citation Count
Functional annotation from predicted protein interaction networks200537
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes200513
Enhanced functional information from predicted protein networks200420
Bioverse: Functional, structural and contextual annotation of proteins and proteomes200325
NAR Web Server Issue 2005NAR Web Server Issue 2003
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

BISCDatabase Content

http://bisc.cse.ucsc.edu [open in a new window]

Share This Link
Protein > Databases

Binary subcomplexes in proteins database (BISC) is a protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BISC: binary subcomplexes in proteins database20111
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsgenetic databases genomics molecular models multiprotein complexes protein databases protein interaction mapping

ChemProtDatabase Content

http://www.cbs.dtu.dk/services/ChemProt/ [open in a new window]

Share This Link
Other Molecules > Databases
Protein > 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.

This content is being maintained by otab.

links directory index: 10
TitlePublication YearGoogle Scholar Citation Count
ChemProt: a disease chemical biology database201110
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsdisease drug discovery factual databases genes humans pharmaceutical preparations protein interaction mapping proteins

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

Share This Link
Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
NAR Web Server Issue 2004
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

ConsensusPathDBDatabase Content

http://cpdb.molgen.mpg.de [open in a new window]

Share This Link
Human Genome > Databases
Model Organisms > Databases
Protein > Databases

ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. ConsensusPathDB offers different ways of utilizing these integrated interaction data, with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
ConsensusPathDB: toward a more complete picture of cell biology201115
NAR Database Issue 2011
downloadLink as XML Link as JSON Link as TSV Link as CSV
user feedback
0
external linksLink on Wikipedia
tagsanimals factual databases gene expression gene regulatory networks genetic databases humans metabolic networks and pathways mice protein interaction mapping signal transduction

Associated Tag Cloud