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BIPSTool Content

http://sbi.imim.es/BIPS.php [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

BIPS (Biana Interolog Prediction Server) webserver predicts putative interactions between proteins based on homologs found in Protein-Protein interaction databases. BIPS relies on data integrated in BIANA.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/ [open in a new window]

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Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

links directory index: 49
TitlePublication YearGoogle Scholar Citation Count
CRP: Cleavage of Radiolabeled Phosphoproteins20039
A strategy for the rapid identification of phosphorylation sites in the phosphoproteome200240
NAR Web Server Issue 2003
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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

DBD2BSTool Content

http://dbd2bs.csie.ntu.edu.tw/ [open in a new window]

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DNA > Structure and Sequence Feature Detection

DBD2BS web server uses the structure of DNA binding domains (DBDs) to predict the corresponding binding sites on DNA. Queries can be specified by a PDB ID or the coordinates of a DNA-binding protein in PDB format. DBD2BS currently maintains a list of 2,176 protein-DNA complexes and 3,135 unbound structures of DNA-binding proteins collected from PDB.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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DILIMOTTool Content

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

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Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

links directory index: 242
TitlePublication YearGoogle Scholar Citation Count
DILIMOT: discovery of linear motifs in proteins200670
Systematic discovery of new recognition peptides mediating protein interaction networks2005172
NAR Web Server Issue 2006
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DIMA 3.0Database Content

http://webclu.bio.wzw.tum.de/dima [open in a new window]

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Protein > Databases

Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
DIMA 3.0: Domain Interaction Map20118
NAR Database Issue 2011
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tagsmutation protein databases protein interaction domains and motifs protein interaction mapping

DIPDatabase Content

http://dip.doe-mbi.ucla.edu/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes

The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and update database entries.

links directory index: 2073
TitlePublication YearGoogle Scholar Citation Count
The Database of Interacting Proteins: 2004 update2004974
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions2002924
DIP: The Database of Interacting Proteins: 2001 update2001175
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ELMTool Content

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

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Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

links directory index: 1035
TitlePublication YearGoogle Scholar Citation Count
ELM--the database of eukaryotic linear motifs201215
ELM: the status of the 2010 eukaryotic linear motif resource201090
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins2003465
NAR Database Issue 2010NAR Web Server Issue 2003
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external linksLink on Wikipedia
tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology computer graphics disease eukaryota eukaryotic cells genetic databases humans information storage and retrieval internet molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins software tertiary protein structure user-computer interface viral proteins

ExPASy Molecular Biology ServerResource Content

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

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Education > Directories and Portals
Protein > Do-it-all Tools for Protein

ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

links directory index: 1342
TitlePublication YearGoogle Scholar Citation Count
ExPASy: The proteomics server for in-depth protein knowledge and analysis20031342
NAR Web Server Issue 2003NAR Web Server Issue 2012
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tagsenzymes gel electrophoresis internet molecular models protein conformation protein databases protein sequence analysis proteins proteomics software systems integration user-computer interface

GlobPlotTool Content

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

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Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

links directory index: 481
TitlePublication YearGoogle Scholar Citation Count
GlobPlot: Exploring protein sequences for globularity and disorder2003481
NAR Web Server Issue 2003
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GPSTool Content

http://csbl.bmb.uga.edu/~ffzhou/gps_web/ [open in a new window]

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Protein > Domains and Motifs

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.

This content is being maintained by ffzhou.

links directory index: 190
TitlePublication YearGoogle Scholar Citation Count
GPS: a comprehensive www server for phosphorylation sites prediction2005109
GPS: a novel group-based phosphorylation predicting and scoring method200481
NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence homology animals binding sites conserved sequence microfilament proteins nerve tissue proteins phosphoproteins phosphorylation protein binding protein kinases protein sequence analysis protein-serine-threonine kinases rats sequence alignment substrate specificity

IBISDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi [open in a new window]

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Protein > Databases

IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query.

links directory index: 33
TitlePublication YearGoogle Scholar Citation Count
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins20121
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites201032
NAR Database Issue 2010
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tagsalgorithms animals binding sites catalytic domain cluster analysis computational biology genetic databases humans protein databases protein interaction mapping protein-tyrosine kinases tertiary protein structure

iELMTool Content

http://i.elm.eu.org [open in a new window]

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Protein > Annotation and Function
Protein > Domains and Motifs

iELM webserver predicts the function and positional interface for short linear motifs important in protein-protein interactions.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count
NAR Web Server Issue 2012
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InterProDatabase Content

http://www.ebi.ac.uk/interpro/index.html [open in a new window]

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Protein > Domains and Motifs

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

links directory index: 3869
TitlePublication YearGoogle Scholar Citation Count
InterPro in 2011: new developments in the family and domain prediction database201211
The InterPro BioMart: federated query and web service access to the InterPro Resource20114
InterPro: the integrative protein signature database2009585
New developments in the InterPro database2007392
InterPro, progress and status in 20052005562
The InterPro Database, 2003 brings increased coverage and new features2003700
InterPro: an integrated documentation resource for protein families, domains and functional sites200299
The InterPro database, an integrated documentation resource for protein families, domains and functional sites2001758
InterPro--an integrated documentation resource for protein families, domains and functional sites2000758
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external linksLink on Wikipedia
tagsalgorithms amino acid repetitive sequences animals computational biology factual databases humans information services metabolic networks and pathways post-translational protein processing protein databases protein sequence analysis proteins search engine sequence alignment systems integration tertiary protein structure

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/ [open in a new window]

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Protein > Domains and Motifs
Protein > Networks & Interactions, Pathways and Enzymes

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

links directory index: 99
TitlePublication YearGoogle Scholar Citation Count
iSPOT: A web tool to infer the interaction specificity of families of protein modules200325
SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family200074
NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html [open in a new window]

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The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

links directory index: 3841
TitlePublication YearGoogle Scholar Citation Count
MEME SUITE: tools for motif discovery and searching2009174
MEME: discovering and analyzing DNA and protein sequence motifs2006507
Meta-MEME: motif-based hidden Markov models of protein families1997223
An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases199757
The megaprior heuristic for discovering protein sequence patterns199628
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool199697
The value of prior knowledge in discovering motifs with MEME1995492
Fitting a mixture model by expectation maximization to discover motifs in biopolymers19942263
NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation base sequence binding sites biopolymers computer communication networks databases as topic dna dna sequence analysis evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases internet mammals markov chains molecular models molecular sequence data nucleic acid repetitive sequences protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements user-computer interface

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