> > Proteomics

Proteomics

This section contains links to general proteomics resources, methods, software, and databases.

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Found 33 links

Displaying 15 links

bioNMFTool Content

http://bionmf.dacya.ucm.es/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression
Expression > Transcript Expression Analysis
Literature > Text Mining and Semantics
Protein > Proteomics

A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

NAR Web Server Issue 2008
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tagsalgorithms cluster analysis computational biology gene expression profiling

DeNovoIDDatabase Content

http://proteomics.mcw.edu/denovoid/

Protein > Proteomics

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

NAR Web Server Issue 2005
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tagsalgorithms amino acids mass spectrometry peptides protein databases protein sequence analysis proteomics

ExPASy Proteomics toolsResource Content

http://us.expasy.org/tools/

Protein > Proteomics

Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.

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GELBANKDatabase Content

http://gelbank.anl.gov/

Expression > Protein Expression
Protein > Protein Expression
Protein > Proteomics

GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available.

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tagsfactual databases gel electrophoresis genome humans hydrogen-ion concentration molecular weight proteome proteomics research design

Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/

Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

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tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

HUPO Proteomics Standards InitiativeResource Content

http://psidev.sourceforge.net/

Protein > Proteomics

HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.

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tagsbiochemistry database management systems guidelines as topic humans internationality mass spectrometry natural language processing peptide mapping protein binding protein databases protein interaction mapping proteins proteomics reference standards

iSARSTTool Content

http://sarst.life.nthu.edu.tw/iSARST/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing
Protein > Proteomics

iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.

NAR Web Server Issue 2009
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tagsprotein databases protein structural homology systems integration

ISOTOPICATool Content

http://coco.protein.osaka-u.ac.jp/isotopica/

Protein > Proteomics

Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.

NAR Web Server Issue 2004
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tagsamino acid sequence base sequence biopolymers carbohydrate sequence ions isotopes mass spectrometry mathematical computing peptide mapping

ISPIDER CentralTool Content

http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl

Protein > Proteomics

The ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from searches for integrative in silico experiments in proteomics.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases proteomics systems integration
setsUniversity of Manchester

JVirGelTool Content

http://www.jvirgel.de/

Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

NAR Web Server Issue 2003
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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics reproducibility of results

KEGG: Kyoto Encyclopedia of Genes and GenomesDatabase Content

http://www.genome.ad.jp/kegg/

Expression > Networks
Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PATHWAY (interaction networks for cellular processes), and LIGAND (chemical compounds and chemical reactions). KEGG Atlas is a new tool for the global analysis of metabolic pathways.

NAR Web Server Issue 2008
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tagsamino acid sequence animals biological models computational biology computer simulation disease factual databases gene expression genes genetic models genome genomics humans japan ligands metabolic networks and pathways metabolism molecular sequence data molecular structure pharmaceutical preparations protein binding proteome sequence homology systems biology systems integration

MASCOT (Matrix Science)Tool Content

http://www.matrixscience.com/

Protein > Biochemical Features
Protein > Proteomics

Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.

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tagsamino acid sequence amino acids factual databases mass spectrometry molecular sequence data molecular weight nucleic acids probability protein biosynthesis proteins

MassNetTool Content

http://massnet.kr

Protein > Do-it-all Tools for Protein
Protein > Proteomics

MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.

NAR Web Server Issue 2008
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tagsmass spectrometry protein databases protein interaction mapping proteins

MassTRIXTool Content

http://masstrix.org

Other Molecules > Metabolites
Protein > Proteomics

With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.

NAR Web Server Issue 2008
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tagsgene expression mass spectrometry metabolic networks and pathways

massXpertTool Content

http://www.massxpert.org

Protein > Proteomics

massXpert is a proteomics-oriented program mainly concerned with protein physico-chemistry and protein/peptide mass spectra simulations.

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tagsdata display mass spectrometry protein conformation proteome

Tags associated with subcategory 'Protein/Proteomics'

mass spectrometry proteins protein databases proteomics protein sequence analysis humans amino acid sequence algorithms animals computational biology proteome systems integration peptides factual databases genomics statistical data interpretation protein conformation molecular weight protozoan proteins plasmodium falciparum statistical models sinorhizobium meliloti genetic databases automatic data processing sensitivity and specificity genetic transcription invertebrate hormones regression analysis open reading frames mitochondrial dna fungal proteins fungal genome peptide fragments saccharomyces cerevisiae protein precursors neuropeptides logistic models terminator codon genetic polymorphism isoelectric point ribosomal proteins amino acid sequence homology protein disulfide-isomerases cattle software design apolipoprotein a-i archaeal proteins bacterial proteins protein biosynthesis probability nucleic acids mice molecular sequence data programming languages natural language processing post-translational protein processing sequence alignment polysaccharides saccharomyces cerevisiae proteins sequence tagged sites ions isotopes molecular models information dissemination reproducibility of results mathematical computing peptide mapping protein folding multiprotein complexes documentation data display carbohydrate sequence biopolymers gel electrophoresis base sequence computer simulation biochemistry binding sites drug discovery quantitation protein array analysis database management systems guidelines as topic alternative splicing bacterial rna electrophoresis genome metabolism japan biological models genetic models brca1 protein molecular structure aplysia bacterial genome gene expression genes pharmaceutical preparations biomolecular nuclear magnetic resonance ligands protein structural homology