Databases

Presented are a number of links, in no particular order, to proteomic and protein databases as well as tools for Mass Spectrometry and Visualisation. These are currently mainly generic or associated with human biology and diseases but will be expanded in future to include other organisms. Please let Pastel BioScience know (resources@pastelbioscience.co.uk) of other databases that may be useful to the proteomics community.


Main Proteomics Databases


Uniprot

ExPaSy | Swissprot

EMBL-EBI | PRIDE

.....Omics Discovery Index

.....Pfam

.....InterPro

.....ProtVista

.....PDBe

.....PDBsum

.....IntAct

.....CATH

.....SCOP

.....SIFTS

.....EMPIAR

.....PIA

.....HMMER

.....Expression Atlas

OMICSDI | linking public omics data sets w/ Omics Discovery Index

THE GPM

GPMDB Proteome Database

PeptideAtlas

MassIVE

PIR | Protein Information Resource

ProteomeXchange

Human Proteome Map

hu.MAP | Human Protein Complex Map

ProteomicsDB | DB using SAP HANA from Technische Universitat Munchen

Human Protein Atlas

TPB Home | the proteome browser

neXtProt | exploring the universe of human proteins

neXtProt - tools | peptide uniqueness checker

APPRIS | annotating principal splice isoforms

Superfamily

Cape & Caper | designed to visualize human proteomic datasets

CHPP | Chromosome-centric Human Proteome Project

PEDANT | Protein Extraction, Description and ANalysis Tool

Proteome Quality Index | using comprehensive database of downloadable proteomes

bioDBnet | integrates biological DBs e.g. Gene, UniProt, Ensembl, GO, Affy, RefSeq etc


Tissue / organelle specifc


MetaMass | tool for meta-analysis of subcellular proteomics data

TissueNet | protein-protein interactions across human tissues

Human Plasma Proteome Project Data Central at Peptide Atlas

Liverbase 2.0

HKUPP | Kidney and Urinary

Salivaomics | salivary omics database

MitProNet | Mitochondrial proteome

MitoMiner | Mitochondrial proteome

MitoCarta2.0 | inventory of mammalian mitochondrial proteins

MPIC | Mitochondrial Protein Import Components

HSPD | Human (Homo sapiens) Sperm Proteome Database

Membranome | structural & functional data of bitopic transmembrane proteins

HTP | resources of the a-helical human transmembrane proteins

MVsCarta | compendium of microvescicles protein components

MetazSecKB | human/animal secretomes plus other subcellular locations

MatrisomeDB | normal and tumor extracellular matrices

COMPARTMENTS | Subcellular localization database

TISSUES | Tissue expression database

PredHSP | Heat Shock proteins and their class


Disease specifc


Alzbiomarker | Alzheimer biomarker measurements from cerebrospinal fluid & blood

DAPD | Diabetes Associated Proteins Database

BiomarkerBase | Amplion

BioPathways at Covance

Diagnostic and Prognostic biomarker database

DISEASES | Disease-gene associations mined from literature


Cancer


Cancer DriverDB | the open database of cancer biomarkers

canSAR v2.0 | Integrated Cancer Drug Discovery Platform, CRUK

TCPA | The Cancer Proteome Atlas

NCI-60 Cancer proteome database

CPTAC | Clinical Proteomic Tumor Analysis Consortium

The CPTAC Assay Protal

CMPD | cancer mutant proteome database

MCLP | functional proteomics of cancer cell lines

CanProVar | germline & somatic variations in the human proteome

MYCbase | Myc assocaited database

Colorectal cancer atlas | quant. & non-quant. protein expression data

Acute Myeloid Leukemia Protein Galaxy


PTM specific


PTM-SD | Post Translational Modification Structural Database

iPTMnet | protein post-translational modifications (PTMs) in systems biology context

ModProt | post-translational modification map of proteome

PTMfunc | functional predictions for protein post-translational modifications

PTMprober | deciphering proteome-specific PTM sites atlas

PIPI | PTM-Invariant peptide identification

Phosphopedia | human phosphorylation sites (>100,000) & phosphopeptides

PhosFate | analysis of human quantitative phosphoproteomics data

PhosphoSitePlus | online resource of PTMs - phosphoryl, ubiquitin, acetyl & methylation

PhoSigNet | systematic resource for phosphorylation mediated signaling network

DeNovoPTM | de novo sequencing with limited no. PTM occurrences per peptide

DAPPLE 2 | PTM sites using data for 19 different PTMs from 16 databases

Peiman | enrichment analysis in post translational modification (PTM) types

FragMixer | auto. phosphopeptide ident. using multiple MS/MS fragment. modes

CPhos DB | identify evolutionarily conserved phosphorylation sites

PhosphoPath | visualization & analysis of quantitative phosphoproteome datasets

Selphi | automated analysis of global phosphoproteomics datasets

iSuc-PseAAC | predicting Lysine succinylation in proteins

SSPKA | species-specific prediction of lysine acetylation

Succ | machine learning approach predict. species-specific succinylation sites

SuccFind | prediction of succinylation sites in proteins

SwissPalm | protein S-palmitoylation database

MDD-SOH | web server for identifying S-sulfenylation sites

PRmePRed | Protein arginine methylation prediction tool

GlyTouCan | the glycan repository

UniCarbkb | knowledge platform for glycoproteomics

GRITS | annotation of glycomics mass spectrometry data

GlycoPep DB | assign glycan comp. to MS data of glycopeptides

GlycoPep ID | assign peptide comp. to CID data of glycopeptides

GlycoPep Evaluator | generate decoy glycopeptides & score ETD data

GlycoMaster DB

XGlycScan

GlycoPepGrader | identifies glycopeptide candidate responsible MS spectrum

GlycoMine | machine learning approach predict. N-, C-, O-link glycosyl.

NetOglyc | neural network predictions of mucin type GalNAc O-glycosylation

O-Gglco proteome DB (Human)

Glycodomain | visual representation of glycosylated proteins

GlycoDigest | a tool for exoglycosidase digestions

CAZy | Carbohydrate-Active enZYmes Database

GAPP | proteogenomic profiling of PTMs in prokaryotes

-----------------------------

STRAP PTM | Software for Differential Comparison of PTMs


Organsim specifc


PathRings | exploration of ortholog and expression data

OrthoDB | hierarchical catalog of orthologs

OMA | orthology database

InParanoid | ortholog groups with inparalogs

OrthoInspector | package dedicated to orthology inference and analysis

ProteINSIDE | proteomics data from ruminants via orthologs

EggNOG | nested orthology inference across 3686 organisms

PaxDb | protein abundance across organisms

PhosphOrtholog | PTMs on proteins orthologous across species

Proteny | tool to analyze synteny at the protein level

NOmESS | homology-driven assembly of NOn-redundant protEin Sequence Sets

--- | excellent list of orthology databases

-----------------------------

ViPTree | the Viral Proteomic Tree server

HIV mutation browser

-----------------------------

psortB | bacterial localization prediction tool

SecretP v2.1 | proteomic analysis of Gram-negative bacterial secreted proteins

MimicMe | predicts host-like proteins (mimics) in pathogenic organisms

SysMO | systems biology of microorganisms

CodaChrome | bacterial proteome comparison with GenBank finished bacterial genomes

EcoCyc | E. coli K-12 database

CHOPIN | database of models of Mycobacterium tuberculosis (Mtb)

CyanOmics | Synechococcus sp. PCC 7002 omics data

VectorBase | invertebrate Vectors of Human Pathogens

PBIT | pipeline builder for ident. of drug targets for infectious diseases

-----------------------------

CYCLoPs | protein abundance & localization changes S. cerevisiae

LoQAtE | localization and quantitation atlas of the yeast proteome

FPD | fungi phosphorylation database

Secretool | fungi

Plant-PrAS | physicochemical, structural properties & novel functional regions

PPDB | Plant Proteome DataBase for A.thaliana & maize

Arabidopsis | SUBA3 subcellular localisation DB

Arabidopsis | ASURE subcellular reference portal

PTIR | predicted tomato interactome resource

SpirPro | spirulina proteome repository

PlantPReS | plant proteome response to stress

Wheat | proteome and sub-proteoms

-----------------------------

TriTrypDB | incl. MS data for Trypanosoma brucei, cruzi & leishmania

toxoMINE | multi omics database for T.gondii

TrypsNETDB | protein interactions for trypanosomatid parasites

PlasmoDB | plasmodium - a bit of proteomics embedded

-----------------------------

Worm PES | C. elegans database resource

DPAV | drosophila proteome atlas viewer

ProtoBug | hierarchical classification of insect proteomes


Metaproteomics


MetaProteomeAnalyzer | analyze & visualize metaproteomics (& proteomics!) data

Sysmo

UniPept

MetaProSIP

MP3 | prediction of pathogenic proteins in metagenomic & genomic datasets

Blazmass | proteomic search engine with ComPIL integration for metaproteomics


Mass Spec Tools


SRM Atlas

MS-Amanda

PRIDEInspector

ProteoWizard

MaxQuant

MaxReport | enhanced result reporting tool for MaxQuant

PD-Nodes | collection of nodes for Thermo Scientific Proteome Discoverer

mzCloud

OpenMS | offers datastructures & algorithms for processing of MS data

ProHits | info management & analysis of MS data with focus on interaction proteomics

UCSF ProteinProspecter | tools for mining sequence databases

Skyline | MacCoss Lab Software - targeted proteomics environment

......Panorama

......BiodiversityPlugin

......MPPReport

......MS1Probe

......MSstats

......MSstatsQC

......Population Variation

......Prego

......Proteotypic Peptide Viewer

......Protter

......Quasar

......SProCoP

Pecan | peptide detection directly from DIA data without the need of a spectral library

BioInfra.Prot | 'free' proteomics analysis consulting services

Percolator | MacCoss lab - peptide identification from shotgun proteomics datasets

PAnDA | MacCoss lab - post analysis data aquisition

Peptide-Shaker | interpretation & identification results from multiple search engines

philosopher | complete toolkit for shotgun proteomics data analysis

BumberDash | Tabb Lab Software for MS analysis

SafeQuant | analysis of quantitative (LFQ,TMT,HRM) proteomics data

MSPLIT | spectral-library search for ident. of mixture spectra of up to 2 peptides

MSPLIT-DIA | spectral-library search for ident. of mixture spectra of up to 10 peptides

ProCon | conversion of commercial formats to mzIdentML 1.1 & PRIDE XML

TOMAHAQ | triggerd offset, Mmultiplexed, acc. mass, high-res., abs. quantification

MSREDUCE | ultrafast reduction of big MS data

NIST | Mass and Fragment Calculator Software

MaConDa | MS Contaminants Database

X!Tandem

Informed Proteomics | algorithms for proteomic mass spectrometry data analysis

iPQF | iTRAQ (& TMT) Protein Quantification based on Features

ProteoSign | protein differential expression analysis

Comet | MS/MS sequence database search tool

Mass-up | mass spectrometry utility for proteomics

Picky | simple method designer for targeted proteomics

SPIRE | visualize proteins & peptides from MS data

Protalizer | automated DIA proteomics data analysis

SpecOMS | all-to-all MS spectra comparisons within minutes

MaRaCluster | fragment rarity metric for clustering fragment spectra

MOPED | mmulti-omics profiling expression database

HiQuant | rapid analysis of large-scale MS protein quantification data

Crux | software toolkit for tandem MS analysis

PepExplorer | similarity-driven tool for analyzing de novo sequencing data

SWATHProphet | software tool for analysis of SWATH (DIA) data

SWATH Atlas | analysis of generated MS data libraries

TopFind | knowledgebase & analysis resource for protein termini & protease processing

Peptracker | tools for management, visualisation & analysis of quantitative information

pyQms | generalized, fast & accurate MS data quantification

PeptideTracker | storing of info on protein concentrations in biological tissues

ProLuCID | fast, sensitive tandem MS-based protein identification program

EasyProt | complete graphical platform for analysis of MS/MS data

MSpC | spectral count based label-free quantitative proteomics

TPP | Trans-Proteomic Pipeline collection of integrated tools for MS/MS proteomics

ProteoRed | java MIAPI API

Perseus | shotgun proteomics data analyses

Peptagram | converts proteomics data into HTML5 visualisation

Diana | algorithm and software tools for DIA-MS data analysis

protExpress | Documentation

STRAP PTM | Differential Comparison of PTMs

ProteoAnnotator

mzXML Plotter & Plotly

ProtBase | Arizona Cancer Centre

POTAMOS | simplifies MS calculations for PTM proteins

msproteomicstools | python module for MS-based proteomics

protk | proteomics toolkit - command line tools in Ruby

PeakLink | peptide peak linking method in LC-MS/MS using wavelet & SVM

MSstats | statistical tool for quantitative MS-based proteomics

SpliceVista | GitHub

RCPA | proteomics tools

MALDIquant | quantitative analysis of maldi MS data

xiNET | visualisation of cross-linking/MS data

xiSPEC | auto. spectra annot., intuitive interac., easy testing of hypoth., export for public.

xiQ | minimalistic software for precursor ion quantitation

mzTab | reporting MS-based proteomics & metabolomics results

MSqRob | robust statistical inference for quantitative LC-MS proteomics

padua 0.1.8 | Python interface for Data Analysis with MaxQuant & Perseus

ProteoSuite | analysis of quantitative mass spectrometry data

seaMass | sparse signal restoration for mass spectrometry

GIRO | groupwise image registration and normalisation

WFMM | wavelet functional mixed models for LC-MS

TRIC | graph-based alignment software for SRM or SWATH-MS

The peptide simplex | sensitive quantitative proteomics

Streaming visualisation of LC-MS raw data and results

MiST | MS interaction STatistics - scoring of affinity purification-MS data

PASS | protein assembler with [very] short sequence peptides

M2Lite | converts msf files to standard mzIdentML format

iMonDB | auto extract, store, manage MS instrument parameters from raw data files

PatternLab | tool(s) for analyzing shotgun proteomic data

Mapsy | python library for MS proteomics data analysis

IPeak | peptide identification pipeline

MzJava | analysis of large scale proteomics & glycomics MS data sets

LogViewer | QC metrics for LTQ-FT and LT-Orbitrap instruments

rapid NOVOR | fast MS spectra protein identification program

PAnalyzer | software tool for protein inference in shotgun proteomics

HiXCorr | high-speed XCorr engine for high-res. spectra

pView | LC-MS/MS Data Viewer and Analyzer

JAMSS | a GUI Java Mass Spectrometry Simulation Suite

MASH | processing of top-down high-resolution mass spectrometry data

TopPIC | top-down MS Based proteoform identification & characterization

MSAcquisition Simulator | data-dependent acquisition simulator

ProSight Lite | matching single candidate protein sequences & modifications

DeuteRater | kinetic curves for deuterated water labeled proteins

Ursgal | Python module - bottom-up proteomics for large-scale analysis

SAAS | Search All, Asses Subset strategy for FDR estimation in shotgun proteomics

ProteoModlR | R Suite for Quantitative Proteomics Pathway Modeling

iMPAQT | a tool for analysis of MRM chromatograms

Neo-pep-tool | neopeptide discovery in proteomics data

pyproteome | package for managing proteomics data

Curatr | creating, curating, and sharing a mass spectral library

Genoppi | integrative analysis of proteomic data & genetics

OpenSlice | web-based API for large scale MS data sharing

Mzmine | MS data processing with main focus on LC-MS data


via Sourceforge

PeptideProphet | validates peptide assignments to MS/MS spectra

SAINT | Significance Analysis of INTeractome

DIA-Umpire | computational analysis pipeline for DIA proteomics data

MS Data Miner | analyze, process, validate, compare, display files from MS software

MSSuite | ProteoStats

IQuant | pipeline for quant. proteomics based upon isobaric tags

APP | automated proteomics pipeline

EXIMS | new peak picking method for EXploring Imaging MS data

MassWiz | novel scoring algorithm with target-decoy analysis pipeline for tandem MS

mapDIA | model-based analysis of quantitative data in DIA-MS

Morpheus | 5 times faster than OMSSA for large human datasets


via Bioconductor

Mass spectrometry and proteomics data analysis

RforProteomics | add package to 'Using R & Bioconductor for proteomics data analysis'

mzR | parser for netCDF, mzXML, mzData and mzML and mzIdentML files

MSnbase | plotting, data manip. & processing of MS proteomics data

pRolocGUI | interactive visualisation of spatial proteomics data

pRoloc | pattern recognition on quant. MS data to infer protein sub-cellular localisation

Synapter | reanalysis of label-free proteomics data acquired on a Synapt G2 MS

msmsTests | statistical tests for label-free LC-MS/MS data by spectral counts

msmsEDA | exploratory data analysis of LC-MS/MS data by spectral counts

Isobar | anal. & quant. of isobarically tagged MSMS proteomics data

proteoQC | R package for proteomics data quality control

MSnID | explor. & assess. of confidence of LC-MSn identif.

sapFinder | variant peptides detection and visualization in shotgun proteomics

specL | peptide spectrum matches for use in targeted proteomics


via MyBioSoftware

ProtMAX | large Shotgun Proteomics Mass Spectrometry data sets

Sipros | database-searching algorithm for peptide and protein identification

JAMSS | Proteomics MS Simulation in Java

SILVER | Stable Isotope Labeling LC-MS data Quantitative Analysis

SIMA | Simultaneous Multiple Alignment of LC/MS Peak Lists

TPP | collection of integrated tools for MS/MS

Specialize | ident. of peptides with complex PTM from tandem MS

ProteinDecision | protein ident. using peptide-mass fingerprinting data

MS-Deconv | deconvolution of top-down spectra

MS-GF+ | database search for peptide identification

MixGF | computing stat. signif. of pept.-spectrum-matches for multiplexed MS/MS Spectra

SpliceDB | incorporation of RNA-seq for MS DB search

Tremolo | spectral library search

MSBayesPro | bayesian protein inference for LC-MS/MS proteomics

DQmodel 0.2 | improved peptide detectability prediction with protein quantity considered

ProteinART | protein inference solutions

ProteinInfer | combinatorial perspective of the protein inference problem

PeptideReranking | with protein-peptide correspondence & precursor peak intensity info.

SRPI | Score Regularization for Peptide Identification

NITPICK | peak identification for MS data

UniNovo | universal tool for de novo peptide sequencing

FEvER | functional information from differential quantitative proteomics datasets

Anubis | automated peptide detection & Quantification in SRM data

SRM QC | a tool for keeping track of SRM instrument performance

SapFinder | variant peptides detection & visualization in shotgun proteomics

CHAMPS | complete homology assisted MS/MS protein sequencing

TBnovo | de novo protein sequencing by combining top-down and bottom-up MS

protViz | R package for quality checks, viz, & analysis of proteomics MS data


-----------------------------

CutDB | a proteolytic event database

CaspDB database

Spliceprot

MitoFates | predicts mitochondrial N-terminal localization signal cleavage position


via Commercial


Proteome Discoverer

Mascot

Spectronaut

PEAKS

Byonic

InDigistion App (iOS)


Visualisation Tools


ProtVista | renders position-based annotations for protein sequences

Protter | interactive protein feature visualization

Peptigram | peptidomics data visualization

ComPPI | compartmentalized protein-protein interaction database

ClueGO | creates, visualizes functionally grouped network of terms/pathways

PTMOracle | Co-visualisation and co-analysis of PTM & PPI data

CIG-P | circular interaction graph for proteomics

msVolcano | dynamic volcano plotting for MS data

JSparklines | visualize numbers in Java tables

pViz.js | visualization of protein sequence features

ProHits-viz | customizable images from protein-protein interaction data

BioJS | viewer for protein sequence features

Scop3D | visualization of sequence variation of a protein on its structure

DOSE | disease ontology semantic and enrichment analysis

TAPIR | visualization software for chromatographic data obtained by MS

NOVA | analysis complexome profiling data

Multiplierz | managing proteomic MS workflows & data analysis

DataShop | data visualisation, exploration & analysis

BatMass | mass spectrometry data visualization

CLMSVault | protein X-linking MS data analysis & visualization

YASARA | molecular-graphics, modeling and simulation program

Solubis | identify mutants that decrease protein aggregation tendency

iCOBRA | compare & visualize performance of methods for estimation or classification

MSviz-ui | the all purpose visualization app for MSViz

MALDIViz | quality checks, visualizations and analysis of MS data


Miscelaneous


DPD | Dark Proteome Database

APPRIS | annotating principal splice isoforms

MissingProteinPedia | to collate 'Missing proteins' defined by neXtProt

Taverna | domain-independent scientific workflow management system

DeNovoGUI | GUI for PepNovo+, DirecTag, pNovo+ (beta) & Novor (beta)

Fasta-O-Matic | sanity check & if needed reformat FASTA files

moCluster | multiple omics data integration & gene set analysis

MI-PVT | systematic visualization of proteins in human chromosomes

YPED | storage, retrieval, & integrated analysis of HTP proteomic data

STATegraEMS | the experiment management system for -omics

PIQMIe | semi-quantitative proteomics data management and analysis

ProteomeScout | repository & analysis resource for PTMs & proteins

AFree 2.0 beta | Fast ALL versus ALL Proteome Comparisons

CrossCheck | open-source, high-throughput database analysis software

Pyteomics | Python tools to handle various sorts of proteomics data

PyPDB | PDB search, data retrieval including BLAST and sequence motif queries

Meme Suite | motif based sequence analaysis tools

MassTodonPy | estimate products of ETD in MS

ShettiMotif | search engine for short linear motifs / domains (SLiM)

EPD | characterising proteome dynamics in both human cells and model organisms

CABRA | cluster and annotate blast results algorithm

SignalP 4.1 | presence & location of signal peptide cleavage sites

TAPAS | alternative splices and protein families

CRAPome | contaminant repository for affinity purification

MoonProt | database of moonlighting proteins

TOPPR | stores high quality processed events for protease data

Proteasix | predict proteases involved in naturally occurring peptide generation

Mechismo | mechanistic interpretations of structural modifications

BioPlex | biophysical interactions of ORFeome-based complexes

NetProt | complex-based feature selection

STRING | protein-protein interaction database

DIP | Database of interacting proteins

XLSearch | probabilistic DB Search Algo for Identifying Cross-Linked Peptides

LMPID | linear motifs mediated protein protein interaction database

PEP-SiteFinder | identify candidate protein-peptide interaction sites

PIPE | protein-protein interaction prediction

PIPE-SITES | protein binding site prediction

InterPred | pipeline to identify & model protein-protein interactions

MIEC-SVM | auto. pipeline for protein peptide/ligand interactions

SpotOn | determination of Hot-Spots at protein-protein interfaces

PCIA | identification of protein complexes in protein-protein interaction networks

ECL | Identification of Cross-Linked Peptides Using Whole Database

SLiMSuite | short linear motifs (SLiMs) in proteins as functional microdomains

MotAn | motif analyzer for Protein 3D Structures

SELPHI | identification of kinase-assoc. networks from global phospho-proteomics data

Crescendo | identifies functional sites in proteins

Spotlite | co-complexed proteins

SFINX | filtering index for co-complex interactomics data analysis

FCP | functional coverage of the proteome

PEPPER | find meaningful pathways/complexes

FunRich | functional enrichment analysis tool

INGA | prediction of protein function

PRINTS | compendium of protein fingerprints

ECOD | Evolutionary Classification of Protein Domains

ProteinCarta | termini tags from 9 organisms

Splicify | proteogenomic ident. of disease specific protein biomarkers from mRNA splicing

pyGeno | python package for personalized proteogenomics

PGTools | analysis and visualization of proteogenomic data

Proteoformer | proteogenomic pipeline delineating true in vivo proteoforms

PPLine | proteogenomic pipeline for SAP/indels & alt. spliced variants discovery

EVpedia | Extracellular Vesicles

pwOmics | pathway-based integration of time-series omics data using public DBs

RaftProt | Mammalian Lipid raft Proteome DB

XLink-DB | data storage & visualization for cross-linking data

Kojak | efficient ident. of cross-linked peptides in complex protein mixtures

ProXL | visualize and share protein Cross-linking Data

FunMod Network Analysis | Cytoscape Plugin

SW# | library for sequence alignment based on CUDA enabled GPUs

DAVID | DB for Annotation, Visualization & Integrated Discovery

NCIP/prot-express | GitHub

PIKE | Protein Information & Knowledge Extractor

ProGeRF | proteome & genome repeat finder tool

customProDB | RNAseq to Fasta

CompOmics

OrthoDB software | compute orthologs on custom data

MPC-bioinformatics | bacterial-proteogenomic-pipeline

PIA | Protein Inference Algorithms fully integrated into PRIDE

PIA | Core-library

SUBAcon | max entropy justif. for Naive Bayes

MetaSPS | de novo protein sequencing

aLFQ | R-package for estimat. abs. protein quant. from label-free LC-MS/MS data

Normalyzer | normalisation of omics datasets

inmembrane | pipeline to predict if a protein is exposed on surface of bacteria

RAIN | automated image alignment for 2-D gel electrophoresis

ProteomeGRID | cluster image computing for Condor

pyProCT | cluster analysis for structural proteomics

RepExplore | technical replicate variance in proteomics data analysis

DisCons | quant. investigating conservation of protein disorder at the amino acid level

Speedb | fast structural protein search on PDB

SIFTER | phylogeny-based protein function prediction

EBprot | bayesian analysis of labeling-based quantitative proteomics data

GProX | integrated analysis & visualization of large proteomics datasets

MSProGene | transcript databases for tandem MS search using RNA-Seq data

PrionW | identifies proteins with gln/asn rich prion-like domains

GalaxyPepDock | Protein-peptide docking based on interaction similarity

pepATTRACT | docking protocol that is fully blind

SANSparallel | interactive homology search against Uniprot

RAPSearch2 | fast protein similarity search

EVcouplings | functional & structural info from evolutionary seq. record

PredSTP | SVM based model to predict seq. cysteine stabilized peptides

SEEK | sharing scientific datasets, models, simulations, processes & research outcomes

SplicePie | analyze non-sequential & multi-step splicing

Data Calibration | max. likelihood calibr. for samples quantified in batches

Hammock/Galaxy | clustering extremely large DBs of short peptide sequences

Hammock | clustering extremely large DBs of short peptide sequences with seq. motifs

Falcon@home | high through-put server for protein structure prediction

ProtSav | protein tertiary structure analysis and validation server

SIM-XL | identification of cross-linked peptides

PDID | Protein-Drug Interaction Database

SecretP v2.0 | a new method for predicting mammalian secreted proteins

CP4P | FDR QC, control procedures and computing of adjusted p-values

ASAP | Amino-acid Sequence Annotation Predictor

SpectroGene | genome annotation using top-down mass spectrometry

PrionW | identifies proteins containing gln/asp rich prion-like domains

MBPpred | prediction of membrane lipid-Binding Proteins

PGx | mapping identified peptides onto their putative genomic coordinates

SEEK | psharing datasets,models or simulations, processes & research outcomes

ELASPIC | predicts stability effects of mutations on protein folding and interactions

GprotPRED | a tool for detection & classification of G-proteins

DFLpred | prediction of disordered flexible linker

PDID | Protein-Drug Interaction Database in Structural Human-like Proteome

MODICT | mutation prediction tool based on 3D models

Hydrocalc | identify distinct characteristics of effector proteins

Epitopemap | visualising epitope predictions (currently MHC binding)for proteomes

qpMerge | Galaxy workflow for non-redundant set of quantifications for phospho-motifs

Dintor | functional annotation of genomic and proteomic data

proBAMsuite | genome-based representation & analysis of proteomics data

arrayQualityMetrics | quality metrics report for microarray data

OOMPA | microarray and proteomics analysis library

PMD | protein microarray database

MAPPI-DAT | PPI data generated from microarray-MAPPIT system

ArrayNinja | unifies planning, visualization, analysis of microarray experiments

Heatmapper | interactively visualize data in form of heat maps

dbDSM | database of deleterious synonymous mutation

FASIL-MS | analysis scripts to quantify heavy-light acetylations

HydroCalc | hydropathy profiles calculated using Kyle-Doolittle scale

DISMS2 | direct proteome-wide distance calculation of LC-MS/MS runs

CombiROC | guided & interactive generation of multimarker panels

IonchanPred 2.0 | prediction of ion channel and their types

Pon-Sol | effects of amino acid substitution on protein solubility

IPC | isoelectric point calculator

Proteome-pI | proteome isoelectric point database

PIP-DB | protein isoelectric point database


-----------------------------


Additional software resources that may be worth looking at beyond those listed above can be found at |

HUPO-PSI | tools implementing mzIdentML

BioDocker | repository for Bioinformatics

CCMS | software tools

SPC | seattle proteome center & transproteomic pipeline

PROWL | Rockefeller software tools

Unipept | proteomics tools

Sourceforge

GitHub

GoogleCode

OmicTools

Bioconductor

MyBiosoftware

MS-Utils



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