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
.....Pfam
.....InterPro
.....ProtVista
.....PDBe
.....PDBsum
.....IntAct
.....CATH
.....SCOP
.....SIFTS
.....EMPIAR
.....PIA
.....HMMER
.....Expression Atlas
OMICSDI | linking public omics data sets w/ Omics Discovery Index
PIR | Protein Information Resource
hu.MAP | Human Protein Complex Map
ProteomicsDB | DB using SAP HANA from Technische Universitat Munchen
TPB Home | the proteome browser
neXtProt | exploring the universe of human proteins
neXtProt - tools | peptide uniqueness checker
APPRIS | annotating principal splice isoforms
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
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
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
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
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
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
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
-----------------------------
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
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
MP3 | prediction of pathogenic proteins in metagenomic & genomic datasets
Blazmass | proteomic search engine with ComPIL integration for metaproteomics
Mass Spec Tools
MaxReport | enhanced result reporting tool for MaxQuant
PD-Nodes | collection of nodes for Thermo Scientific Proteome Discoverer
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
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
Perseus | shotgun proteomics data analyses
Peptagram | converts proteomics data into HTML5 visualisation
Diana | algorithm and software tools for DIA-MS data analysis
STRAP PTM | Differential Comparison of PTMs
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
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 dataCuratr | 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
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
MitoFates | predicts mitochondrial N-terminal localization signal cleavage position
via Commercial
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 featuresScop3D | 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
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
PIKE | Protein Information & Knowledge Extractor
ProGeRF | proteome & genome repeat finder tool
OrthoDB software | compute orthologs on custom data
MPC-bioinformatics | bacterial-proteogenomic-pipeline
PIA | Protein Inference Algorithms fully integrated into PRIDE
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
SPC | seattle proteome center & transproteomic pipeline
PROWL | Rockefeller software tools
