Protein Identification

&

Characterization

AACompIdent

AACompIdent

AACompIdent

AACompIdent TagIdent

To find the putative protein family if querying a new sequence has failed using alignment methods

By neglecting the order of amino acid residues in a sequence, it uses the amino acid composition

144 properties like mol.wt, hydrophobicity, average charge etc., are weighted individually and are used as query vector

PROPSEARCH

PROPSEARCH-DISTANCE

Tool for identification by peptide mapping or peptideSequencing

PepSea

PepMAPPER: Takes peptide mass as the input

Mascot: Can take the following as input, 1) Peptide mass fingerprint 2) Sequence query 3) MS/MS ion search

Peptide mass fingerprinting tools

PepMAPPER

MASCOT

MASCOT

To identify peptides that from unspecific cleavage of proteins from their experimental masses

Takes chemical modifications, post-translational modifications(PTM) and protease autolytic cleavage in account

Findpept

TMAP

TMHMM

TMPRED

TopPred2

PHDhtm

DAS

Transmembrane helices prediction

Compute pI/Mw: Calculates pI and mol.wt

ProtParam: • Computation of physical and chemical parameters for a protein sequence• Computed parameters include, Mol.Wt, Theoretical pI, amino acid composition, atomic composition, estimated half-life etc.,

Primary structure analysis and prediction

PHDacc: Simple hydrophobicity analysis

ProtScale: • Computation of physical and chemical parameters for a protein sequence• Computed parameters include, Mol.Wt, Theoretical pI, amino acid composition, atomic composition, estimated half-life etc.,

Hydrophobicity prediction

Identifies possible PEST regions

PEST

Chou-Fasman methodGOR (Garnier, Osguthorpe and Robson) MethodNearest Neighbour MthodHidden Markov ModelsNeural networksSOPMA (self-Optimized Prediction method based on MSA)

Secondary structure prediction

Relative frequencies of each Amino acid in different secondary structures

Less accurate than GOR method

Amino acid propensities is the basis

Chou-Fasman method

Ala, Glu, Leu, Met Helix formers

Pro, Gly Helix breakers

Amino acid propensities

Four out of six amino acids have high probability >1.03 α helix

Three out of five amino acids with a probability of >1.00 β Sheet

Predictive values

Amino acid propensities & conditional probabilities are the basis

GOR Method