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Protein Identification

There are several techniques which are used for the identification of a protein structure such as optical rotatory dispersion, X-ray crystallography, spectroscopy and nuclear magnetic resonance, these techniques are powerful in determining the structural features of protein but they require many hours of highly skilled and technically dedicated work environments. There are several computational techniques which allow for the biological discovery based on the protein sequences only and/or on their comparison to protein families. 

There are three main methods to identify protein and its structural features. 

1) Protein Identity Based on Composition: 

This involves the methods and online packages such as AA Compident, AA Compsim and Propsearch.. (AA stands for Amino Acid). 
AA Compident: It uses the amino acid composition of the unknown protein to identify known proteins of the same composition. 
AA Compsim: Instead of using the experimentally derived amino acid composition, it uses the sequence of a SWISS-PROT protein. A theoretical pI and molecular weight are computed. 
PropSearch: this method is robust and various physical properties are used in performing the analysis. 

2) Physical properties based on sequence:

There are 4 methods to identify the physical properties of a protein based on sequence. PeptideMass, TGREASE, SAPS and Compute pI/MQ and ProtParam.
PeptideMass: It is used for the peptide mapping experiments and it determines the cleavage products of a protein after treatment with protease or other chemical reagent. 
TGREASE: calculates the hydrophobicity of a protein along its length. 
SAPS: It provides the extensive statistical information for any given query sequence. It stands for Statistical Analysis of Protein Sequences. 
Computer pI/MW: It calculates the isoelectric point and molecular weight of an input sequence. 
ProtParam: It calculates the molecular weight, isoelectric point, overall amino acid composition, a theoretical extinction coefficient and grand average hydrophobicity.

3) Protein Structure Prediction: 

For the prediction of secondary structures of a given protein, several online servers like JPRED, PSIPRED are used. 

Using servers like Modeler, primer and Swiss prot, the homology modelling for protein sequences showing similarity to other sequences are predicted. 

I-Tasser and Rossetta are the Ab-initio structure prediction servers which are used for the protein sequences that hardly share any similarity to known protein structures. 
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