Bioinformatics based database and tools for protein analysis:

a. Sequence analysis: Similarity searching using protein sequences are performed using BLASTP analysis tool at the NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome) and a detailed description of BLASTP is provided in the section on BLAST.

Several online bioinformatics tool for protein analysis have been made available at Expasy (http://www.expasy.org/). Some of these tools are:

1. PANDIT Plus:for resources related to domain structure and protein families (/). Another such tool and database is the ()http://panditplus.org PROSITE http://prosite.expasy.org/


2. ProtParam: This tool has been developed for prediction of physical (such as Molecular weight) and chemical (such as pI) properties of proteins (http://web.expasy.org/protparam/)


3. PSORT: A tool for predicting the sub-cellular localization of proteins (http://www.psort.org/)


4. Coiled–Coil Prediction: for prediction of coiled-coil regions (http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_lupas.html)

b.    Structure prediction of proteins: NMR spectroscopy Protein structure prediction is one of the major challenge areas in bioinformatics. Most of the structures that have been solved accurately are based either on or Although there is information available that the primary sequence gives rise to secondary which in turn folds into tertiary and eventually quaternary structure, no precise algorithm has been developed that can predict all protein structures. Using computational tools, three strategies have been proposed for protein structure prediction,X-ray crystallography.

1. Homology modeling


2. Fold recognition or Threading, and


3. Ab-initio prediction

SWISS-MODEL Workspace http://www.expasy.org/ is a homology based protein structure prediction program.

PHYRE2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index) is a fold recognition based protein structure prediction tool

HMMSTR/Rosetta (http://robetta.bakerlab.org) and now available as ROBETTA (http://robetta.bakerlab.org/) is an ab-initio protein structure prediction tool