Methods

Calculating Physico-chemical properties. ProtParam is the appropriate tool for calculating physico-chemical properties. It can give datum like molecular weight, extinction coefficient, instability index and half-life. ProtParam can be accessed at http://web.expasy.org/protparam/.

Transmembrane Segment Prediction. For a primary structure analysis of protein, THMM, is a program that predicts transmembrane segments in protein. It also tells about the portion of proteins that are probably inside and outside the cell. The online database can be accessed at http://www.cbs.dtu.dk/services/TMHMM/.

Detecting PROSITE signature matches. To detect which functional group or protein will help in increasing the functional diversity of proteome, a trusted protein database was used (http://prosite.expasy.org/scanprosite/). ScanProsite is a web-based tool in determining which prosite pattern a certain sequence is located. It is also designed for checking if other proteins contain the same sequence.

Identifying Protein Domains. InterProScan a tool that combines different protein signature recognition methods and allows the comparison of a certain sequence from the InterPro, a domain database that includes most of the major domain collections available online. For InterProScan, visit the website www.ebi.ac.uk/InterProScan/.

Locating Coiled-coil Region. In determining the coiled-coil region of the given protein structure, go to http://ch.embnet.org/software/COILS_form.html . COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score.

In computing ang representing the profile produced by any amino acid scale on a selected protein, ProtScale was used. It is a two-dimensional plot wherein the hydrophobicity of a protein is given account to. This concerns major and minor peaks that are responsible in the determination of the hydrophobic site. ProtScale is available at http://web.expasy.org/protscale/.

Motifs determination. Motif scanning means finding all known motifs that occur in a sequence, Motifscan can be accessed at http://myhits.isb-sib.ch/cgi-bin/motif_scan. In using this database, the result must be filtered and shown using PROSITE profiles.

Predicting cleavage sites. PeptideCutter (http://web.expasy.org/peptide_cutter/) was used in predicting potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. This tool can be helpful in determining whether the chosen protein can interact with the available enzyme in the database. Enzymes can be chosen all at once, and can also be chosen one at a time depending on how the user wants in to be.

Prediction of the secondary structure PSIPRED is a popular structure prediction method to accurately predict the secondary structure of any protein. It can say how many alpha helix and beta sheets are in there in a protein structure. PsiPred can be obtained by accessing to

www.bioinf.cs.ucl.ac.uk/psipred/.

Prediction of the tertiary structure Dihedral angles between C-C (, psi) and N-C (, phi) of amino acid residues and empirical distribution of data points in a protein structure are determined using Ramachandran plot software (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php). Partial-double-bond makes the peptide planar, it limits the rotation around C-N bond making it to have a two alpha-carbons, C, O, N and H among them in one plane.

Therefore, the third angle which is omega () is constant at 1800. These three angles are the most significant local structure parameter that governs the protein folding.

Prediction of the quarternary structure SWISS-MODEL is a structural bioinformatics web-server dedicated to homology

modeling of protein 3D structures. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. SWISS-MODEL can be access at

http://swissmodel.expasy.org/.