TumorHPD Help
TumorHPD is a user friendly webserver where user can submit their query as peptide, protein and multiple peptide sequences in batch mode. Detailed information about each method is given below:

Peptide

There user can predict the tumor homing ability of the submitted peptide on the basis of SVM based prediction method. The mutants of the originally submitted peptide are generated.

Secondary Structure Prediction

User can also predict secondary structure of the query peptide by clicking on secondary structure option (It usually takes bit longer to calculate secondary structure, so have patience). For further information about secondary structure prediction, plesae refer original article

The various letters used in secondary strcture representation are given below: H = Alpha helix E = Beta strand C = Coil

Stepwise description of Peptide module is given below

Input sequence:- User can paste the peptide sequence directly into the input box. Sequences must be entered in the single letter code. All the non-natural amino acids and characters will be ignored from the peptide sequence. User can select from the different SVM based models (NTCT5- for peptides of short length; NTCT10- for the peptides having length more than 10 residues; Whole peptide- for peptides of any length; NTCT5 Up to 10 residues- specific for the peptide of 4-10 residue length) for predicting the tumor homing peptides at particular threshold( range -1 to 1) provided for user. All possible mutants (containing tumor homing ability in the form of SVM score and user selected physicochemical properties) for user submitted peptide will be generated. Original peptide and its mutants are shown in tabular form. The red colored residue in mutants depicts the substituted residue. The results can be sorted in ascending as well as descending order of their values. This will help to identify best putative tumor homing peptide (i.e., with highest SVM score) from the list of peptides. Best putative tumor homing peptide can further be used to generate all possible mutants to get still more tumor homing peptides.

Protein
There user can identify tumor homing regions from the protein (should be submitted in single letter code) of interest. Possible peptides are generated from the protein using overlapping window concept. The snapshot given below gives a very brief idea about this module.
The results from Protein module may be generated in following two modes:
Tabular Mode
The brief description is given below: Paste the protein (in single letter code) in the input box. After submission, all possible peptides are generated containing putative tumor homing ability (in the form of SVM score) with physicochemical properties. Results are displayed in tabular form having desired physicochemical properties choosen by the user. Mutants of the fragments with tumor homing properties can be generated further by just clicking on the fragment. The later will help to generate best putative tumor homing peptides.
Graphic Mode
The results are displayed in two patterns, one showing the whole protein results for four physicochemical properties (i.e., SVM score, Hydrophobicity, Hydrophilicity, Charge, Molecular weight). Clicking upon a particular physicochemical property e.g., on the basis of SVM score (at a particular threshold), no. of peaks will decide possible tumor homing peptides present in protein sequence.
The other pattern is displayed for fragments which are generated from the submitted protein. Physicochemical properties (SVM score, Hydrophobicity, Hydrophilicity, Charge, Molecular weight) and the peptides fragments for that protein are displayed. On clicking the peptide fragments, the physicochemical properties are displayed in graphical form.

Batch

Through this module, user can submit more than one peptide sequence (either by pasting the peptide sequences in text box or uploading the file containing peptide sequences) in FASTA format only. Thus, it will be helpful in high-throughput screening of peptides. Further, all the possible mutants may be generated for the original peptide (just clicking on it).