Keyword Search

This option provides a straightforward way to search using a single word. Users can enter a sequence (e.g., CSNIDARAC), motif (e.g., WYY), target tumor (e.g., Breast cancer), target cell (e.g., Endothelial cell), or cell lines (e.g., MDA-MB) as used in the experiments.

The results will be displayed based on the selected fields, such as the sequence, research article details, PMID, etc.

Advance Search

This page allows complex queries in the TumorHoPe database using multiple fields and logical operators.

• Select a field, enter a value, and choose an operator (AND, OR, NOT).
• Add terms to build your query.
• Edit the Query Box directly if needed.
• Click Search to run or Clear to reset.
• Download results using Download CSV.

For full documentation, visit the HELP page.

Peptide Search

Users can search a query sequence against the entire database. The results will display either peptides that exactly match the query or peptides that partially match the provided sequence.

Major Fields

This interface enables users to browse the database by the following key fields:

• Target Tumor
• Cell Line
• Year of Publication
• Target Site

Amino Acid Frequency and Composition

Filter sequences by amino acid frequency and composition. For example, setting Lysine values between 3 and 23 will retrieve all sequences with Lysine counts in that range. You can combine this with other amino acid criteria (e.g., Glycine between 4 and 18) to further refine the results. This method also applies to filtering by amino acid composition as well as physical property frequency and composition.

Physicochemical Property Frequency and Composition

Retrieve tumor homing peptides based on the frequency of specific residue types. You can:

• Filter by residue types such as positive charge, negative charge, or polar residues.
• Adjust default minimum and maximum values to customize your search range.
• Example: Set an aromatic property range between 2 and 8 to display all peptides within that range.
• Combine multiple property criteria (e.g., aromatic property and positive charge) for more refined results.

Physicochemical Property Values

Display tumor homing peptides that fall within user-defined ranges for the following properties:

• Hydrophobicity
• Hydrophilicity
• Net Charge
• Isoelectric Point
• Molecular Weight

Enter the desired minimum and maximum values for each property to retrieve peptides that match your criteria.

Secondary Structure Composition

Retrieve peptides based on the percentage composition of four different secondary structural states:

• Helix (H)
• Beta Sheet (E)
• Turn (T)
• Coil (C)

Define the minimum and maximum percentage values for each structural type to filter the results.

Secondary Structure Prediction

Submit a peptide sequence from the database to receive its predicted secondary structural state.

3D Structures

Three-dimensional structures of all tumor homing peptides have been predicted using the PEPstr tool.

BLAST 🔗

Perform a similarity-based search of a query sequence against the Tumor Homing Peptide database using BLAST.

• Enter the query sequence using single-letter amino acid codes.
• The tool returns all peptides from the database that show similarity to the query.

Smith-Waterman

This tool identifies regions of local similarity between the query peptide and peptides in the database.

• Performs pairwise alignments by comparing all possible segments.
• Optimizes similarity scores to provide precise alignment results.

Identical Residues

Compares the query sequence with each peptide in the database to determine exact residue matches.

• The sequence is aligned step-by-step with all database peptides.
• The tool returns the count of identical residues for each pair.

Peptide Mapping

Slide the query peptide across all database sequences to find the best alignment with the highest number of identical residues.

Physical Properties

Calculate physical properties of a given peptide, including:

• Hydrophobicity
• Hydrophilicity
• Net Charge
• Isoelectric Point
• Molecular Weight