structure of peptides, we have predicted tertiary structure of tumor homing peptides using software PEPstr [15]. PEPstr is a state of art method for predicting structure of bioactive peptides. It is a de-novo method which builds a tertiary structure from predicted secondary structure and tight turns [15]. In addition, secondary structures of these peptides have also been predicted from predicted tertiary structure using software DSSP [16]. In our database, we maintain both secondary and tertiary structure of each peptide in PDB format. In order to understand the nature of the peptide, it is imperative to know the constituents of each peptide. Therefore, in-house PERL scripts have been used for computing frequency and composition of each type of amino acid residue in all the peptides. This information is very useful to understand which residues/ motifs are preferred in tumor homing peptides. Apart from amino acid frequency and composition, users may also want to know which types of residues are preferred like charged, polar, hydrophobic, etc. Therefore, we have computed frequency and composition of each class (aromatic, aliphatic, positively charged, negatively charged, neutral, polar and hydrophobic) of residues. This information is very useful to know which peptides are dominated by positively charged residues. We have also computed overall physicochemical properties (hydrophobicity, hydrophilicity molecular weight, iso-electric point and net charge) of each peptide [17,18]. All above information is stored in the database as secondary data for analysis and browsing of peptides based on their properties. Implementation of tools Apart from the collection of tumor homing peptides and their targets, a wide variety of information can be generated using the various online software/tools provided with TumorHoPe. Follow- ing are the main tools provided with the TumorHoPe database. Data searching TumorHoPe is integrated with a user friendly interface for retrieving data from the database. A brief description of these interfaces is as follows: Keyword Search. This interface allows users to search their query in most of the fields of database (e.g., peptide sequence, motif, target tumor, target cell, source clone). One of the powerful features of this interface is that it allows users to select fields they wish to display in their results. Complex Search. Advance search allows users to search the whole database in a stepwise manner. A query can be submitted using the following five steps: (i) fill the field name; (ii) choose any of four match operators ( = , ., ,, and LIKE); (iii) fill the value, (iv) choose between two condition operators (AND & OR); and (v) press to add another query. Users are able to add multiple queries to search the database. In summary, advance search allows users to perform more complex queries in TumorHoPe. Peptide Search. This interface is designed for searching a peptide sequence in the database. It allows two types of queries: (i) Containing peptide: it is for searching user defined peptide sequence in tumor homing peptides, and (ii) Exact search: it allows user to search tumor homing peptides, which are 100 percent identical to user’s peptide. Browsing tools We have designed powerful browsing facility that allows a user to browse data using various options. A brief description of interfaces designed for browsing are as follows: Major Fields. This interface allows a user to browse database on the following four major fields: (i) target tumor; (ii) cell lines; (iii) Tumor Homing Peptides Repository year of publication; and (iv) target site. As shown in Figure 2, it provides a number of peptides for different types of target tumor, target site and cell lines. Amino Acid Frequency. This option is designed for searching or extracting peptides, which have desired frequency of specific type of residues. For example, user may search all peptides that have two Arg and three Ala. This is useful option of searching peptides dominated by particular type of residues. Amino Acid Composition. This interface allows users to extract peptides from the database based on their amino acid composition. For example, user can search all the peptides that have all Arg residues by specifying 100% composition of Arg. User can easily extract tumor homing peptides with desired amino acid composition. Physicochemical Property Frequency. User can extract tumor homing peptides with desired frequency of certain types of residues like, positively charged, negatively charged polar aliphatic, aromatic residues, etc. For example, user can easily extract all tumor homing peptides that have more than four positively charged residues. Physicochemical Property Composition. This interface allows users to extract tumor homing peptides with desired composition of different types of residues like, positively charged, negatively charged, polar residues, etc. For example, user can easily extract all tumor homing peptides that have more than 80% positively charged residues. Physicochemical Property Value. We have also computed physicochemical properties of each tumor homing peptide like hydrophobicity, hydrophilicity, net charge, iso-electric point. This tool allows users to extract tumor homing peptides with desired physicochemical properties. For example, user can search all peptides having net positive charge and molecular weight in the desired range [17,18]. Structure based browsing tools In this database, predicted secondary and tertiary structure of each peptide has been stored. Three interfaces have been developed to extract structural information of tumor homing peptides. A brief description of these interfaces is as follows: Secondary Structure (SS) composition. This interface allows users to browse peptides based on their secondary structure composition. We have assigned four types of secondary structure states (H-helix, E-beta strand, T-turn and C-coil) from DSSP. User can search tumor homing peptides with desired composition of these four types of secondary structure states. For example, user can search peptides that have more than 60% residues in the helix state. Secondary Structure (SS) Search. This interface allows users to search segment of particular secondary structure states. 3D structure. This interface is designed to browse tertiary structure of tumor homing peptides. It also allows user to search results on any field. First, it displays structure of peptide as static image. This image is clickable, and on click, it launches Jmol (http://www.jmol.org) after loading structure of peptides. This allows user to visualize 3D structure in any format or size/ orientation supported by Jmol. Web-Based Tools A number of web-based tools have been integrated in this database to facilitate further analysis of peptides. A brief description of these tools is as follows: Blast Search. We have integrated BLAST search tool [19] that allows users to perform similarity based search against tumor homing peptides. This option allows users to submit one or more PLoS ONE | www.plosone.org 3 April 2012 | Volume 7 | Issue 4 | e35187