Tumor Homing Peptides Repository Figure 1. Overall architecture of TumorHoPe database. doi:10.1371/journal.pone.0035187.g001 the malignant tissue, chemo-resistance of the cancer cells can be overcome or reduced [13]. Despite the huge therapeutic potential of tumor homing peptides, till date, there is no database or bioinformatics method for designing of effective tumor homing peptides. In order to facilitate scientific community, we have made a systematic attempt to collect and compile experimentally validated tumor homing peptides. Materials and Methods Data collection and compilation Data for TumorHoPe database is manually collected from published papers, patents, and web sites by using a combination of keywords like tumor homing peptides and tumor targeting peptides (Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/). Ex- perimentally validated sequences were collected from published literature. Sequences were also collected from the patents which are available at websites of United States Patent and Trademark Office and World Intellectual Property Organization. Database Architecture and Web interface TumorHoPe is built on Apache HTTP server 2.2 with MySQL server 5.1.47 as the back end and the PHP 5.2.9, HTML and JavaScript as the front end. Apache, MySQL and PHP are preferred as these are open-source softwares and platform independent. The architecture of TumorHoPe database is shown in Figure 1. Organization of data TumorHoPe is a manually curated database which provides comprehensive information about peptides that target, bind to, and or home to tumor. Data for each peptide can be categorized as primary (e.g. peptide sequence, PubMed ID (PMID) and experimental details) and secondary data (e.g. secondary/tertiary structure, amino acid composition, frequency and physicochemical properties). Each peptide is assigned a unique entry number, and information is divided into different tables. Each table provides unique information. Primary Data. Primary data contains general information of tumor homing peptides. All the information is extracted manually from various resources, mainly from publications and patents. As shown in the Figure 1, database provides comprehensive information on each peptide using more than 15 types of fields. Main fields are described as follows: (i) Sequence: it contains amino acid sequence of tumor homing peptide; (ii) Target tumor: it contains the name of tumor targeted by peptide; (iii) Target cell: it is type of cells targeted by peptide; (iv) Phage/library: It provides details of phage display library; (v) in vitro/ex vivo: it provides details of experiment carried out in in vitro and ex vivo conditions; (vi) Clone name: it provides information of clones of tumor homing peptides obtained by phage display technology against various tumors; (vii) Payloads: it provides information of conjugate attached with the peptide for imaging or drug delivery; (viii) Tumor homing/Tumor targeting peptides : it provides information whether peptide has been used in vivo experiment (tumor homing) or has been used in vitro experiments (tumor targeting). Secondary Data. In the past, it has been shown that efficacy of tumor homing peptide depends on its structure [14]. Therefore, understanding of tertiary structure of these peptides is a prerequisite. Since these peptide structures are not available in Protein Data Bank (PDB) and existing methods for predicting tertiary structure of protein are unsuitable for predicting tertiary PLoS ONE | www.plosone.org 2 April 2012 | Volume 7 | Issue 4 | e35187