SeqX:: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures -: art. no. 170

Background: The interacting residues of protein and nucleic acid sequences are close to each other - they are co-located. Structure databases ( like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB) contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results: SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s) c. defines a distance from these atoms ( 3 - 15 angstrom). The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom( s); provides a DotPlot-like visualization ( Residues Contact Map), and calculates the frequency of every possible residue pairs ( Residue Contact Table) in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections ( up to 60% when tested on dsDNA). Results obtained on protein structures showed highly significant correlations with results obtained from literature ( p < 0.0001, n = 210, four different subsets). The co-location frequency of physico-chemically compatible amino acids is significantly higher than is calculated and expected in random protein sequences ( p < 0.0001, n = 80). Conclusion: The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements: http:// janbiro. com/ Downloads. html SeqX, Java J2SE Runtime Environment 5.0 ( available from [ see Additional file 1] http:// www. sun. com) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors.