SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures.
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 A). 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).


CONCLUSIONS
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.
Biro
Jan C
JC
Homulus Foundation, San Francisco, CA 94105-1649, USA. jan.biro@sbcglobal.net
Fördös
Gergely
G
D000595:Amino Acid Sequence; D002874:Chromosome Mapping / Q000295:instrumentation*; D019295:Computational Biology / Q000295:instrumentation; D003626:Data Display; D005189:False Positive Reactions; D010446:Peptide Fragments / Q000737:chemistry* / Q000235:genetics*; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013223:Statistics as Topic; D014584:User-Computer Interface
D010446:Peptide Fragments; D011506:Proteins