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

Abstract

BackgroundThe 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.ResultsSeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The usera. 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 Å). 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).ConclusionThe 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 SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] ) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors.

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

“…A JAVA tool called SeqForm, developed by us, was used to select sequence residues in predefined phases (every third in our case) and for residue replacements [12]. Amino acid collocations were detected and evaluated by another tool, SeqX [13].…”

NAPS: Network Analysis of Protein Structures

“…Con-Struct Map ( 16 ), CMWeb ( 17 ) and CMA ( http://ligin.weizmann.ac.il/cma/ ) allows structural comparison of proteins by analysing the contact maps, and CMA also supports analysis of protein complexes. Standalone programs such as SeqX ( 18 ), Protmap2D ( 19 ) and CMview ( 20 ) allow construction and basic analysis of contact maps. RING provides several methods for the construction of residue interaction network, which can be analysed using Cytoscape ( 21 ).…”

Design and Production of Specifically High Affinity Reacting Peptides (SHARP®-s)

“…However new bioinformatics tools [39] and a large protein structure database (PDB) became available. Statistical analyzes of amino-acid colocations in real protein structures revealed that the redundant Genetic Code contains even information necessary to protein folding and interactions [40,41].…”