SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures
<p>Abstract</p> <p>Background</p> <p>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-lo...
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| Format: | Article |
| Language: | English |
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BMC
2005-07-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/6/170 |
| _version_ | 1818036824998674432 |
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| author | Fördös Gergely Biro Jan C |
| author_facet | Fördös Gergely Biro Jan C |
| author_sort | Fördös Gergely |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user</p> <p>a. selects a structure from PDB;</p> <p>b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s)</p> <p>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).</p> <p>Conclusion</p> <p>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.</p> <p>Availability and requirements</p> <p><url>http://janbiro.com/Downloads.html</url> SeqX, Java J2SE Runtime Environment 5.0 (available from [see <supplr sid="S1">Additional file 1</supplr>] <url>http://www.sun.com</url>) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors.</p> <suppl id="S1"> <title> <p>Additional File 1</p> </title> <text> <p>SeqX_1.041_05601.jar. see this article</p> </text> <file name="1471-2105-6-170-S1.jar"> <p>Click here for file</p> </file> </suppl> |
| first_indexed | 2024-12-10T07:17:06Z |
| format | Article |
| id | doaj.art-b7154bb735a948e79789b6bd3d0ab249 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T07:17:06Z |
| publishDate | 2005-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b7154bb735a948e79789b6bd3d0ab2492022-12-22T01:57:54ZengBMCBMC Bioinformatics1471-21052005-07-016117010.1186/1471-2105-6-170SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structuresFördös GergelyBiro Jan C<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user</p> <p>a. selects a structure from PDB;</p> <p>b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s)</p> <p>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).</p> <p>Conclusion</p> <p>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.</p> <p>Availability and requirements</p> <p><url>http://janbiro.com/Downloads.html</url> SeqX, Java J2SE Runtime Environment 5.0 (available from [see <supplr sid="S1">Additional file 1</supplr>] <url>http://www.sun.com</url>) and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors.</p> <suppl id="S1"> <title> <p>Additional File 1</p> </title> <text> <p>SeqX_1.041_05601.jar. see this article</p> </text> <file name="1471-2105-6-170-S1.jar"> <p>Click here for file</p> </file> </suppl>http://www.biomedcentral.com/1471-2105/6/170 |
| spellingShingle | Fördös Gergely Biro Jan C SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures BMC Bioinformatics |
| title | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures |
| title_full | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures |
| title_fullStr | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures |
| title_full_unstemmed | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures |
| title_short | SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures |
| title_sort | seqx a tool to detect analyze and visualize residue co locations in protein and nucleic acid structures |
| url | http://www.biomedcentral.com/1471-2105/6/170 |
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