SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design
<p>Abstract</p> <p>Background</p> <p>The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2005-09-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/6/223 |
| _version_ | 1811250194447073280 |
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| author | Preissner Robert Jaeger Ines S Goede Andrean |
| author_facet | Preissner Robert Jaeger Ines S Goede Andrean |
| author_sort | Preissner Robert |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being prevailant. Conventional mapping techniques with arrays of synthetic peptides have limitations with regard to the location of discontinuous or non-linear binding sites of proteins.</p> <p>Results</p> <p>We present a structure-based approach to the design of peptide libraries that mimic the whole surface or a particular region of a protein. Neighbouring sequence segments are linked by short spacers to conserve local conformation. To this end, we have developed SUPERFICIAL, a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions.</p> <p>Conclusion</p> <p>Based on 3D structures, SUPERFICIAL may help to negotiate some of the existing limitations, since binding sites consisting of several linear pieces can now be detected.</p> |
| first_indexed | 2024-04-12T15:59:40Z |
| format | Article |
| id | doaj.art-b5265411e6844fb8a5bbe66805b7a0b0 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T15:59:40Z |
| publishDate | 2005-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-b5265411e6844fb8a5bbe66805b7a0b02022-12-22T03:26:14ZengBMCBMC Bioinformatics1471-21052005-09-016122310.1186/1471-2105-6-223SUPERFICIAL – Surface mapping of proteins via structure-based peptide library designPreissner RobertJaeger Ines SGoede Andrean<p>Abstract</p> <p>Background</p> <p>The determination of protein surfaces and the detection of binding sites are essential to our understanding of protein-protein interactions. Such binding sites can be characterised as linear and non-linear, the non-linear sites being prevailant. Conventional mapping techniques with arrays of synthetic peptides have limitations with regard to the location of discontinuous or non-linear binding sites of proteins.</p> <p>Results</p> <p>We present a structure-based approach to the design of peptide libraries that mimic the whole surface or a particular region of a protein. Neighbouring sequence segments are linked by short spacers to conserve local conformation. To this end, we have developed SUPERFICIAL, a program that uses protein structures as input and generates library proposals consisting of linear and non-linear peptides. This process can be influenced by a graphical user interface at different stages, from the surface computation up to the definition of spatial regions.</p> <p>Conclusion</p> <p>Based on 3D structures, SUPERFICIAL may help to negotiate some of the existing limitations, since binding sites consisting of several linear pieces can now be detected.</p>http://www.biomedcentral.com/1471-2105/6/223 |
| spellingShingle | Preissner Robert Jaeger Ines S Goede Andrean SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design BMC Bioinformatics |
| title | SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design |
| title_full | SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design |
| title_fullStr | SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design |
| title_full_unstemmed | SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design |
| title_short | SUPERFICIAL – Surface mapping of proteins via structure-based peptide library design |
| title_sort | superficial surface mapping of proteins via structure based peptide library design |
| url | http://www.biomedcentral.com/1471-2105/6/223 |
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