{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,24]],"date-time":"2025-11-24T06:50:18Z","timestamp":1763967018276},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats: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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats: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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats: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.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-223","type":"journal-article","created":{"date-parts":[[2005,9,9]],"date-time":"2005-09-09T18:13:37Z","timestamp":1126289617000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["SUPERFICIAL \u2013 Surface mapping of proteins via structure-based peptide library design"],"prefix":"10.1186","volume":"6","author":[{"given":"Andrean","family":"Goede","sequence":"first","affiliation":[]},{"given":"Ines S","family":"Jaeger","sequence":"additional","affiliation":[]},{"given":"Robert","family":"Preissner","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,9,9]]},"reference":[{"issue":"10","key":"548_CR1","doi-asserted-by":"publisher","first-page":"5772","DOI":"10.1073\/pnas.1030237100","volume":"100","author":"B Ma","year":"2003","unstructured":"Ma B, Elkayam T, Wolfson H, Nussinov R: Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. 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