{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T15:53:40Z","timestamp":1771602820844,"version":"3.50.1"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Solvent exposure of amino acid residues of proteins plays an important role in understanding and predicting protein structure, function and interactions. Solvent exposure can be characterized by several measures including solvent accessible surface area (ASA), residue depth (RD) and contact numbers (CN). More recently, an orientation-dependent contact number called half-sphere exposure (HSE) was introduced by separating the contacts within upper and down half spheres defined according to the C\u03b1-C\u03b2 (HSE\u03b2) vector or neighboring C\u03b1-C\u03b1 vectors (HSE\u03b1). HSE\u03b1 calculated from protein structures was found to better describe the solvent exposure over ASA, CN and RD in many applications. Thus, a sequence-based prediction is desirable, as most proteins do not have experimentally determined structures. To our best knowledge, there is no method to predict HSE\u03b1 and only one method to predict HSE\u03b2.<\/jats:p><jats:p>Results: This study developed a novel method for predicting both HSE\u03b1 and HSE\u03b2 (SPIDER-HSE) that achieved a consistent performance for 10-fold cross validation and two independent tests. The correlation coefficients between predicted and measured HSE\u03b2 (0.73 for upper sphere, 0.69 for down sphere and 0.76 for contact numbers) for the independent test set of 1199 proteins are significantly higher than existing methods. Moreover, predicted HSE\u03b1 has a higher correlation coefficient (0.46) to the stability change by residue mutants than predicted HSE\u03b2 (0.37) and ASA (0.43). The results, together with its easy C\u03b1-atom-based calculation, highlight the potential usefulness of predicted HSE\u03b1 for protein structure prediction and refinement as well as function prediction.<\/jats:p><jats:p>Availability and implementation: The method is available at http:\/\/sparks-lab.org.<\/jats:p><jats:p>Contact: \u00a0yuedong.yang@griffith.edu.au or yaoqi.zhou@griffith.edu.au<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv665","type":"journal-article","created":{"date-parts":[[2015,11,15]],"date-time":"2015-11-15T01:38:21Z","timestamp":1447551501000},"page":"843-849","source":"Crossref","is-referenced-by-count":87,"title":["Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins"],"prefix":"10.1093","volume":"32","author":[{"given":"Rhys","family":"Heffernan","sequence":"first","affiliation":[{"name":"1 Signal 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