{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T21:53:20Z","timestamp":1720302800814},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ions are essential component of the cell and frequently are found bound to various macromolecules, in particular to proteins. A binding of an ion to a protein greatly affects protein\u2019s biophysical characteristics and needs to be taken into account in any modeling approach. However, ion\u2019s bounded positions cannot be easily revealed experimentally, especially if they are loosely bound to macromolecular surface.<\/jats:p>\n               <jats:p>Results: Here, we report a web server, the BION web server, which addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult to predict. The BION is easy to use web server that requires only coordinate file to be inputted, and the user is provided with various, but easy to navigate, options. The coordinate file with predicted bound ions is displayed on the output and is available for download.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/compbio.clemson.edu\/bion_server\/<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <jats:p>Contact: \u00a0ealexov@clemson.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt032","type":"journal-article","created":{"date-parts":[[2013,2,5]],"date-time":"2013-02-05T01:24:52Z","timestamp":1360027492000},"page":"805-806","source":"Crossref","is-referenced-by-count":13,"title":["BION web server: predicting non-specifically bound surface ions"],"prefix":"10.1093","volume":"29","author":[{"given":"Marharyta","family":"Petukh","sequence":"first","affiliation":[{"name":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taylor","family":"Kimmet","sequence":"additional","affiliation":[{"name":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"},{"name":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emil","family":"Alexov","sequence":"additional","affiliation":[{"name":"1 Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA and 2Department of Computer Sciences, Clemson University, Clemson, SC 29634, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,2,3]]},"reference":[{"key":"2023012810314520100_btt032-B1","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1002\/prot.21587","article-title":"Prediction of transition metal-binding sites from apo protein structures","volume":"70","author":"Babor","year":"2008","journal-title":"Proteins"},{"key":"2023012810314520100_btt032-B2","volume-title":"Metal Ions in Biochemistry","author":"Bhattacharya","year":"2005"},{"key":"2023012810314520100_btt032-B3","doi-asserted-by":"crossref","first-page":"3168","DOI":"10.1021\/ja0209722","article-title":"First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT\/CDM calculations","volume":"125","author":"Dudev","year":"2003","journal-title":"J. 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