{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T02:02:40Z","timestamp":1773885760967,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In many proteins, helix\u2013helix interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining associations between protein units. However, the determination of a set of rules that guide helix\u2013helix interaction has been elusive. In order to gain further insight into the helix\u2013helix interface, we have developed a comprehensive package of tools for analyzing helix\u2013helix packing in proteins. These tools are available at . They include quantitative measures of the helix interaction surface area and helix crossing angle, as well as several methods for visualizing the helical interaction. These methods can be used for analysis of individual protein conformations or to gain insight into dynamic changes in helix interactions. For the latter purpose, a direct interface from entries in the Molecular Motions Database to the HIT site has been provided.<\/jats:p>\n               <jats:p>Contact: \u00a0Mark.Gerstein@yale.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl274","type":"journal-article","created":{"date-parts":[[2006,10,24]],"date-time":"2006-10-24T14:16:03Z","timestamp":1161699363000},"page":"2735-2738","source":"Crossref","is-referenced-by-count":9,"title":["Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins"],"prefix":"10.1093","volume":"22","author":[{"given":"Anne E. Counterman","family":"Burba","sequence":"first","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University \u00a0 New Haven, CT 06520, USA"}]},{"given":"Ursula","family":"Lehnert","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University \u00a0 New Haven, CT 06520, USA"}]},{"given":"Eric Z.","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University \u00a0 New Haven, CT 06520, USA"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"Department of Molecular Biophysics and Biochemistry, Yale University \u00a0 New Haven, CT 06520, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,10,23]]},"reference":[{"key":"2023012408414644800_b1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/prot.10071","article-title":"Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers","volume":"47","author":"Adamian","year":"2002","journal-title":"Proteins"},{"key":"2023012408414644800_b2","doi-asserted-by":"crossref","first-page":"780","DOI":"10.1006\/jmbi.1997.1279","article-title":"Helix packing in membrane proteins","volume":"272","author":"Bowie","year":"1997","journal-title":"J. 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