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A three\u2010dimensional structural model of the KN\u2010BJ2 serine proteinase was built by homology modeling using the snake venom plasminogen activator TSV\u2010PA as a major template and porcine kallikrein as additional structural support. A set of intrinsic buried waters was included in the model and its behavior under dynamic conditions was molecular dynamics simulated, revealing a most interesting similarity pattern to kallikrein. The benzamidine\u2010based thrombin inhibitors \u03b1\u2010NAPAP, 3\u2010TAPAP, and 4\u2010TAPAP were docked into the refined model, allowing for a more insightful functional characterization of the enzyme and a better understanding of the reported comparatively low affinity of KN\u2010BJ2 toward those inhibitors.<\/jats:p>","DOI":"10.1110\/ps.04746804","type":"journal-article","created":{"date-parts":[[2004,8,20]],"date-time":"2004-08-20T22:23:44Z","timestamp":1093040624000},"page":"2355-2369","source":"Crossref","is-referenced-by-count":10,"title":["On the modeling of snake venom serine proteinase interactions with benzamidine\u2010based thrombin inhibitors"],"prefix":"10.1002","volume":"13","author":[{"given":"Elsa S.","family":"Henriques","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nelson","family":"Fonseca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Jo\u00e3o","family":"Ramos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2009,1]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_2_6_3_1","doi-asserted-by":"crossref","first-page":"20085","DOI":"10.1016\/S0021-9258(18)54894-8","article-title":"Crystallographic analysis at 3.0\u2010\u00c5 resolution of the binding to human thrombin of four active site\u2010directed inhibitors","volume":"266","author":"Banner D.W.","year":"1991","journal-title":"J. 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