[{"doi":"10.1007/978-3-540-30219-3_19","date_updated":"2026-05-29T12:02:16Z","status":"public","oa":1,"publisher":"Springer Nature","abstract":[{"text":"We give an algorithm that locally improves the fit between two proteins modeled as space-filling diagrams. The algorithm defines the fit in purely geometric terms and improves by applying a rigid motion to one of the two proteins. Our implementation of the algorithm takes between three and ten seconds and converges with high likelihood to the correct docked configuration, provided it starts at a position away from the correct one by at most 18 degrees of rotation and at most 3.0Angstrom of translation. The speed and convergence radius make this an attractive algorithm to use in combination with a coarse sampling of the six-dimensional space of rigid motions.","lang":"eng"}],"title":"Local search heuristic for rigid protein docking","quality_controlled":"1","publication_identifier":{"eisbn":["9783540302193"],"isbn":["9783540230182"]},"main_file_link":[{"open_access":"1","url":"https://www.math.unm.edu/~vageli/courses/Ma504/matlab/project/pdf/docking_RMSD.pdf"}],"article_processing_charge":"No","day":"01","type":"conference","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Proceedings of the 4th International Workshop of Algorithms in Bioinformatics","date_created":"2018-12-11T12:06:17Z","date_published":"2004-10-01T00:00:00Z","_id":"3988","year":"2004","publist_id":"2136","extern":"1","OA_place":"repository","alternative_title":["Lecture Notes in Computer Science"],"citation":{"short":"V. Choi, P. Agarwal, H. Edelsbrunner, J. Rudolph, in:, Proceedings of the 4th International Workshop of Algorithms in Bioinformatics, Springer Nature, 2004, pp. 218–229.","ama":"Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid protein docking. In: <i>Proceedings of the 4th International Workshop of Algorithms in Bioinformatics</i>. Vol 3240. Springer Nature; 2004:218-229. doi:<a href=\"https://doi.org/10.1007/978-3-540-30219-3_19\">10.1007/978-3-540-30219-3_19</a>","apa":"Choi, V., Agarwal, P., Edelsbrunner, H., &#38; Rudolph, J. (2004). Local search heuristic for rigid protein docking. In <i>Proceedings of the 4th International Workshop of Algorithms in Bioinformatics</i> (Vol. 3240, pp. 218–229). Bergen, Norway: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-540-30219-3_19\">https://doi.org/10.1007/978-3-540-30219-3_19</a>","ista":"Choi V, Agarwal P, Edelsbrunner H, Rudolph J. 2004. Local search heuristic for rigid protein docking. Proceedings of the 4th International Workshop of Algorithms in Bioinformatics. WABI: 4th International Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science, vol. 3240, 218–229.","ieee":"V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic for rigid protein docking,” in <i>Proceedings of the 4th International Workshop of Algorithms in Bioinformatics</i>, Bergen, Norway, 2004, vol. 3240, pp. 218–229.","chicago":"Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph. “Local Search Heuristic for Rigid Protein Docking.” In <i>Proceedings of the 4th International Workshop of Algorithms in Bioinformatics</i>, 3240:218–29. Springer Nature, 2004. <a href=\"https://doi.org/10.1007/978-3-540-30219-3_19\">https://doi.org/10.1007/978-3-540-30219-3_19</a>.","mla":"Choi, Vicky, et al. “Local Search Heuristic for Rigid Protein Docking.” <i>Proceedings of the 4th International Workshop of Algorithms in Bioinformatics</i>, vol. 3240, Springer Nature, 2004, pp. 218–29, doi:<a href=\"https://doi.org/10.1007/978-3-540-30219-3_19\">10.1007/978-3-540-30219-3_19</a>."},"OA_type":"green","intvolume":"      3240","scopus_import":"1","acknowledgement":"Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from Duke University and NIH under grant R01 GM61822-01.","publication_status":"published","author":[{"last_name":"Choi","full_name":"Choi, Vicky","first_name":"Vicky"},{"last_name":"Agarwal","full_name":"Agarwal, Pankaj","first_name":"Pankaj"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Rudolph, Johannes","last_name":"Rudolph","first_name":"Johannes"}],"conference":{"name":"WABI: 4th International Workshop on Algorithms in Bioinformatics","start_date":"2004-09-17","location":"Bergen, Norway","end_date":"2004-09-21"},"volume":3240,"month":"10","language":[{"iso":"eng"}],"page":"218 - 229","oa_version":"Preprint"}]