Local search heuristic for rigid protein docking
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.
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Author
Choi, Vicky;
Agarwal, Pankaj;
Edelsbrunner, HerbertISTA 
;
Rudolph, Johannes
;
Rudolph, JohannesSeries Title
Lecture Notes in Computer Science
Abstract
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.
Publishing Year
Date Published
2004-10-01
Proceedings Title
Proceedings of the 4th International Workshop of Algorithms in Bioinformatics
Publisher
Springer Nature
Acknowledgement
Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from Duke University and NIH under grant R01 GM61822-01.
Volume
3240
Page
218 - 229
Conference
WABI: 4th International Workshop on Algorithms in Bioinformatics
Conference Location
Bergen, Norway
Conference Date
2004-09-17 – 2004-09-21
ISBN
IST-REx-ID
Cite this
Choi V, Agarwal P, Edelsbrunner H, Rudolph J. Local search heuristic for rigid protein docking. In: Proceedings of the 4th International Workshop of Algorithms in Bioinformatics. Vol 3240. Springer Nature; 2004:218-229. doi:10.1007/978-3-540-30219-3_19
Choi, V., Agarwal, P., Edelsbrunner, H., & Rudolph, J. (2004). Local search heuristic for rigid protein docking. In Proceedings of the 4th International Workshop of Algorithms in Bioinformatics (Vol. 3240, pp. 218–229). Bergen, Norway: Springer Nature. https://doi.org/10.1007/978-3-540-30219-3_19
Choi, Vicky, Pankaj Agarwal, Herbert Edelsbrunner, and Johannes Rudolph. “Local Search Heuristic for Rigid Protein Docking.” In Proceedings of the 4th International Workshop of Algorithms in Bioinformatics, 3240:218–29. Springer Nature, 2004. https://doi.org/10.1007/978-3-540-30219-3_19.
V. Choi, P. Agarwal, H. Edelsbrunner, and J. Rudolph, “Local search heuristic for rigid protein docking,” in Proceedings of the 4th International Workshop of Algorithms in Bioinformatics, Bergen, Norway, 2004, vol. 3240, pp. 218–229.
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.
Choi, Vicky, et al. “Local Search Heuristic for Rigid Protein Docking.” Proceedings of the 4th International Workshop of Algorithms in Bioinformatics, vol. 3240, Springer Nature, 2004, pp. 218–29, doi:10.1007/978-3-540-30219-3_19.
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