---
OA_place: repository
OA_type: green
_id: '3988'
abstract:
- lang: eng
  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.
acknowledgement: Supported by NSF under grant CCR-00-86013, BGT Postdoc Program from
  Duke University and NIH under grant R01 GM61822-01.
alternative_title:
- Lecture Notes in Computer Science
article_processing_charge: No
author:
- first_name: Vicky
  full_name: Choi, Vicky
  last_name: Choi
- first_name: Pankaj
  full_name: Agarwal, Pankaj
  last_name: Agarwal
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Johannes
  full_name: Rudolph, Johannes
  last_name: Rudolph
citation:
  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>'
  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>.
  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.
  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.'
  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>.
  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.
conference:
  end_date: 2004-09-21
  location: Bergen, Norway
  name: 'WABI: 4th International Workshop on Algorithms in Bioinformatics'
  start_date: 2004-09-17
date_created: 2018-12-11T12:06:17Z
date_published: 2004-10-01T00:00:00Z
date_updated: 2026-05-29T12:02:16Z
day: '01'
doi: 10.1007/978-3-540-30219-3_19
extern: '1'
intvolume: '      3240'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.math.unm.edu/~vageli/courses/Ma504/matlab/project/pdf/docking_RMSD.pdf
month: '10'
oa: 1
oa_version: Preprint
page: 218 - 229
publication: Proceedings of the 4th International Workshop of Algorithms in Bioinformatics
publication_identifier:
  eisbn:
  - '9783540302193'
  isbn:
  - '9783540230182'
publication_status: published
publisher: Springer Nature
publist_id: '2136'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local search heuristic for rigid protein docking
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 3240
year: '2004'
...