Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS

Korb, Oliver; Stützle, Thomas; Exner, Thomas E.

Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS

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Date

2009

Authors

Korb, Oliver

Stützle, Thomas

Exner, Thomas E.

Project

Plants-Software

Collections

Chemie
Zukunftskolleg

Publication type

Journal article

Published in

Journal of Chemical Information and Modelling ; 49 (2009), 1. - pp. 84-96. - ISSN 1549-9596. - eISSN 1549-960X

Abstract

In this paper we present two empirical scoring functions, PLANTS(CHEMPLP) and PLANTS(PLP), designed for our docking algorithm PLANTS (Protein-Ligand ANT System), which is based on ant colony optimization (ACO). They are related, regarding their functional form, to parts of already published scoring functions and force fields. The parametrization procedure described here was able to identify several parameter settings showing an excellent performance for the task of pose prediction on two test sets comprising 298 complexes in total. Up to 87% of the complexes of the Astex diverse set and 77% of the CCDC/Astex clean listnc (noncovalently bound complexes of the clean list) could be reproduced with root-mean-square deviations of less than 2 A with respect to the experimentally determined structures. A comparison with the state-of-the-art docking tool GOLD clearly shows that this is, especially for the druglike Astex diverse set, an improvement in pose prediction performance. Additionally, optimized parameter settings for the search algorithm were identified, which can be used to balance pose prediction reliability and search speed.

Subject (DDC)

540 Chemistry

Cite This

ISO 690

KORB, Oliver, Thomas STÜTZLE, Thomas E. EXNER, 2009. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS. In: Journal of Chemical Information and Modelling. 49(1), pp. 84-96. ISSN 1549-9596. eISSN 1549-960X. Available under: doi: 10.1021/ci800298z

BibTex

@article{Korb2009Empir-1095,
  year={2009},
  doi={10.1021/ci800298z},
  title={Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS},
  number={1},
  volume={49},
  issn={1549-9596},
  journal={Journal of Chemical Information and Modelling},
  pages={84--96},
  author={Korb, Oliver and Stützle, Thomas and Exner, Thomas E.}
}

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Bibliography of Konstanz

Yes