Application of Inductive Logic Programming to Structure-Based Drug Design

David Pierre Louis Enot; Ross Donald King

doi:10.1007/978-3-540-39804-2_16

Application of Inductive Logic Programming to Structure-Based Drug Design

David Pierre Louis Enot
, Ross Donald King

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (ISBN)

5 Citations (Scopus)

Abstract

Developments in physical and biological technology have resulted in a rapid rise in the amount of data available on the 3D structure of protein-ligand complexes. The extraction of knowledge from this data is central to the design of new drugs. We extended the application of Inductive Logic Programming (ILP) in drug design to deal with such structure-based drug design (SBDD) problems. We first expanded the ILP pharmacophore representation to deal with protein active sites. Applying a combination of the ILP algorithm Aleph, and linear regression, we then formed quantitative models that can be interpretated chemically. We applied this approach to two test cases: Glycogen Phosphorylase inhibitors, and HIV protease inhibitors. In both cases we observed a significant (P < 0.05) improvement over both standard approaches, and use of only the ligand. We demonstrate that the theories produced are consistent with the existing chemical literature.

Original language	English
Title of host publication	Knowledge Discovery in Databases: PKDD 2003
Subtitle of host publication	7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings
Publisher	Springer Nature
Pages	156-167
Number of pages	12
ISBN (Electronic)	978-3-540-39804-2
ISBN (Print)	978-3-540-20085-7
DOIs	https://doi.org/10.1007/978-3-540-39804-2_16
Publication status	Published - 2003
Event	7th European Conference on Principles and Practice of Knowledge Discovery in Databases - Cavtat-Dubrovnik, Croatia Duration: 22 Sept 2003 → 26 Sept 2003

Publication series

Name	Lecture Notes in Computer Science
Publisher	Springer
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	7th European Conference on Principles and Practice of Knowledge Discovery in Databases
Country/Territory	Croatia
City	Cavtat-Dubrovnik
Period	22 Sept 2003 → 26 Sept 2003

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1007/978-3-540-39804-2_16

http://hdl.handle.net/2160/145

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Enot, D. P. L., & King, R. D. (2003). Application of Inductive Logic Programming to Structure-Based Drug Design. In Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings (pp. 156-167). (Lecture Notes in Computer Science). Springer Nature. https://doi.org/10.1007/978-3-540-39804-2_16

Enot, David Pierre Louis ; King, Ross Donald. / Application of Inductive Logic Programming to Structure-Based Drug Design. Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings. Springer Nature, 2003. pp. 156-167 (Lecture Notes in Computer Science).

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abstract = "Developments in physical and biological technology have resulted in a rapid rise in the amount of data available on the 3D structure of protein-ligand complexes. The extraction of knowledge from this data is central to the design of new drugs. We extended the application of Inductive Logic Programming (ILP) in drug design to deal with such structure-based drug design (SBDD) problems. We first expanded the ILP pharmacophore representation to deal with protein active sites. Applying a combination of the ILP algorithm Aleph, and linear regression, we then formed quantitative models that can be interpretated chemically. We applied this approach to two test cases: Glycogen Phosphorylase inhibitors, and HIV protease inhibitors. In both cases we observed a significant (P < 0.05) improvement over both standard approaches, and use of only the ligand. We demonstrate that the theories produced are consistent with the existing chemical literature.",

author = "Enot, \{David Pierre Louis\} and King, \{Ross Donald\}",

note = "Enot, D. and King, R. D. (2003) Application of Inductive Logic Programming to Structure-Based Drug Design. 7th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD '03). Springer LNAI 2838 p156-167; 7th European Conference on Principles and Practice of Knowledge Discovery in Databases ; Conference date: 22-09-2003 Through 26-09-2003",

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Enot, DPL & King, RD 2003, Application of Inductive Logic Programming to Structure-Based Drug Design. in Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings. Lecture Notes in Computer Science, Springer Nature, pp. 156-167, 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, 22 Sept 2003. https://doi.org/10.1007/978-3-540-39804-2_16

Application of Inductive Logic Programming to Structure-Based Drug Design. / Enot, David Pierre Louis; King, Ross Donald.
Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings. Springer Nature, 2003. p. 156-167 (Lecture Notes in Computer Science).

Research output: Chapter in Book/Report/Conference proceeding › Conference Proceeding (ISBN)

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T1 - Application of Inductive Logic Programming to Structure-Based Drug Design

AU - Enot, David Pierre Louis

AU - King, Ross Donald

N1 - Enot, D. and King, R. D. (2003) Application of Inductive Logic Programming to Structure-Based Drug Design. 7th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD '03). Springer LNAI 2838 p156-167

PY - 2003

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N2 - Developments in physical and biological technology have resulted in a rapid rise in the amount of data available on the 3D structure of protein-ligand complexes. The extraction of knowledge from this data is central to the design of new drugs. We extended the application of Inductive Logic Programming (ILP) in drug design to deal with such structure-based drug design (SBDD) problems. We first expanded the ILP pharmacophore representation to deal with protein active sites. Applying a combination of the ILP algorithm Aleph, and linear regression, we then formed quantitative models that can be interpretated chemically. We applied this approach to two test cases: Glycogen Phosphorylase inhibitors, and HIV protease inhibitors. In both cases we observed a significant (P < 0.05) improvement over both standard approaches, and use of only the ligand. We demonstrate that the theories produced are consistent with the existing chemical literature.

AB - Developments in physical and biological technology have resulted in a rapid rise in the amount of data available on the 3D structure of protein-ligand complexes. The extraction of knowledge from this data is central to the design of new drugs. We extended the application of Inductive Logic Programming (ILP) in drug design to deal with such structure-based drug design (SBDD) problems. We first expanded the ILP pharmacophore representation to deal with protein active sites. Applying a combination of the ILP algorithm Aleph, and linear regression, we then formed quantitative models that can be interpretated chemically. We applied this approach to two test cases: Glycogen Phosphorylase inhibitors, and HIV protease inhibitors. In both cases we observed a significant (P < 0.05) improvement over both standard approaches, and use of only the ligand. We demonstrate that the theories produced are consistent with the existing chemical literature.

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SN - 978-3-540-20085-7

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Enot DPL, King RD. Application of Inductive Logic Programming to Structure-Based Drug Design. In Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases, Cavtat-Dubrovnik, Croatia, September 22-26, 2003. Proceedings. Springer Nature. 2003. p. 156-167. (Lecture Notes in Computer Science). doi: 10.1007/978-3-540-39804-2_16

Application of Inductive Logic Programming to Structure-Based Drug Design

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