Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking

Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to impro...
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Autor*in:	Boxin Guan [verfasserIn] Changsheng Zhang [verfasserIn] Jiaxu Ning [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2017

Schlagwörter:	Protein–ligand docking Pharmaceutical development Genetic algorithm AutoDock Crossover elitist preservation

Übergeordnetes Werk:	In: AMB Express - SpringerOpen, 2011, 7(2017), 1, Seite 11
Übergeordnetes Werk:	volume:7 ; year:2017 ; number:1 ; pages:11

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.1186/s13568-017-0476-0

Katalog-ID:	DOAJ023162538

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520			\|a Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.
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spelling	10.1186/s13568-017-0476-0 doi (DE-627)DOAJ023162538 (DE-599)DOAJf28aa4225bba4c90a563ccd55ed312d1 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QR1-502 Boxin Guan verfasserin aut Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems. Protein–ligand docking Pharmaceutical development Genetic algorithm AutoDock Crossover elitist preservation Biotechnology Microbiology Changsheng Zhang verfasserin aut Jiaxu Ning verfasserin aut In AMB Express SpringerOpen, 2011 7(2017), 1, Seite 11 (DE-627)665672926 (DE-600)2621432-5 21910855 nnns volume:7 year:2017 number:1 pages:11 https://doi.org/10.1186/s13568-017-0476-0 kostenfrei https://doaj.org/article/f28aa4225bba4c90a563ccd55ed312d1 kostenfrei http://link.springer.com/article/10.1186/s13568-017-0476-0 kostenfrei https://doaj.org/toc/2191-0855 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2017 1 11
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allfieldsSound	10.1186/s13568-017-0476-0 doi (DE-627)DOAJ023162538 (DE-599)DOAJf28aa4225bba4c90a563ccd55ed312d1 DE-627 ger DE-627 rakwb eng TP248.13-248.65 QR1-502 Boxin Guan verfasserin aut Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems. Protein–ligand docking Pharmaceutical development Genetic algorithm AutoDock Crossover elitist preservation Biotechnology Microbiology Changsheng Zhang verfasserin aut Jiaxu Ning verfasserin aut In AMB Express SpringerOpen, 2011 7(2017), 1, Seite 11 (DE-627)665672926 (DE-600)2621432-5 21910855 nnns volume:7 year:2017 number:1 pages:11 https://doi.org/10.1186/s13568-017-0476-0 kostenfrei https://doaj.org/article/f28aa4225bba4c90a563ccd55ed312d1 kostenfrei http://link.springer.com/article/10.1186/s13568-017-0476-0 kostenfrei https://doaj.org/toc/2191-0855 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 7 2017 1 11
language	English
source	In AMB Express 7(2017), 1, Seite 11 volume:7 year:2017 number:1 pages:11
sourceStr	In AMB Express 7(2017), 1, Seite 11 volume:7 year:2017 number:1 pages:11
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topic_facet	Protein–ligand docking Pharmaceutical development Genetic algorithm AutoDock Crossover elitist preservation Biotechnology Microbiology
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authorswithroles_txt_mv	Boxin Guan @@aut@@ Changsheng Zhang @@aut@@ Jiaxu Ning @@aut@@
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callnumber-first	T - Technology
author	Boxin Guan
spellingShingle	Boxin Guan misc TP248.13-248.65 misc QR1-502 misc Protein–ligand docking misc Pharmaceutical development misc Genetic algorithm misc AutoDock misc Crossover elitist preservation misc Biotechnology misc Microbiology Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
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topic	misc TP248.13-248.65 misc QR1-502 misc Protein–ligand docking misc Pharmaceutical development misc Genetic algorithm misc AutoDock misc Crossover elitist preservation misc Biotechnology misc Microbiology
topic_unstemmed	misc TP248.13-248.65 misc QR1-502 misc Protein–ligand docking misc Pharmaceutical development misc Genetic algorithm misc AutoDock misc Crossover elitist preservation misc Biotechnology misc Microbiology
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title	Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
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title_full	Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
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title_sort	genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
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title_auth	Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
abstract	Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.
abstractGer	Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.
abstract_unstemmed	Abstract Protein–ligand docking plays an important role in computer-aided pharmaceutical development. Protein–ligand docking can be defined as a search algorithm with a scoring function, whose aim is to determine the conformation of the ligand and the receptor with the lowest energy. Hence, to improve an efficient algorithm has become a very significant challenge. In this paper, a novel search algorithm based on crossover elitist preservation mechanism (CEP) for solving protein–ligand docking problems is proposed. The proposed algorithm, namely genetic algorithm with crossover elitist preservation (CEPGA), employ the CEP to keep the elite individuals of the last generation and make the crossover more efficient and robust. The performance of CEPGA is tested on sixteen molecular docking complexes from RCSB protein data bank. In comparison with GA, LGA and SODOCK in the aspects of lowest energy and highest accuracy, the results of which indicate that the CEPGA is a reliable and successful method for protein–ligand docking problems.
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title_short	Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking
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Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking

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