Molegear: A Java-based platform for evolutionary de novo molecular design

Yunhan Chu; Xuezhong He

doi:10.3390/molecules24071444

Molegear: A Java-based platform for evolutionary de novo molecular design

Yunhan Chu, Xuezhong He^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

A Java-based platform, MoleGear, is developed for de novo molecular design based on the chemistry development kit (CDK) and other Java packages. MoleGear uses evolutionary algorithm (EA) to explore chemical space, and a suite of fragment-based operators of growing, crossover, and mutation for assembling novel molecules that can be scored by prediction of binding free energy or a weighted-sum multi-objective fitness function. The EA can be conducted in parallel over multiple nodes to support large-scale molecular optimizations. Some complementary utilities such as fragment library design, chemical space analysis, and graphical user interface are also integrated into MoleGear. The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design.

Original language	English
Article number	1444
Journal	Molecules
Volume	24
Issue number	7
DOIs	https://doi.org/10.3390/molecules24071444
State	Published - 11 Apr 2019
Externally published	Yes

Keywords

De novo design
Drug molecules
Evolutionary algorithm
Fitness
Multi-objective function

UN SDGs

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

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10.3390/molecules24071444

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title = "Molegear: A Java-based platform for evolutionary de novo molecular design",

abstract = "A Java-based platform, MoleGear, is developed for de novo molecular design based on the chemistry development kit (CDK) and other Java packages. MoleGear uses evolutionary algorithm (EA) to explore chemical space, and a suite of fragment-based operators of growing, crossover, and mutation for assembling novel molecules that can be scored by prediction of binding free energy or a weighted-sum multi-objective fitness function. The EA can be conducted in parallel over multiple nodes to support large-scale molecular optimizations. Some complementary utilities such as fragment library design, chemical space analysis, and graphical user interface are also integrated into MoleGear. The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design.",

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author = "Yunhan Chu and Xuezhong He",

note = "Publisher Copyright: {\textcopyright} 2019 by the authors.",

year = "2019",

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day = "11",

doi = "10.3390/molecules24071444",

language = "英语",

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AU - Chu, Yunhan

AU - He, Xuezhong

PY - 2019/4/11

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AB - A Java-based platform, MoleGear, is developed for de novo molecular design based on the chemistry development kit (CDK) and other Java packages. MoleGear uses evolutionary algorithm (EA) to explore chemical space, and a suite of fragment-based operators of growing, crossover, and mutation for assembling novel molecules that can be scored by prediction of binding free energy or a weighted-sum multi-objective fitness function. The EA can be conducted in parallel over multiple nodes to support large-scale molecular optimizations. Some complementary utilities such as fragment library design, chemical space analysis, and graphical user interface are also integrated into MoleGear. The candidate molecules as inhibitors for the human immunodeficiency virus 1 (HIV-1) protease were designed by MoleGear, which validates the potential capability for de novo molecular design.

KW - De novo design

KW - Drug molecules

KW - Evolutionary algorithm

KW - Fitness

KW - Multi-objective function

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Molegear: A Java-based platform for evolutionary de novo molecular design

Abstract

Keywords

UN SDGs

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