Department of Chemical Engineering, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
Molecules. 2019 Apr 11;24(7):1444. doi: 10.3390/molecules24071444.
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.
一个基于 Java 的平台 MoleGear 是为从头分子设计开发的，它基于化学开发工具包（CDK）和其他 Java 包。 MoleGear 使用进化算法（EA）来探索化学空间，并使用一系列基于片段的生长、交叉和突变算子来组装新的分子，这些分子可以通过预测结合自由能或加权和多目标适应度函数来评分。EA 可以在多个节点上并行进行，以支持大规模的分子优化。MoleGear 还集成了一些补充工具，如片段库设计、化学空间分析和图形用户界面。通过 MoleGear 设计了人免疫缺陷病毒 1（HIV-1）蛋白酶抑制剂的候选分子，验证了从头分子设计的潜在能力。
