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7. Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model

Author

Li, Yaqin, Li, Lingli, Xu, Yongjin, and Yu, Yi

Subjects
Quantitative Biology - Biomolecules, Computer Science - Machine Learning
Abstract

De novo molecular design has facilitated the exploration of large chemical space to accelerate drug discovery. Structure-based de novo method can overcome the data scarcity of active ligands by incorporating drug-target interaction into deep generative architectures. However, these strategies are bottlenecked by the small fraction of experimentally determined protein or complex structures. In addition, the cost of molecular generation is computationally expensive due to 3D representations of both molecule and protein. Here, we demonstrate a widely used and fast protein sequence-based reinforcement learning (RL) model for drug discovery. In the generative model, one of the reward components, a binding affinity predictor, is based on 1D protein sequence and molecular SMILES. As a proof of concept, the RL model was utilized to design molecules for four targets. The generated compounds showed bioactivities by the validation of both QSAR and molecular docking with experimental 3D binding pockets. We also found that the performance of generated molecules depends on the selection of data source training for the binding predictor. Furthermore, drug design for a kinase without any experimental structure, CDK20, was studied by our model. With only 1D protein sequence as input, the generated novel compounds showed favorable binding affinity based on the AlphaFold predicted structure.

Published
2022

17. Exploring the Curriculum Development in Content and Language Integrated Learning: A Systematic Review

Author

Li, Lingli, Huang, Fuquan, Chen, Siyu, Pan, Leiqiong, Zeng, Wenjie, and Wu, Xiaoqi

Abstract

Content and language integrated learning (CLIL) is a booming innovation pervading many educational settings. The global spread of CLIL is being practiced in classrooms the world over. Nevertheless, there is still a lack of systematic curricula for CLIL, despite its widespread adoption. Furthermore, the majority of teachers are implementing CLIL without the support of suitable published materials or resource banks. To explore and explain the curriculum development in CLIL, 281 studies from 2009 to 2019 were reviewed systematically, focusing on peer-reviewed English-language journals. We identified studies through using 'Content and Language Integrated Learning' and CLIL as the search terms in the ProQuest Research Library and EBSCO host databases. Selected articles were organized into five inquiry areas and analyzed thematically, inspired by the curriculum development model proposed by Pawlas and Oliva: 1) CLIL philosophy; 2) CLIL goals; 3) CLIL plan; 4) CLIL implementation; and 5) CLIL evaluation. Based on these themes, Boyer's scholarship of integration was introduced to propose a holistic model for CLIL curriculum development.

Published
2020

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