Computer-aided understanding and engineering of enzymatic selectivity

L Wu, L Qin, Y Nie, Y Xu, YL Zhao - Biotechnology Advances, 2022 - Elsevier
Abstract Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric
synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally …

Mimicking Enzymes: The quest for powerful catalysts from simple molecules to nanozymes

Y Lyu, P Scrimin - ACS Catalysis, 2021 - ACS Publications
Enzymes are highly evolved catalysts that perform their tasks with high efficiency. 1 Hence,
they may constitute a very attractive reference in the development of a synthetic catalyst. The …

ADMETboost: a web server for accurate ADMET prediction

H Tian, R Ketkar, P Tao - Journal of molecular modeling, 2022 - Springer
The absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties are
important in drug discovery as they define efficacy and safety. In this work, we applied an …

UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: a comparison study

F Trozzi, X Wang, P Tao - The Journal of Physical Chemistry B, 2021 - ACS Publications
Proteins are the molecular machines of life. The multitude of possible conformations that
proteins can adopt determines their free-energy landscapes. However, the inherently high …

[HTML][HTML] Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET

SK Jayasekara, HD Joni, B Jayantha… - Computational and …, 2023 - Elsevier
Polyethylene terephthalate (PET) is the largest produced polyester globally, and less than
30% of all the PET produced globally (∼ 6 billion pounds annually) is currently recycled into …

A novel neural network-based alloy design strategy: Gated recurrent unit machine learning modeling integrated with orthogonal experiment design and data …

J Yin, Q Lei, X Li, X Zhang, X Meng, Y Jiang, L Tian… - Acta Materialia, 2023 - Elsevier
Abstract Machine learning-aided alloy design has recently attracted broad interest among
the materials science community. However, the prediction accuracy of general machine …

Enhancing conformational sampling for intrinsically disordered and ordered proteins by Variational autoencoder

JJ Zhu, NJ Zhang, T Wei, HF Chen - International Journal of Molecular …, 2023 - mdpi.com
Intrinsically disordered proteins (IDPs) account for more than 50% of the human proteome
and are closely associated with tumors, cardiovascular diseases, and neurodegeneration …

Explore protein conformational space with variational autoencoder

H Tian, X Jiang, F Trozzi, S **ao… - Frontiers in molecular …, 2021 - frontiersin.org
Molecular dynamics (MD) simulations have been actively used in the study of protein
structure and function. However, extensive sampling in the protein conformational space …

[HTML][HTML] Understanding the effectiveness of enzyme pre-reaction state by a quantum-based machine learning model

S Luo, L Liu, CJ Lyu, B Sim, Y Liu, H Gong… - Cell Reports Physical …, 2022 - cell.com
Prediction of enzymatic stereochemistry is a significant challenge in computational chemistry
because of targeting very small energy gaps in highly complicated macromolecular systems …

Machine learning models predict calculation outcomes with the transferability necessary for computational catalysis

C Duan, A Nandy, H Adamji… - Journal of Chemical …, 2022 - ACS Publications
Virtual high-throughput screening (VHTS) and machine learning (ML) have greatly
accelerated the design of single-site transition-metal catalysts. VHTS of catalysts, however …