From predicting to decision making: Reinforcement learning in biomedicine

X Liu, J Zhang, Z Hou, YI Yang… - Wiley Interdisciplinary …, 2024 - Wiley Online Library
Reinforcement learning (RL) is one important branch of artificial intelligence (AI), which
intuitively imitates the learning style of human beings. It is commonly derived from solving …

Experimental NOE, chemical shift, and proline isomerization data provide detailed insights into amelotin oligomerization

SC Chiliveri, Y Shen, JL Baber, J Ying… - Journal of the …, 2023 - ACS Publications
Amelotin is an intrinsically disordered protein (IDP) rich in Pro residues and is involved in
hydroxyapatite mineralization. It rapidly oligomerizes under physiological conditions of pH …

Protein multimer structure prediction via prompt learning

Z Gao, X Sun, Z Liu, Y Li, H Cheng, J Li - arXiv preprint arXiv:2402.18813, 2024 - arxiv.org
Understanding the 3D structures of protein multimers is crucial, as they play a vital role in
regulating various cellular processes. It has been empirically confirmed that the multimer …

[HTML][HTML] Deep confident steps to new pockets: Strategies for docking generalization

G Corso, A Deng, B Fry, N Polizzi, R Barzilay… - ArXiv, 2024 - ncbi.nlm.nih.gov
Accurate blind docking has the potential to lead to new biological breakthroughs, but for this
promise to be realized, docking methods must generalize well across the proteome. Existing …

Simulation toolkits at the molecular scale for trans-scale thermal signaling

I Kurisaki, M Suzuki - Computational and Structural Biotechnology Journal, 2023 - Elsevier
Thermogenesis is a physiological activity of releasing heat that originates from intracellular
biochemical reactions. Recent experimental studies discovered that externally applied heat …

Deep Reinforcement Learning for Modelling Protein Complexes

Z Gao, T Feng, J You, C Zi, Y Zhou, C Zhang… - arXiv preprint arXiv …, 2024 - arxiv.org
AlphaFold can be used for both single-chain and multi-chain protein structure prediction,
while the latter becomes extremely challenging as the number of chains increases. In this …

Domain-based protein docking with extremely large conformational changes

C Christoffer, D Kihara - Journal of molecular biology, 2022 - Elsevier
Proteins are key components in many processes in living cells, and physical interactions
with other proteins and nucleic acids often form key parts of their functions. In many cases …

Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD

C Christoffer, D Kihara - Proteomics, 2023 - Wiley Online Library
Proteins and nucleic acids are key components in many processes in living cells, and
interactions between proteins and nucleic acids are often crucial pathway components. In …

Syndock: N rigid protein docking via learnable group synchronization

Y Ji, Y Bian, G Fu, P Zhao, P Luo - arXiv preprint arXiv:2305.15156, 2023 - arxiv.org
The regulation of various cellular processes heavily relies on the protein complexes within a
living cell, necessitating a comprehensive understanding of their three-dimensional …

Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling

X Ding, X Chen, EE Sullivan, TF Shay, V Gradinaru - Molecular Therapy, 2024 - cell.com
Deep-learning-based methods for protein structure prediction have achieved
unprecedented accuracy, yet their utility in the engineering of protein-based binders remains …