Recent trends in biocatalysis

D Yi, T Bayer, CPS Badenhorst, S Wu… - Chemical Society …, 2021 - pubs.rsc.org
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the
integration of multidisciplinary technologies, natural enzymatic reactions are constantly …

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

K Leppek, R Das, M Barna - Nature reviews Molecular cell biology, 2018 - nature.com
RNA molecules can fold into intricate shapes that can provide an additional layer of control
of gene expression beyond that of their sequence. In this Review, we discuss the current …

The HDOCK server for integrated protein–protein docking

Y Yan, H Tao, J He, SY Huang - Nature protocols, 2020 - nature.com
Abstract The HDOCK server (http://hdock. phys. hust. edu. cn/) is a highly integrated suite of
homology search, template-based modeling, structure prediction, macromolecular docking …

Accurate RNA 3D structure prediction using a language model-based deep learning approach

T Shen, Z Hu, S Sun, D Liu, F Wong, J Wang, J Chen… - Nature …, 2024 - nature.com
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved
challenge. Determining RNA 3D structures is crucial for understanding their functions and …

RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

J Singh, J Hanson, K Paliwal, Y Zhou - Nature communications, 2019 - nature.com
The majority of our human genome transcribes into noncoding RNAs with unknown
structures and functions. Obtaining functional clues for noncoding RNAs requires accurate …

Assessment of three‐dimensional RNA structure prediction in CASP15

R Das, RC Kretsch, AJ Simpkin… - Proteins: Structure …, 2023 - Wiley Online Library
The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we
report assessments of RNA structure predictions in CASP15, the first CASP exercise that …

RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

FARFAR2: improved de novo rosetta prediction of complex global RNA folds

AM Watkins, R Rangan, R Das - Structure, 2020 - cell.com
Predicting RNA three-dimensional structures from sequence could accelerate
understanding of the growing number of RNA molecules being discovered across biology …

RNA-Puzzles Round V: blind predictions of 23 RNA structures

F Bu, Y Adam, RW Adamiak, M Antczak… - Nature …, 2024 - nature.com
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA three-dimensional structure prediction. With agreement from structural biologists, RNA …

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Z Miao, RW Adamiak, M Antczak, MJ Boniecki… - Rna, 2020 - rnajournal.cshlp.org
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of
RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are …