Navigating the landscape of enzyme design: from molecular simulations to machine learning

J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …

[HTML][HTML] Applications of molecular dynamics simulation in structure prediction of peptides and proteins

H Geng, F Chen, J Ye, F Jiang - Computational and structural …, 2019 - Elsevier
Compared with rapid accumulation of protein sequences from high-throughput DNA
sequencing, obtaining experimental 3D structures of proteins is still much more difficult …

DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction

G Terashi, X Wang, D Prasad, T Nakamura, D Kihara - Nature Methods, 2024 - nature.com
Three-dimensional structure modeling from maps is an indispensable step for studying
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …

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 …

Structural predictions of protein–DNA binding: MELD-DNA

R Esmaeeli, A Bauzá, A Perez - Nucleic Acids Research, 2023 - academic.oup.com
Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and
functional genome. Yet, our structural understanding of how proteins interact with DNA is …

Protein storytelling through physics

E Brini, C Simmerling, K Dill - Science, 2020 - science.org
BACKGROUND Understanding biology, particularly at the level of actionable drug
discovery, is often a matter of develo** accurate stories about how proteins work. This …

Advances in free-energy-based simulations of protein folding and ligand binding

A Perez, JA Morrone, C Simmerling, KA Dill - Current opinion in structural …, 2016 - Elsevier
Highlights•Molecular dynamics is reaching longer timescales faster than Moore's law's
rate.•Improved sampling algorithms, force fields and computers drive advances.•At current …

Protein structure prediction using Rosetta in CASP12

S Ovchinnikov, H Park, DE Kim… - Proteins: Structure …, 2018 - Wiley Online Library
We describe several notable aspects of our structure predictions using Rosetta in CASP12
in the free modeling (FM) and refinement (TR) categories. First, we had previously …

Adenylyl cyclase signalling complexes–Pharmacological challenges and opportunities

ML Halls, DMF Cooper - Pharmacology & therapeutics, 2017 - Elsevier
Signalling pathways involving the vital second messanger, cAMP, impact on most significant
physiological processes. Unsurprisingly therefore, the activation and regulation of cAMP …

From inhibition to degradation: targeting the antiapoptotic protein myeloid cell leukemia 1 (MCL1)

JW Papatzimas, E Gorobets, R Maity… - Journal of medicinal …, 2019 - ACS Publications
Protein–protein interactions (PPIs) have emerged as significant targets for therapeutic
development, owing to their critical nature in diverse biological processes. An ideal PPI …