The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins

V Agarwal, AC McShan - Nature Chemical Biology, 2024 - nature.com
Artificial intelligence-driven advances in protein structure prediction in recent years have
raised the question: has the protein structure-prediction problem been solved? Here, with a …

Metabolic engineering of model microorganisms for the production of xanthophyll

N Wang, H Peng, C Yang, W Guo, M Wang, G Li, D Liu - Microorganisms, 2023 - mdpi.com
Xanthophyll is an oxidated version of carotenoid. It presents significant value to the
pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and …

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

N Giri, J Cheng - Nature Communications, 2024 - nature.com
Accurately building 3D atomic structures from cryo-EM density maps is a crucial step in cryo-
EM-based protein structure determination. Converting density maps into 3D atomic …

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

A Dhakal, R Gyawali, L Wang, J Cheng - Scientific Data, 2023 - nature.com
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of
biological macromolecular complexes. Picking single-protein particles from cryo-EM …

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference

SE Hoff, FE Thomasen, K Lindorff-Larsen… - PLOS Computational …, 2024 - journals.plos.org
Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a
challenging problem of outstanding importance. Current refinement methods often generate …

All-Atom Biomolecular Simulation in the Exascale Era

TL Beck, P Carloni, DN Asthagiri - Journal of Chemical Theory and …, 2024 - ACS Publications
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML
techniques, that model biomolecular motions over unprecedented length and time scales …

Cryo2structdata: A large labeled cryo-em density map dataset for ai-based modeling of protein structures

N Giri, L Wang, J Cheng - Scientific Data, 2024 - nature.com
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new
era of structural biology, enabling the routine determination of large biological molecules …

Advancing cryo-electron microscopy data analysis through accelerated simulation-based flexible fitting approaches

O Miyashita, F Tama - Current Opinion in Structural Biology, 2023 - Elsevier
Flexible fitting based on molecular dynamics simulation is a technique for structure modeling
from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution …

Improving protein–ligand interaction modeling with cryo-em data, templates, and deep learning in 2021 ligand model challenge

N Giri, J Cheng - Biomolecules, 2023 - mdpi.com
Elucidating protein–ligand interaction is crucial for studying the function of proteins and
compounds in an organism and critical for drug discovery and design. The problem of …

Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method

T Włodarski, JO Streit, A Mitropoulou, LD Cabrita… - Scientific Reports, 2024 - nature.com
Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for the
determination of structures of complex biological molecules. The accurate characterisation …