The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins
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 …
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 …
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
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 …
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
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of
biological macromolecular complexes. Picking single-protein particles from cryo-EM …
biological macromolecular complexes. Picking single-protein particles from cryo-EM …
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a
challenging problem of outstanding importance. Current refinement methods often generate …
challenging problem of outstanding importance. Current refinement methods often generate …
All-Atom Biomolecular Simulation in the Exascale Era
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML
techniques, that model biomolecular motions over unprecedented length and time scales …
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
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 …
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 …
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
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 …
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 …
determination of structures of complex biological molecules. The accurate characterisation …