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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 …
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 …
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
Three-dimensional structure modeling from maps is an indispensable step for studying
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …
proteins and their complexes with cryogenic electron microscopy. Although the resolution of …
RNA-Puzzles Round V: blind predictions of 23 RNA structures
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 three-dimensional structure prediction. With agreement from structural biologists, RNA …
Structural predictions of protein–DNA binding: MELD-DNA
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 …
functional genome. Yet, our structural understanding of how proteins interact with DNA is …
Protein storytelling through physics
BACKGROUND Understanding biology, particularly at the level of actionable drug
discovery, is often a matter of develo** accurate stories about how proteins work. This …
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
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 …
rate.•Improved sampling algorithms, force fields and computers drive advances.•At current …
Protein structure prediction using Rosetta in CASP12
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 …
in the free modeling (FM) and refinement (TR) categories. First, we had previously …
Adenylyl cyclase signalling complexes–Pharmacological challenges and opportunities
Signalling pathways involving the vital second messanger, cAMP, impact on most significant
physiological processes. Unsurprisingly therefore, the activation and regulation of cAMP …
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 …
development, owing to their critical nature in diverse biological processes. An ideal PPI …