Exploring and learning the universe of protein allostery using artificial intelligence augmented biophysical and computational approaches
Allosteric mechanisms are commonly employed regulatory tools used by proteins to
orchestrate complex biochemical processes and control communications in cells. The …
orchestrate complex biochemical processes and control communications in cells. The …
Emerging methods and applications to decrypt allostery in proteins and nucleic acids
PR Arantes, AC Patel, G Palermo - Journal of molecular biology, 2022 - Elsevier
Many large protein-nucleic acid complexes exhibit allosteric regulation. In these systems,
the propagation of the allosteric signaling is strongly coupled to conformational dynamics …
the propagation of the allosteric signaling is strongly coupled to conformational dynamics …
UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: A comparison study
Proteins are the molecular machines of life. The multitude of possible conformations that
proteins can adopt determines their free-energy landscapes. However, the inherently high …
proteins can adopt determines their free-energy landscapes. However, the inherently high …
[HTML][HTML] Delineating the activation mechanism and conformational landscape of a class BG protein-coupled receptor glucagon receptor
Y Wang, M Li, W Liang, X Shi, J Fan, R Kong… - Computational and …, 2022 - Elsevier
Class BG protein-coupled receptors (GPCRs) are important targets in the treatment of
metabolic syndrome and diabetes. Although multiple structures of class B GPCRs–G protein …
metabolic syndrome and diabetes. Although multiple structures of class B GPCRs–G protein …
Drug design targeting active posttranslational modification protein isoforms
Modern drug design aims to discover novel lead compounds with attractable chemical
profiles to enable further exploration of the intersection of chemical space and biological …
profiles to enable further exploration of the intersection of chemical space and biological …
Allosteric regulation at the crossroads of new technologies: multiscale modeling, networks, and machine learning
GM Verkhivker, S Agajanian, G Hu… - Frontiers in molecular …, 2020 - frontiersin.org
Allosteric regulation is a common mechanism employed by complex biomolecular systems
for regulation of activity and adaptability in the cellular environment, serving as an effective …
for regulation of activity and adaptability in the cellular environment, serving as an effective …
From deep mutational mapping of allosteric protein landscapes to deep learning of allostery and hidden allosteric sites: zooming in on “allosteric intersection” of …
G Verkhivker, M Alshahrani, G Gupta, S Xiao… - International Journal of …, 2023 - mdpi.com
The recent advances in artificial intelligence (AI) and machine learning have driven the
design of new expert systems and automated workflows that are able to model complex …
design of new expert systems and automated workflows that are able to model complex …
Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain
The conformational-driven allosteric protein diatom Phaeodactylum tricornutum
aureochrome 1a (PtAu1a) differs from other light–oxygen–voltage (LOV) proteins for its …
aureochrome 1a (PtAu1a) differs from other light–oxygen–voltage (LOV) proteins for its …
[HTML][HTML] Dynamics of hydrogen bonds in the secondary structures of allosteric protein Avena Sativa phototropin 1
Abstract The Light-Oxygen-Voltage 2 (LOV2) domain of Avena Sativa phototropin 1
(AsLOV2) protein is one of the most studied domains in the field of designing photoswitches …
(AsLOV2) protein is one of the most studied domains in the field of designing photoswitches …
Unraveling the energetic significance of chemical events in enzyme catalysis via machine-learning based regression approach
The bacterial enzyme class of β-lactamases are involved in benzylpenicillin acylation
reactions, which are currently being revisited using hybrid quantum mechanical molecular …
reactions, which are currently being revisited using hybrid quantum mechanical molecular …