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Applications of Molecular Dynamics Simulation in Protein Study
Membranes, 2022 Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study ...
San Ming Wang +2 more
exaly +2 more sources
Introductory Tutorials for Simulating Protein Dynamics with GROMACS. [PDF]
J Phys Chem BAtomistic molecular dynamics (MD) simulations have become an indispensable tool for investigating the structure, dynamics, and energetics of biomolecules.
Lemkul JA.
europepmc +2 more sources
Developing a molecular dynamics force field for both folded and disordered protein states
Proceedings of the National Academy of Sciences of the United States of America, 2018 Significance Many proteins that perform important biological functions are completely or partially disordered under physiological conditions. Molecular dynamics simulations could be a powerful tool for the structural characterization of such proteins ...
David E Shaw +2 more
exaly +2 more sources
Protein Dynamics and Enzymatic Catalysis
Journal of Physical Chemistry B, 2023 This Perspective presents a review of our work and that of others in the highly controversial topic of the coupling of protein dynamics to reaction in enzymes. We have been involved in studying this topic for many years.
Steven D. Schwartz
semanticscholar +1 more source
Protein dynamics: The future is bright and complicated!
Structural Dynamics, 2023 Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions ...
Kwangho Nam, M. Wolf-Watz
semanticscholar +1 more source
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinform., 2021 Summary ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community.
She Zhang +8 more
semanticscholar +1 more source
Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status
Radiation, 2022 Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases.
Tiziana Mancini +5 more
semanticscholar +1 more source
Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics
bioRxiv, 2021 Time-lagged independent component analysis (tICA) is a widely used dimension reduction method for the analysis of molecular dynamics (MD) trajectories and has proven particularly useful for the construction of protein dynamics Markov models.
Steffen Schultze, H. Grubmüller
semanticscholar +1 more source
Engineering the protein dynamics of an ancestral luciferase
Nature Communications, 2021 Protein dynamics are often invoked in explanations of enzyme catalysis, but their design has proven elusive. Here we track the role of dynamics in evolution, starting from the evolvable and thermostable ancestral protein AncHLD-RLuc which catalyses both ...
A. Schenkmayerova +16 more
semanticscholar +1 more source
Targeting Ras-binding domain of ELMO1 by computational nanobody design
Communications Biology, 2023 Structural analysis of the Ras-binding domain (RBD) of ELMO1 alone and in complex with the activator RhoG enables rational engineering and validation of a nanobody targeting ELMO1 RBD.
Chunlai Tam +11 more
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