Results 91 to 100 of about 7,568,994 (301)

Machine Learning with and for Molecular Dynamics Simulations

CHIMIA, 2019
From simple clustering techniques to more sophisticated neural networks, the use of machine learning has become a valuable tool in many fields of chemistry in the past decades.
Sereina Riniker, Shuzhe Wang, Patrick Bleiziffer, Lennard Böselt, Carmen Esposito   +4 more
doaj   +1 more source

Malformin A1–mediated cytotoxicity in ovarian cancer cells occurs through pyroptosis and autophagy

FEBS Open Bio, EarlyView.
This study investigated the effects of the natural compound Malformin A1 (MA1) on the cytoskeleton that regulates cell proliferation and migration. Disruption of the cytoskeleton can impair these processes and promote cancer cell death. MA1 disrupted cytoskeletal organization, induced DNA damage, inflammation, activated autophagy, and pyroptosis ...
Nada Abdullah Hassan, Ikram A. Burney, Shika Hanif Malgundkar, Siva Ramamoorthy, Ressin Varghese, Mohamed A. Al‐Kindi, Hamad Al Riyami, Shadia Al Bahlani, Sergey Dobretsov, Syed Imran Hassan, Benjamin K. Tsang, Yahya Tamimi   +11 more
wiley   +1 more source

Identifying and characterising a plant GH1 β‐glucosidase that exhibits hydrolytic activity on N‐linked glucopyranoside

FEBS Open Bio, EarlyView.
We report the first β‐glucosidase with demonstrated hydrolytic activity on an N‐linked glycopyranoside. The enzyme, native to maize, was biochemically characterised for this novel reaction, and structural modelling of the enzyme–substrate complex revealed several clues to the underlying reduced catalytic rate relative to its native O‐glycopyranoside ...
Hani Gharabli, Carlotta Chiesa, Maher Abou Hachem, Ditte Hededam Welner   +3 more
wiley   +1 more source

Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

, 2007
A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al.
Mark, AE, Vendruscolo, Michele, Mark, Alan E., Vendruscolo, M, Alan E. Mark, Periole, X, Periole, Xavier, Xavier Periole, Michele Vendruscolo   +8 more
core   +1 more source

Structural studies and functional engineering of NanX: an anhydro‐sialic acid transporter from Escherichia coli

FEBS Open Bio, EarlyView.
Biophysical characterisation shows that NanX, a membrane transport protein from the major facilitator superfamily (MFS), forms both monomers and dimers after purification. AlphaFold modelling and substrate docking provide information on residues likely involved in substrate recognition for NanX and another MFS member, NanT.
Michael C. Newton‐Vesty, Kelsi R. Hall, Zachary D. Tillett, Liam S. Turk, James S. Davies, Michael J. Currie, Hamish G. Brown, Sepideh Valimehr, Peter D. Mace, Andrew E. Whitten, Santosh Panjikar, Eric Hanssen, Rachel A. North, Renwick C.J. Dobson   +13 more
wiley   +1 more source

Determining the structure of interfacial peptide films: comparing neutron reflectometry and molecular dynamics simulations

, 2014
The peptides AM1 and Lac21E self-organize into switchable films at an air-water interface. In an earlier study, it was proposed that both AM1 and Lac21E formed monolayers of α-helical peptides based on consistency with neutron reflectivity data.
Xue, Ying, Mark, Alan E., Poger, D., Middelberg, A., He, Lizhong, Poger, David, He, L., Middelberg, Anton P. J., Ying Xue, David Poger, Alan E. Mark, Mark, A., Lizhong He, Anton P. J. Middelberg, Xue, Y.   +14 more
core   +1 more source

Continuous Finite Element Methods of Molecular Dynamics Simulations

Modelling and Simulation in Engineering, 2015
Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems.
Qiong Tang, Luohua Liu, Yujun Zheng
doaj   +1 more source

Reliability and reproducibility checklist for molecular dynamics simulations

Communications Biology, 2023
We present a checklist to improve the reliability and reproducibility of molecular dynamics simulations and related methods.
doaj   +1 more source

Adenosine triphosphate as a modulator of protein interactions and stability

FEBS Open Bio, EarlyView.
ATP is best known as the cell's energy currency, but it also shapes how proteins fold, interact, aggregate and form biomolecular condensates. This review explains the emerging physical principles behind these effects, including weak binding to charged protein regions, magnesium‐dependent behaviour and concentration‐dependent control of protein ...
Shuyuan Tan, Robin Curtis
wiley   +1 more source

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion Binding from atomistic molecular dynamics simulations [PDF]

, 2014
The multidrug and toxic compound extrusion transporters extrude a wide variety of substrates out of both mammalian and bacterial cells via the electrochemical gradient of protons and cations across the membrane.
Khalid, Syma, Syma Khalid, Leung, Yuk Ming, Yuk Ming Leung, Holdbrook, Daniel A., Thomas J. Piggot, Piggot, Thomas J., Daniel A. Holdbrook   +7 more
core   +1 more source