Results 81 to 90 of about 8,716,920 (283)

Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

, 2010
We have developed CUDA-enabled version of a general purpose molecular dynamics simulation code for GPU. Implementation details including parallelization scheme and performance optimization are described.
이식, 오광진, 명훈주
core  

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

Molecular Dynamics Simulation of High Density DNA Arrays

Computation, 2018
Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural ...
Rudolf Podgornik, Julija Zavadlav, Matej Praprotnik   +2 more
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

Molecular Components and Molecular Modelling for Asphalt: A Review

Advanced Physics Research
Asphalt is a complex, heterogeneous organic mixture increasingly used in modern pavement. With the rising traffic load and sustainable strategies, developing high‐performance asphalt materials becomes crucial, which relies on the understanding of the ...
Zhijin Wang, Yuanbin Zhou, Jiandong Zhang, Xinlv Ji, Haifei Zhan   +4 more
doaj   +1 more source

Recent insights into the molecular mechanism of ubiquinol oxidation by cytochrome bc1

FEBS Open Bio, EarlyView.
The review reflects on the mechanism of the catalytic reaction in cytochrome bc1: the electron bifurcation that involves the separation of two electrons derived from the quinol oxidation to opposite sides of the enzyme across the membrane. This review summarizes the long‐standing effort to understand the mechanism of quinol oxidation catalyzed by ...
Anna Wójcik‐Augustyn, Artur Osyczka, Marcin Sarewicz   +2 more
wiley   +1 more source

Neurochemical Endpoints to Inform Early‐Stage Trials of Spinocerebellar Ataxia 2 and 3 in a Multisite Setting

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Neurochemical levels measured by brain MR spectroscopy (MRS) have been proposed as endpoints for clinical trials in early‐stage spinocerebellar ataxia (SCA) trials. We tested their trial‐readiness by quantifying neurochemicals in three affected brain regions in early‐stage cohorts of SCA2 and SCA3, examining their reproducibility in ...
James M. Joers, Yaqiao Wei, Dinesh K. Deelchand, Adam Berrington, Young Woo Park, Guita Banan, Michal Povazan, Jens T. Rosenberg, André J. W. van der Kouwe, Tetsuo Ashizawa, Khalaf O. Bushara, Chiadi U. Onyike, Sub H. Subramony, Jeremy D. Schmahmann, Brian J. Soher, Peter B. Barker, Thomas H. Mareci, Eva‐Maria Ratai, Lynn E. Eberly, Gülin Öz   +19 more
wiley   +1 more source

Re‐Purposing Sapropterin (Kuvan) for ACTA2‐Related Multisystemic Smooth Muscle Dysfunction Syndrome: A Translational Mechanistic and First‐In‐Human Therapeutic Report

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Multisystemic smooth muscle dysfunction syndrome (MSMDS) is an ultra‐rare, ACTA2‐related disorder characterized by severe cerebrovascular disease, aortic aneurysms, and smooth muscle dysfunction. Using molecular dynamics simulations and in silico drug screening, we identified that sapropterin dihydrochloride (Kuvan) is a candidate capable of ...
Moran Hausman‐Kedem, Noa Bielopolski, Vijai Krishnan, Shane Wald‐Altman, Shelly I Shrian, Omer Bar‐Yosef, Livia Kapusta, Claire Shamber, Patricia L. Musolino, Miguel Weil   +9 more
wiley   +1 more source

Network Pharmacology, Molecular Docking and Dynamics Simulation Reveal the Anti-Colitis Mechanism of Smilax glabra Roxb.

Clinical and Experimental Gastroenterology
Yuan Cui,1,2 Jingyi Hu,1 Yanan Li,1 Yiheng Tong,1 Hong Shen1 1Department of Gastroenterology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210001, People’s Republic of China ...
Cui Y, Hu J, Li Y, Tong Y, Shen H
doaj  

In Silico Discovery and Preliminary In Vitro Evaluation of a SETDB1-Related Candidate Compound Associated with Early Osteogenic Effects

Future Pharmacology
Background/Objectives: Osteoporosis remains a clinically important metabolic bone disorder with limited bone-forming therapeutic options. SET domain bifurcated protein 1 (SETDB1) is involved in osteogenic epigenetic regulation, but small-molecule ...
Zongchang Li, Sixian Zhang, Shu Chen, Qinke Meng, Zhe Lv, Zhilei Niu, Jun Li, Xi Chen   +7 more
doaj   +1 more source