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From Stefan Doerr Introduction Proteins are essential in the regulation of most of the processes in a cell. They do so by interacting with other molecules, including other proteins. Protein-protein interactions have been the subject of study for a long time using both experimental and computational methods, however they have eluded the atomic-level analysis and

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By Gerard Martinez-Rosell Introduction ACEMD was introduced in the field of Molecular Dynamics (MD) back in 2008. Its release, together with other MD engines, revolutionized the simulation throughput by leveraging the intrinsic parallelism present in a specific computer processor termed GPU (Graphic Processor Unit). Using a cluster of GPUs or a distributed network like GPUGRID

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By Alex Perálvarez-Marín Introduction: In Wang et al. we have studied and described an intermediate step of the molecular mechanism of sugar transport thanks to the possibility to run several MD simulation replicates in the 100 ns range using a single GPU-based desktop running ACEMD. Our solvated membrane protein system embedded in the lipid bilayer

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What has been achieved in Molecular Dynamics and Acellera contribution. Acellera celebrates its 10th anniversary. A decade focusing on molecular dynamics (MD) and dedicated to improve this technique as a strong partner of biophysical approaches. Objectively, molecular dynamics is the only technique allowing to study conformational changes and interaction at atomistic level, to quantify binding

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By Franck Chevalier Introduction: Molecular recognition is rarely a two-body protein-ligand problem, as it often involves the dynamic interplay of multiple molecules that together control the binding process. Myo-inositol monophosphatase (IMPase), a drug target for bipolar disorder, depends on 3 Mg2+ ions as cofactor for its catalytic activity. Although the crystallographic pose of the pre-catalytic

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