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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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By Franck Chevalier Introduction on kinetics Quest for new drug discovery usually involves a clear understanding of ligand binding to its receptor. Free binding energy helps to rank compounds and allows to select those based on their target affinity. Drug discovery programs focused on optimization of target affinity as a proxy of in-vivo efficacy Within

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