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Showing 1 to 11 of 11 for “"Protein-protein docking"”.
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Graphics processing unit accelerated coarse-grained protein-protein docking
… of the Kim-Hummer coarse-grained model for protein docking simulations, using a Replica Exchange Monte-Carlo (REMC) method. Our highly parallel implementation vastly increases the size- and time scales accessible to molecular simulation. We describe in detail the complex process of migrating …
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Addition of flexible linkers to GPU-accelerated coarse-grained simulations of protein-protein docking
Multiprotein complexes are responsible for many vital cellular functions, and understanding their formation has many applications in medical research. Computer simulation has become a valuable tool in the study of biochemical processes, but simulation of large molecular structures such as proteins …
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Enhancing protein-protein docking by new approaches to protein flexibility and scoring of docking hypotheses
… Verständnis von biologischen Funktionen können Proteindockingverfahren angewandt werden. Die Simulation der Interaktion von Proteinen ermöglicht einen Einblick in die Mechanismen dieser Funktionen. Viele Dockingansätze modellieren Proteine als feste Körper. Proteine sind jedoch flexibel. …
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Improving protein docking with binding site prediction
Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, …
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Analysis of molecular interactions in the presence of side chain flexibility
Protein-protein and protein-ligand interactions are ubiquitous in biology. For many proteins, these interactions can be well simulated by assuming rigid body association, resulting in powerful predictions from protein-protein docking. These methods have also been applied to sample ensembles of …
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The Interaction of Cofilin with the Actin Filament
… in all cells, understanding how actin-binding-proteins: ABPs) bind and how their regulating mechanisms work is not only important to the basics of cytoskeletal pathways, but also to understanding associated diseases and creating possible therapeutics to combat them. Cofilin is an ABP that plays …
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Computational Study on MFP MexA in MexAB-OprM and RND transporter AcrB in AcrAB-TolC Efflux Pumps
… and an undetermined number of Membrane Fusion Proteins (MFPs), which are essential for the stability and functionality of the pumps. In our study we focused on the two major efflux pumps expressed in P.aeruginosa and E.coli / Salmonella, MexAB-OprM and AcrAB-TolC respectively. In particular, we …
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Protein kinases: Structure modeling, inhibition, and protein-protein interactions
<p>Human protein kinases belong to a large and diverse enzyme family that contains more than 500 members. Deregulation of protein kinases is associated with many disorders, and this is why protein kinases are attractive targets for drug discovery. Due to the high conservation of the ATP binding …
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Multicomponent Complexes, Structural Proteomes, Drug Discovery For Cancer Gene Census And SARS CoV-2
… biology is expensive and time-consuming, a protein modelling algorithm such as a MODELLER can reduce the ample space between the sequence and structural annotation in less time. Thus, solving protein structures with reliable or high accuracy quality assessment can be achieved …
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Interactions of Proteins with Membranes: Insights from Molecular Dynamics Simulations
Membrane proteins play a crucial role in numerous biological processes, including signal transduction, molecular transport, and cell recognition. Due to their involve- ment in fundamental physiological functions and their relevance as pharmacological targets, understanding their structure and …