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Showing 1 to 20 of 21 for “"Protein docking"”.
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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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Improving Protein Docking Using Efficient Sustainable Evolutionary Algorithm
<p>AutoDock is a widely used automated protein docking program in structure-based drug-design. Different search algorithms, such as Simulated Annealing, traditional Genetic Algorithm and Lamarckian Genetic Algorithm are used in AutoDock. However, the docking performance of these algorithms is still …
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DOCKGROUND Protein Docking Benchmark Sets and Assessment Resource
Proteins and nucleic acids are key components of cellular functions. To better understand these functions, it is essential to study protein-protein and protein-nucleic acids interactions at the structural level. Compared to the number of currently known proteins, there are relatively few …
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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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Identifying a Target Protein and Ligands for Autoimmune Disorders
… display an overexpression of master regulatory protein HIF-1 HIF-1is a transcription factor for pro-inflammatory cytokine interleukin-17A (IL-17A), which is highly involved in inflammatory reactions within the body. To search for a treatment for SLE, computer aided drug discovery techniques were …
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The pathway of electron transfer within the nitrogenase complex
… that, within the current view of component protein docking and nitrogenase catalysis, are likely to be involved in inter- or intra-molecular electron transfer. Intermolecular electron transfer was probed by substituting charged residues that, within the model for component protein docking …
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Algorithms for Derivative-Free Optimization
… derivative-free solvers, including B&M, to the protein-ligand docking problem. Results show that B&M delivers satisfactory ligand conformations, even outperforming the state-of-the-art protein docking software AutoDock.
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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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Modeling protein flexibility using collective modes of motion: Applications to drug design
… the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids or small molecules (ligands) and …
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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 modeling of protein-protein and protein-peptide interactions
Protein-protein and protein-peptide interactions play a central role in various aspects of the structural and functional organization of the cell. While the most complete structural characterization is provided by X-ray crystallography, many biological interactions occur in complexes that will not …
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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 …
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Regulating the stabilities of NOD1 and NOD2, two innate immune receptors, with sugars and chaperones
… binding oligomerization domain containing proteins 1 and 2 (NOD1 and NOD2), members of the NOD-like receptor family (NLRs). These NLRs recognize different fragments from bacterial cell wall peptidoglycan (PG) using their C-terminal leucine rich repeat (LRR) domains and then signal the body …
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Bioinformatic Analysis of the Interaction Of EVC And EVC2 Proteins
<p>Protein to protein interactions are significant to various biological processes, functioning, and the regulation of cells and organisms. Proteins perform essential cellular tasks and often work together in complexes, enabling specific functions like enzymatic activity, signal transduction, DNA …
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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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