Molecular dynamics simulations
Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
... Degradation of certain proteins through the ubiquitin-proteasome pathway is a common strategy taken by the key modulators responsible for stress responses. Kelch-like ECH-associated protein-1(Keap1), a substrate adaptor ...
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The gating mechanism of the human aquaporin 5 revealed by molecular dynamics simulations.
... Aquaporins are protein channels located across the cell membrane with the role of conducting water or other small sugar alcohol molecules (aquaglyceroporins). The high-resolution X-ray structure of the human aquaporin 5 ...
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Vibrational G peak splitting in laterally functionalized single wall carbon nanotubes: Theory and molecular dynamics simulations
... In order to test the hypothesis described above, we employed molecular dynamics simulations to investigate the effects of lateral functionalization in vibrational modes of SWCNTs. Our calculations ...
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Effects of Nitrogen Atoms on Mechanical Properties of Graphene by Molecular Dynamics Simulations
... using molecular dynamics simulations,” Lecture Notes in Engineering and Computer Science: Proceedings of the International MultiConference of Engineers and Computer Scientists 2012, IMECS 2012, 14–16 ...
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Docking and Molecular Dynamics Simulations in Potential Drugs Discovery: An Application to Influenza Virus M2 Protein
... algorythm. Molecular dynamics simulations allow side chains and ligand to be more ...Thus, molecular dynamics simulations of the transmembrane region of M2 protein tetramer in ...
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Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets
... drugs. Molecular modelling techniques have been used as tools to develop new ...docking simulations were carried out using AutoDock Vina ...to molecular dynamics simulations in vacuum ...
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Different inward and outward conduction mechanisms in NaVMs suggested by molecular dynamics simulations.
... by molecular dynamics simulations and free energy ...structural dynamics of the protein, especially the flexibility of SF and its fundamental role in kinetics underpinning ion selectivity, ...
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Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
... Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic ...
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Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62.
... Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of ...
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Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study.
... few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross ...atomistic molecular ...
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Structural basis of type 2A von Willebrand disease investigated by molecular dynamics simulations and experiments.
... study, molecular dynamics simulations suggest that the A2 domain unfolds under tensile force progressively through a series of ...by simulations to destabilize the A2 domain and facilitate ...
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Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.
... In this work, we investigated the influence of chirality of crizotinib on its MTH1 Inhibitory activity by the use of molecular dynamics simulations and binding free energy calculations. The ...
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Dynamics of the contact between a ruthenium surface with a single nanoasperity and a flat ruthenium surface: Molecular dynamics simulations
... the dynamics of the contact between a pair of surfaces (with properties designed to mimic ruthenium) via molecular dynamics ...such simulations suggest that contact behavior is highly ...
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Mechanism of deep-sea fish α-actin pressure tolerance investigated by molecular dynamics simulations.
... Deep-sea fish actins from C. armatus (Arm) and C. yaquinae (Yaq) have specific substitutions (Q137K and V54A [Arm] or I67P [Yaq]) not found in actins of terrestrial animals or species of shallow-water fish. Although the ...
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Towards the design of new and improved drilling fluid additives using molecular dynamics simulations
... Nevertheless, KCl was commonly used in associ- ation with partially-hydrolyzed polyacrylamide (PHPA) as a swelling inhibitor additive in WBDFs throughout the 1960s (Bloys et al. 1994) and its use continues to this day. ...
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An interaction potential for materials and molecular dynamics simulations.
... quando tratamos de materiais onde a distribuição eletrônica ou a ligação química em torno do átomo muda significativamente durante os movimentos dos átomos que são de interesse na simulação. Por outro lado, uma grande ...
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Study of the affinity between the protein kinase PKA and peptide substrates derived from kemptide using molecular dynamics simulations and MM/GBSA.
... first, molecular structures representing the complexes in solvent media were subjected to MD simulations, and second, a binding affinity between PKA and substrate was predicted using MM-GBSA free energy ...
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Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations
... ular dynamics through structure-based models (SB) is an effective tool for assessing the tridimensional arrangement of chimeric enzymes as well as for inferring the functional practicability before experimental ...
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IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
... Molecular simulation protocols (docking and MD simulations) start with an initial 3D model of the system, which can be obtained from NMR or crystallographic data, collected in the Protein Data Bank (PDB) ...
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Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
... study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding ...
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