[PDF] Top 20 An interaction potential for materials and molecular dynamics simulations.
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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 ... See full document
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Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study.
... activities and numerous diseases suggests a strong therapeutic potential for these systems ...the interaction between PHD fingers and non methylated histone tails, as several experimental ... See full document
13
Successful application of virtual screening and molecular dynamics simulations against antimalarial molecular targets
... other molecular target ...capture and integrate relevant information in an easily accessible format to identify and prioritise potential ...integration and mining of emerging ... See full document
10
Insight into the intermolecular recognition mechanism between Keap1 and IKKβ combining homology modelling, protein-protein docking, molecular dynamics simulations and virtual alanine mutation.
... laevis and Homo sapiens (Figure ...Keap1 and IKKβ in Homo sapiens, the homology model of human IKKβ was built depending on the crystal structure of Xenopus laevis’ IKKβ (Figure ...identity and high ... See full document
13
Towards the design of new and improved drilling fluid additives using molecular dynamics simulations
... CVFF and Teppen ...9–6 potential where the Teppen force-field was used and a 12–6 Lennard-Jones potential for the larger systems simulated using the ClayFF and CVFF ...(Hockney ... See full document
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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.
... plays an important role in drug metabo- lism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, ...51, and 62 were performed, and ... See full document
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The mechanisms of substrates interaction with the active site of Mycobacterium tuberculosis tyrosyl-tRNA synthetase studied by molecular dynamics simulations
... Materials and methods. Initial structures. Structu- re of the MtTyrRS dimer in free state was prepared ac- cording to the scheme described in our previous work [28]. The crystallographic structures of ... See full document
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Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.
... unliganded and ligand-bound forms, even with a trapped nicotinoyl thioester ...intermediates and allowed for a more complete under- standing of the reaction mechanism of ...mechanism and the active ... See full document
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Mapping the structural and dynamical features of kinesin motor domains.
... 3HQD) and ADP (PDB code: ...ATP and nucleotide free simulation starting ...[51] and evaluated with the DOPE score [52] to yield the ADP simulation starting ...accelerated molecular ... See full document
13
A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1).
... of an intracellular calcium storage organelle, the sarcoplasmic ...hyperthermia, an adverse reaction to general ...the molecular basis of RyR1 dysfunction remains largely unknown because of the lack ... See full document
10
Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations
... simple and reliable ...regions and studied with normal mode analysis [13], molecular dynamics (MD) [14–16] or Monte Carlo simulations [17] have provided not only successful data ... See full document
9
Docking and Molecular Dynamics Simulations in Potential Drugs Discovery: An Application to Influenza Virus M2 Protein
... Abstract: Molecular docking is a common method for searching new potential ...is molecular dynamics simulations of protein-ligand ...envelope and endosomal membrane, thereby ... See full document
9
Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues.
... Molecular dynamics analysis used the modeling package GROMACS ...apo- and holoprotein crystal structures (PDB entry 1XXC and 1XXA, respectively) were prepared by standard methods in YASARA ... See full document
12
Computational of the substrate binding mode in III oxidase
... A and B rings of coproporphyrinogen III in the heme biosynthetic ...site and the initial substrate protonation state) remain poorly ...The molecular dynamics simulations described in ... See full document
26
IDENTIFICATION OF PHARMACOLOGICAL TARGETS COMBINING DOCKING AND MOLECULAR DYNAMICS SIMULATIONS
... favorable interaction presents the greatest frequency of occurrence; thus, a statistical analysis of the complex’s crystal structure is performed, focusing on inter-atomic contacts and ...databases ... See full document
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J. Braz. Chem. Soc. vol.17 número7
... enzyme and a homology model of parasite’s enzyme, both in complex with glycine, as N-glycine-[3-hydroxy-2-methyl-5- phosphonooxymethyl-pyridin-4-yl-methane] and 5-formyl-6-hydrofolic acid, to design ... See full document
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Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution
... protein potential energy surface, the remaining analysis is focused on the correspondence between the results obtained from the current EDA with the experimen- tally-derived PCA of ...ED3 and PC1 from Sim1, ... See full document
22
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 ...nanoasperity and a flat ruthenium surface. The results of such ... See full document
11
J. Braz. Chem. Soc. vol.13 número6
... Molecular Interaction Potentials (MIP) are frequently used for the comparison of series of compounds displaying related biological ...are interaction energies between the considered compounds ... See full document
5
Recycled materials for the investment casting process
... Instytut Technik Wytwarzania Politechniki Warszawskiej, ul. Recykling materia ł owy by ł ukierunkowany po pierwsze na zmniejszenie ilo ci odpadów w odlewniach precyzyjnych, po drugie u[r] ... See full document
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