molecular dynamics (MD)
Validation of molecular dynamics simulation
... of molecular systems is playing an ever growing role in academic and industrial ...and molecular biology, computer simulation is already a part of daily ...the molecular dynamics ~ MD ! ...
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Thermostat Algorithms for Molecular Dynamics Simulations
... particular molecular dynamics (MD) simu- lations, have nowadays become a common tool for investigating the properties of polymer [1] and (bio-)molecular systems [2, 3, 4, 5, 6, ...
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An integrated approach towards the development of novel antifungal agents containing thiadiazole: synthesis and a combined similarity search, homology modelling, molecular dynamics and molecular docking study
... Molecular docking is a value added tool in computer aided drug design. It helps us to understand inhibi- tion mechanism of a drug or drug candidate against its target. Ligand similarity search is one of the ...
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Computational Protein Design and Molecular Dynamics Simulations: A Study of Membrane Proteins, Small Peptides and Molecular Systems
... well-established molecular dynamics simulation techniques that have been extensively used to study structure, function and dynamics of biologically relevant ...particular molecular problems ...
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In silico Molecular Docking and Molecular Dynamics Applications in the Designing of a New Mosquito Repellent from the Plant Calotropis gigantea Targeting the Odorant Binding Protein of Culex quinquefasciatus
... during molecular dynamics simulation for 100ps is shown in ...and molecular dynamics performed on potential ligands to the Odorant Binding Protein of the mosquito Anopheles gambiae (AgOBP1) ...
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Hydrogen-Deuterium Exchange Mass Spectrometry and Molecular Dynamics Simulations for Studying Protein Structure and Dynamics
... Classical models of allostery envision that effector binding triggers conformational changes that cause distant target binding sites to open or close. 1,2,4 Recent studies have expanded this view by emphasizing the role ...
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Molecular dynamics pre simulations for nanoscale computational fluid dynamics
... as molecular layering and velocity slip near to liquid–solid interfaces, seemingly precludes efficient con- tinuum computational fluid dynamics ...accurate molecular dynamics (MD) simulations ...
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Molecular dynamics pre-simulations for nanoscale computational fluid dynamics
... as molecular layering and velocity slip near to liquid–solid interfaces, seemingly precludes efficient con- tinuum computational fluid dynamics ...accurate molecular dynamics (MD) simulations ...
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Molecular dynamics simulation of amphiphilic aggregates
... The Molecular dynamics (MD) simulation technique is a powerful tool to study amphiphile ...motion. Molecular interaction energy and the free energy profiles can be also calculated from simulation ...
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Human Prion Protein Conformational Changes Susceptibility: A Molecular Dynamics Simulation Study
... making it more prone to adopt an abnormal misfolded structure, the majority of cases reported among general population are sporadic in wild-type organisms. Thus, in this work we studied the dynamics and stability ...
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Towards Predictive Molecular Dynamics Simulations of DNA: Role of Electrostatics and of the Cell Environment.
... The relationship between DNA sequence and structure is a subject of considerable interest, and its understanding is believed important for essential cellular processes such as replication and transcription. The ...
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Molecular Dynamics Simulation of Diffusion of Gases and Liquids in Conditions of Phase Transition
... in molecular systems of Lennard-Jones particles have been calcu- lated by the molecular dynamics method in a wide range of density and temperature of the ...
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Article Relative contributions of Solubility and Mobility to the Stability of Amorphous Solid Dispersions of poorly soluble drugs: A Molecular Dynamics Simulation study
... perform Molecular Dynamics simulations to determine properties of blends of eight different polymer-small molecule drug combinations for which stability data is available from a consistent set of literature ...
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Molecular dynamics and physical stability of coamorphous ezetimib and indapamide mixtures
... Low physical stability is the main reason limiting the widespread use of amorphous pharmaceuticals. One approach to overcome this problem is to mix these drugs with various excipients. In this study coamorphous drug–drug ...
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Molecular dynamics and protein function
... When molecular dynam- ics simulations are a routine part of structural biology, it will become clearer what refinements and extensions of the methodology are most needed to im- prove the results and to perfect the ...
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Molecular dynamic simulation of V176G mutation associated with Gerstmann–Sträussler–Scheinker at elevated temperature
... on molecular dynamics (MD) as it can not only replicate the environmental conditions needed for inducing change in protein structure but can also show the changes unfolding in real ...
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Different interface orientations of pentacene and PTCDA induce different degrees of disorder
... The molecular dynamic (MD) simulations of the interfaces between PTCDA and pentacene have been performed with the atomistic molecular dynamics package GROMACS (Stockholm Center for Biomem- brane ...
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Paper 06-2011-2
... Specifically, molecular dynamics (MD), dissipate particle dynamics (DPD), elastic network model (ELM) and immersed molecular electrokinetic finite element method (IMEFEM) are introduced with ...
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1 Computational insight into the effect of natural
... Molecular Dynamics (MD) simulations; 4) preferential binding sites of ligands and their effect on 47.. amyloid structure-dynamics[18] on Aβ fragments and full-length single[r] ...
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Multiscale Simulations of Phosphatidylinositol Bisphosphate: Understanding Its Biological Role Through Physical Chemistry
... and molecular dynamics (MD) simulations are able to provide a multiscale view of the physical chemistry of PPIs that is inaccessible to almost all experimental ...
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