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   Articles with "umbrella sampling" as a keyword



Self-healing umbrella sampling: convergence and efficiency

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recommendations! Published in 2017 at "Statistics and Computing"

DOI: 10.1007/s11222-015-9613-2

Abstract: The Self-Healing Umbrella Sampling (SHUS) algorithm is an adaptive biasing algorithm which has been proposed in Marsili et al. (J Phys Chem B 110(29):14011–14013, 2006) in order to efficiently sample a multimodal probability measure. We show… read more here.

Keywords: algorithm; healing umbrella; umbrella sampling; self healing ... See more keywords

Free Energy Calculation of Membrane Permeation - Simulation Results Suggest Relaxation of Headgroup-Solute Interactions is the Slowest Degree of Freedom

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recommendations! Published in 2017 at "Biophysical Journal"

DOI: 10.1016/j.bpj.2016.11.1258

Abstract: Molecular Dynamics (MD) simulations have been extensively used to investigate membrane-solute interactions. Understanding the interactions associated with solute translocation across lipid bilayers facilitates prediction of passive permeation rates of cell membranes, which is a very… read more here.

Keywords: energy; permeation; solute interactions; umbrella sampling ... See more keywords
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Vitamin E does not Preferentially Bind to Polyunsaturated Lipids as Revealed by Umbrella Sampling MD Simulations

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recommendations! Published in 2017 at "Biophysical Journal"

DOI: 10.1016/j.bpj.2016.11.445

Abstract: Alpha-tocopherol (αtoc) is the active form of vitamin E that is retained in the human body. It is a lipid-soluble antioxidant, which protects polyunsaturated fatty acids (PUFA) by terminating a chain of chemical reactions that… read more here.

Keywords: vitamin preferentially; toc; preferentially bind; bind polyunsaturated ... See more keywords

Umbrella Sampling MD Simulations for Retention Prediction in Peptide Reversed-phase Liquid Chromatography.

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recommendations! Published in 2024 at "Analytical chemistry"

DOI: 10.1021/acs.analchem.4c05428

Abstract: Reversed-phase liquid chromatography (RPLC) is an essential tool for separating complex mixtures such as proteolytic digests in bottom-up proteomics. There is growing interest in methods that can predict the RPLC retention behavior of peptides and… read more here.

Keywords: umbrella sampling; retention; reversed phase; retention prediction ... See more keywords

Umbrella Sampling Simulations Measure Switch Peptide Binding and Hydrophobic Patch Opening Free Energies in Cardiac Troponin

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recommendations! Published in 2022 at "Journal of chemical information and modeling"

DOI: 10.1021/acs.jcim.2c00508

Abstract: The cardiac troponin (cTn) complex is an important regulatory protein in heart contraction. Upon binding of Ca2+, cTn undergoes a conformational shift that allows the troponin I switch peptide (cTnISP) to be released from the… read more here.

Keywords: hydrophobic patch; umbrella sampling; switch peptide; troponin ... See more keywords

Determination of Equilibrium Adsorbed Morphologies of Surfactants at Metal-Water Interfaces Using a Modified Umbrella Sampling-Based Methodology.

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recommendations! Published in 2022 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.2c00078

Abstract: Surfactants adsorb to metal-water interfaces in various morphologies, including self-assembled monolayers (SAMs), cylindrical and spherical micelles, or hemimicelles. Current molecular simulation methods are unable to efficiently sample the formation of these morphologies because of the… read more here.

Keywords: modified umbrella; methodology; umbrella sampling; water ... See more keywords

Do All Paths Lead to Rome? How Reliable is Umbrella Sampling Along a Single Path?

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recommendations! Published in 2024 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.4c00134

Abstract: Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free energies of protein-ligand and protein-protein complexes. A routinely used method for binding free energy calculations with MD is umbrella sampling (US), which calculates… read more here.

Keywords: umbrella sampling; binding free; along single; protein ... See more keywords

Parameter Optimization Method in Multidimensional Umbrella Sampling.

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recommendations! Published in 2024 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.4c00282

Abstract: Umbrella sampling (US) is an effective method for calculating free-energy landscapes (FELs). However, the complexity of controlling the sampling positions complicates multidimensional FEL calculations. In this study, we proposed a method for controlling sampling by… read more here.

Keywords: method; umbrella sampling; fel; point ... See more keywords
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Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations

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recommendations! Published in 2024 at "Scientific Reports"

DOI: 10.1038/s41598-024-62743-3

Abstract: Although the use of the tyrosine kinase inhibitors (TKIs) has been proved that it can save live in a cancer treatment, the currently used drugs bring in many undesirable side-effects. Therefore, the search for new… read more here.

Keywords: umbrella sampling; tyrosine kinase; kinase inhibitors; pyridine derivatives ... See more keywords

Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein.

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recommendations! Published in 2022 at "Soft matter"

DOI: 10.1039/d2sm00888b

Abstract: The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in biomolecular systems. Due to long time scales involved in the transition, it is challenging to study… read more here.

Keywords: umbrella sampling; finite temperature; temperature string; collective variables ... See more keywords

Umbrella sampling: A powerful method to sample tails of distributions

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recommendations! Published in 2017 at "Monthly Notices of the Royal Astronomical Society"

DOI: 10.1093/mnras/sty2140

Abstract: We present the umbrella sampling (US) technique and show that it can be used to sample extremely low probability areas of the posterior distribution that may be required in statistical analyses of data. In this… read more here.

Keywords: sample; sampling powerful; powerful method; umbrella windows ... See more keywords