Cargando…

Free‐energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

Previous free‐energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central...

Descripción completa

Detalles Bibliográficos
Autores principales:	Graf, Michael M. H., Maurer, Manuela, Oostenbrink, Chris
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	John Wiley and Sons Inc. 2016
Materias:	Full Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082540/ https://www.ncbi.nlm.nih.gov/pubmed/27634475 http://dx.doi.org/10.1002/jcc.24488

Ejemplares similares

Comparison of free‐energy methods using a tripeptide‐water model system
por: Maurer, Manuela, et al.
Publicado: (2018)

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
por: Reif, Maria M, et al.
Publicado: (2014)

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A
por: Maurer, Manuela, et al.
Publicado: (2016)

Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS)
por: Perthold, Jan Walther, et al.
Publicado: (2020)

Saturation Mutagenesis by Efficient Free-Energy Calculation
por: Jandova, Zuzana, et al.
Publicado: (2017)

Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations
por: Nagy, Gabor, et al.
Publicado: (2012)

Simulation of Reversible Protein–Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints
por: Perthold, Jan Walther, et al.
Publicado: (2017)

Synthesis of trifunctional cyclo-β-tripeptide templates
por: Stein, Frank, et al.
Publicado: (2012)

QSAR Study on Antioxidant Tripeptides and the Antioxidant Activity of the Designed Tripeptides in Free Radical Systems
por: Chen, Nan, et al.
Publicado: (2018)

Free-Energy Calculations for Bioisosteric Modifications of A(3) Adenosine Receptor Antagonists
por: Jandova, Zuzana, et al.
Publicado: (2019)

Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation
por: Chen, Ruiyao, et al.
Publicado: (2021)

Calculating free energies of organic molecules on insulating substrates
por: Gaberle, Julian, et al.
Publicado: (2017)

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex
por: Zhang, Ivy, et al.
Publicado: (2023)

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
por: Dolenc, Jožica, et al.
Publicado: (2005)

Structural modification of the tripeptide KPV by reductive “glycoalkylation” of the lysine residue
por: Songok, Abigael C., et al.
Publicado: (2018)

Overcoming inefficient cellobiose fermentation by cellobiose phosphorylase in the presence of xylose
por: Chomvong, Kulika, et al.
Publicado: (2014)

Luminescent supramolecular hydrogels from a tripeptide and nitrogen-doped carbon nanodots
por: Cringoli, Maria C, et al.
Publicado: (2017)

Binaphthyl-anchored antibacterial tripeptide derivatives with hydrophobic C-terminal amino acid variations
por: Bremner, John B, et al.
Publicado: (2012)

Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis
por: Siebert, David C B, et al.
Publicado: (2019)

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes
por: Turupcu, Aysegül, et al.
Publicado: (2017)

Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods
por: Denarie, Laurent, et al.
Publicado: (2018)

Water in protein hydration and ligand recognition
por: Maurer, Manuela, et al.
Publicado: (2019)

The effect of different cutoff schemes in molecular simulations of proteins
por: Diem, Matthias, et al.
Publicado: (2020)

Tripeptide analysis of protein structures
por: Anishetty, Sharmila, et al.
Publicado: (2002)

Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
por: Chauhan, Jagat S, et al.
Publicado: (2010)

Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
por: Kaus, Joseph W., et al.
Publicado: (2015)

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation
por: Miao, Yinglong, et al.
Publicado: (2015)

Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
por: Matsunaga, Yasuhiro, et al.
Publicado: (2022)

Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling
por: Iida, Shinji, et al.
Publicado: (2016)

New small γ-turn type N-primary amino terminal tripeptide organocatalyst for solvent-free asymmetric aldol reaction of various ketones with aldehydes
por: Thiyagarajan, Rajkumar, et al.
Publicado: (2021)

Overcoming inefficiencies arising due to the impact of the modifiable areal unit problem on single-aggregation disease maps
por: Tuson, Matthew, et al.
Publicado: (2020)

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies
por: Casas, Alexis, et al.
Publicado: (2022)

Controversy of Peptide Cyclization from Tripeptide
por: Lin, Chung-Yin, et al.
Publicado: (2021)

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level
por: Olsson, Martin A., et al.
Publicado: (2016)

Prevention of Disease and Inefficiency
Publicado: (1912)

The Percentage of Militarily Inefficients
Publicado: (1919)

Inefficiency of Thymol as an Antiseptic
por: Andrews, Edmund
Publicado: (1882)

On the use of multiple‐time‐step algorithms to save computing effort in molecular dynamics simulations of proteins
por: Pechlaner, Maria, et al.
Publicado: (2021)

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach
por: Burusco, Kepa K, et al.
Publicado: (2015)

Inefficient Building Electrification Will Require Massive Buildout of Renewable Energy and Seasonal Energy Storage
por: Buonocore, Jonathan J., et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_986c90uqonfehoemrdea4mp660