Convergence of Molecular Dynamics Simulation of Protein Native States: Feasibility vs Self-Consistency Dilemma.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Chemical Theory and Computation

• Publication date

  2016-01-26

• Fields of study

  Biology, Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1021/acs.jctc.5b00999PMID 26765584
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme.

  2015cited by this paper
• Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

  2015cited by this paper
• The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin.

  2015cited by this paper
• Understanding the thermostability and activity of Bacillus subtilis lipase mutants: insights from molecular dynamics simulations.

  2015cited by this paper
• Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations.

  2014cited by this paper
• The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase.

  2014cited by this paper
• Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.

  2014cited by this paper
• Indolicidin binding induces thinning of a lipid bilayer.

  2014cited by this paper
• Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

  2013cited by this paper
• Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase

  2013cited by this paper
• How conformational flexibility stabilizes the hyperthermophilic elongation factor G-domain.

  2013cited by this paper
• Flexibility of the bacterial chaperone trigger factor in microsecond-timescale molecular dynamics simulations.

  2013cited by this paper
• Do Homologous Thermophilic-Mesophilic Proteins Exhibit Similar Structures and Dynamics at Optimal Growth Temperatures? A Molecular Dynamics Simulation Study

  2013cited by this paper
• PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

  2013cited by this paper
• Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

  2012cited by this paper
• Will molecular dynamics simulations of proteins ever reach equilibrium?

  2012cited by this paper
• H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

  2012cited by this paper
• Importance of V3 Loop Flexibility and Net Charge in the Context of Co-Receptor Recognition. A Molecular Dynamics Study on HIV gp120

  2012cited by this paper
• Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation.

  2011cited by this paper
• Automated sampling assessment for molecular simulations using the effective sample size.

  2010cited by this paper
• Comparing geometric and kinetic cluster algorithms for molecular simulation data.

  2010cited by this paper
• Atomic-Level Characterization of the Structural Dynamics of Proteins

  2010cited by this paper
• Crystal structure of cold shock protein 1 from Thermus thermophilus HB8

  2010cited by this paper
• Long-timescale molecular dynamics simulations of protein structure and function.

  2009cited by this paper
• Convergence and Heterogeneity in Peptide Folding with Replica Exchange Molecular Dynamics.

  2009cited by this paper
• Quantifying uncertainty and sampling quality in biomolecular simulations.

  2009cited by this paper
• Understanding Structural/Functional Properties of Immunoconjugates for Cancer Therapy by Computational Approaches

  2008cited by this paper
• Structure and dynamics of the anti-AMCV scFv(F8): effects of selected mutations on the antigen combining site.

  2008cited by this paper
• Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.

  2007cited by this paper
• On the structural convergence of biomolecular simulations by determination of the effective sample size.

  2007cited by this paper
• Solution Structure of chemotaxi protein CheW from Escherichia coli

  2007cited by this paper
• Configurational entropy elucidates the role of salt‐bridge networks in protein thermostability

  2007cited by this paper
• Convergence of molecular dynamics simulations of membrane proteins

  2007cited by this paper
• Comparison of multiple Amber force fields and development of improved protein backbone parameters

  2006cited by this paper
• Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations.

  2006cited by this paper
• Ensemble-based convergence analysis of biomolecular trajectories.

  2006cited by this paper
• A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules

  2006cited by this paper
• Protein flexibility: multiple molecular dynamics simulations of insulin chain B.

  2006cited by this paper
• Molecular dynamics and protein function.

  2005cited by this paper
• Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain.

  2005cited by this paper
• H++: a server for estimating pKas and adding missing hydrogens to macromolecules

  2005cited by this paper
• Effects of Calcium Binding on Structure and Autolysis Regulation in Trypsins. A Molecular Dynamics Investigation.

  2005cited by this paper
• Helical shifts generate two distinct conformers in the atomic resolution structure of the CheA phosphotransferase domain from Thermotoga maritima.

  2004cited by this paper
• Three‐dimensional model of a substrate‐bound SARS chymotrypsin‐like cysteine proteinase predicted by multiple molecular dynamics simulations: Catalytic efficiency regulated by substrate binding

  2004cited by this paper
• Conformational sampling and dynamics of membrane proteins from 10‐nanosecond computer simulations

  2004cited by this paper
• An electrostatic basis for the stability of thermophilic proteins

  2004cited by this paper
• Protein dynamics in a family of laboratory evolved thermophilic enzymes.

  2003cited by this paper
• Molecular dynamics simulations of biomolecules

  2002cited by this paper
• Assessing equilibration and convergence in biomolecular simulations

  2002cited by this paper
• Convergence of sampling in protein simulations.

  2002cited by this paper
• Steered molecular dynamics and mechanical functions of proteins.

  2001cited by this paper
• Steered molecular dynamics investigations of protein function.

  2001cited by this paper
• Flexibility of the murine prion protein and its Asp178Asn mutant investigated by molecular dynamics simulations.

  2001cited by this paper
• Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations

  1999cited by this paper
• Molecular dynamics study of unbinding of the avidin-biotin complex.

  1997cited by this paper
• Recovery of protein structure from contact maps.

  1997cited by this paper
• CHARGE SCREENING AND THE DIELECTRIC CONSTANT OF PROTEINS : INSIGHTS FROM MOLECULAR DYNAMICS

  1996cited by this paper
• Simulation of activation free energies in molecular systems

  1996cited by this paper
• A smooth particle mesh Ewald method

  1995cited by this paper
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

  1992cited by this paper
• Comparison of simple potential functions for simulating liquid water

  1983cited by this paper

• Long-range coupling regulates stator dynamics in the bacterial flagellar motor

  2025cites this paper
• Structural elucidation of four fungal hydrophobins belonging to classes I and II: Results from Alphafold and accelerated molecular dynamics simulations

  2025cites this paper
• AutoSIM: Redesigning and automating umbrella sampling for biomolecular conformational transitions.

  2025cites this paper
• Computational electrophysiology simulation study of the Dengue virus viroporins.

  2025cites this paper
• Second‐order allosteric control as a mechanism for compensatory mutations in B‐cell translocation gene 2

  2025cites this paper
• Exploring protein structural ensembles: Integration of sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling methods

  2024cites this paper
• Evidence that the cold- and menthol-sensing functions of the human TRPM8 channel evolved separately

  2024cites this paper
• A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta

  2024cites this paper
• Investigating the Aryl Hydrocarbon Receptor Agonist/Antagonist Conformational Switch Using Well-Tempered Metadynamics Simulations

  2024cites this paper
• RNA-binding tunes the conformational plasticity and intradomain stability of TDP-43 tandem RNA recognition motifs

  2024cites this paper
• Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.

  2024cites this paper
• Atomistic Simulations of Sarcomere Proteins.

  2024cites this paper
• Simulations predict preferred Mg2+ coordination in a nonenzymatic primer-extension reaction center

  2024cites this paper
• Interacting myosin head dynamics and their modification by 2'-deoxy-ADP.

  2024cites this paper
• A Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions.

  2024cites this paper
• Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics

  2023cites this paper
• Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities.

  2023cites this paper
• Allosteric regulatory control in dihydrofolate reductase is revealed by dynamic asymmetry

  2023cites this paper
• DELTD: An R Package for Kernel Density Estimation using Lifetime Distributions

  2023cites this paper
• Critical Assessment of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins.

  2023cites this paper
• IDP Force Fields Applied to Model PPII-Rich 33-mer Gliadin Peptides.

  2023cites this paper
• Molecular Dynamics Methods for Antibody Design.

  2023cites this paper
• LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories

  2022cites this paper
• On the Uses of PCA to Characterise Molecular Dynamics Simulations of Biological Macromolecules: Basics and Tips for an Effective Use.

  2022cites this paper
• Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace.

  2022cites this paper
• RHAMNETIN IS A BETTER INHIBITOR OF SARS-COV-2 2’-O-METHYLTRANSFERASE THAN DOLUTEGRAVIR: A COMPUTATIONAL PREDICTION

  2022cites this paper
• Self-Consistent Equations Governing the Dynamics of Non-equilibrium Binary Colloidal Systems

  2021cites this paper
• The role of temperature in the binding of the disordered epitope region of human thrombopoietin to antibody: A molecular dynamics simulations study.

  2021cites this paper
• Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants

  2021cites this paper
• Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract

  2021cites this paper
• Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations.

  2020cites this paper
• The Maximum Caliber Variational Principle for Nonequilibria.

  2020cites this paper
• Energy Landscape Mapping and Replica Exchange Molecular Dynamics of an Adsorbed Peptide.

  2020cites this paper
• Variance of Atomic Coordinates as a Dynamical Metric to Distinguish Proteins and Protein-Protein Interactions in Molecular Dynamics Simulations.

  2020cites this paper
• An analytical theory to describe sequence-specific inter-residue distance profiles for polyampholytes and intrinsically disordered proteins.

  2020cites this paper
• Optimization of Molecular Dynamics Simulations of c-MYC1-88—An Intrinsically Disordered System

  2020cites this paper
• Enzyme Dynamics: Looking Beyond a Single Structure

  2020cites this paper
• Thermosensitive Hydration of Four Acrylamide-Based Polymers in Coil and Globule Conformations

  2020cites this paper
• Modulation of post-powerstroke dynamics in myosin II by 2'-deoxy-ADP.

  2020cites this paper
• Altered structure and dynamics of pathogenic cytochrome c variants correlate with increased apoptotic activity

  2020cites this paper
• In Silico Identification of Potential Allosteric Inhibitors of the SARS-CoV-2 Helicase

  2020cites this paper
• In Silico Identification of the Potential Natural Inhibitors of SARS-CoV-2 Guanine-N7 Methyltransferase.

  2020cites this paper
• Studying equilibria of polymers in solution by direct molecular dynamics simulations: poly(N-isopropylacrylamide) in water as a test case

  2019cites this paper
• Confirmation of the formation of salt bridges in the denatured state of CutA1 protein using molecular dynamics simulations

  2019cites this paper
• Dynamical coring of Markov state models.

  2019cites this paper
• Investigating the stability of dengue virus envelope protein dimer using well‐tempered metadynamics simulations

  2019cites this paper
• Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier

  2019cites this paper
• Conformational states of Zika virus non-structural protein 3 determined by molecular dynamics simulations with small-angle X-Ray scattering data.

  2019cites this paper
• Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates.

  2019cites this paper
• In silico investigation of hepatitis c virus: a novel perspective into targeted viral inhibition of NS3 helicase, NS 3/4a protease and NS5b RNA dependent RNA polymerase.

  2019cites this paper
• Predicting the Binding Mode of 2-Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory.

  2018cites this paper
• Mechanistic insights from replica exchange molecular dynamics simulations into mutation induced disordered-to-ordered transition in Hahellin, a βγ-crystallin

  2018cites this paper
• Communication: Introducing prescribed biases in out-of-equilibrium Markov models

  2018cites this paper
• Temperature-induced collapse of a disordered peptide observed by three sampling methods in molecular dynamics simulations.

  2018cites this paper
• Validating Molecular Dynamics Simulations against Experimental Observables in Light of Underlying Conformational Ensembles.

  2018cites this paper
• High throughput nonparametric probability density estimation

  2018cites this paper
• Ancient Thioredoxins Evolved to Modern Day Stability-Function Requirement by Altering Native State Ensemble

  2018cites this paper
• Strategy for Stabilization of CutA1 Proteins Due to Ion-Ion Interactions at Temperatures of over 100 °C.

  2018cites this paper
• Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes

  2017cites this paper
• A toolkit to quantify the sampling quality of molecular dynamics trajectories: studying highly flexible biomolecules

  2017influential citation
• Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

  2017cites this paper
• All-Atom Simulations Reveal Protein Charge Decoration in the Folded and Unfolded Ensemble Is Key in Thermophilic Adaptation.

  2017cites this paper
• Quantitative Assessment of Molecular Dynamics Sampling for Flexible Systems.

  2017cites this paper
• Impact of Cu(II) Binding on Structures and Dynamics of Aβ42 Monomer and Dimer: Molecular Dynamics Study.

  2016cites this paper
• Mode localization in the cooperative dynamics of protein recognition.

  2015cites this paper