Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

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Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method is …
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scholarly articleQ13442814

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P818arXiv ID0803.3861
P356DOI10.1103/PHYSREVLETT.100.020603
P3181OpenCitations bibliographic resource ID1819023
P698PubMed publication ID18232845

P50authorGiovanni BussiQ38318410
Alessandro BarducciQ45938114
Michele ParrinelloQ479473
P433issue2
P407language of work or nameEnglishQ1860
P577publication date2008-01-18
P1433published inPhysical Review LettersQ2018386
P1476titleWell-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
P478volume100

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Q35020584Residues remote from the binding pocket control the antagonist selectivity towards the corticotropin-releasing factor receptor-1.
Q37588671Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics.
Q38273116Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example
Q57471905Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study
Q41898399Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study.
Q36120365Role of water and steric constraints in the kinetics of cavity-ligand unbinding
Q53152881Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.
Q35749668Sampling protein motion and solvent effect during ligand binding
Q44355977Sampling the structure of calcium carbonate nanoparticles with metadynamics
Q51825475Sculpting bespoke mountains: Determining free energies with basis expansions.
Q28546876Secondary Structure of Rat and Human Amylin across Force Fields
Q47725009Self-consistent calculation of protein folding pathways
Q60488223Serendipitous isolation of a disappearing conformational polymorph of succinic acid challenges computational polymorph prediction
Q30404965Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
Q51612601Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation
Q33660041Simulating Protein Mediated Hydrolysis of ATP and Other Nucleoside Triphosphates by Combining QM/MM Molecular Dynamics with Advances in Metadynamics
Q89736005Simulation of Calcium Phosphate Prenucleation Clusters in Aqueous Solution: Association beyond Ion Pairing
Q52324930Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy
Q45957121Simultaneous escaping of explicit and hidden free energy barriers: application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling.
Q47580994Single-pass incremental force updates for adaptively restrained molecular dynamics.
Q46557517Single-sweep methods for free energy calculations
Q92132423Small molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer
Q56940528Solid-liquid interface free energy through metadynamics simulations
Q47599911Some connections between importance sampling and enhanced sampling methods in molecular dynamics.
Q37632922Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB.
Q77319354Specific Material Recognition by Small Peptides Mediated by the Interfacial Solvent Structure
Q36710407Spectral gap optimization of order parameters for sampling complex molecular systems
Q46623101Stacking disorder in ice I.
Q38880205Stereoselective binding of agonists to the β2-adrenergic receptor: insights into molecular details and thermodynamics from molecular dynamics simulations.
Q50096197Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces
Q38681625String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems
Q50931767Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations.
Q47754291Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Q96946563Structural basis of CXC chemokine receptor 2 activation and signalling
Q41894087Structural effects of methionine oxidation on isolated subdomains of human fibrin D and αC regions
Q35228394Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2.
Q52607744Structure and Dynamics of DNA and RNA Double Helices Obtained from the CCG and GGC Trinucleotide Repeats.
Q44873785Structure and Dynamics of DNA and RNA Double Helices of CAG and GAC Trinucleotide Repeats
Q51143652Structure and Li+ ion transport in a mixed carbonate/LiPF6 electrolyte near graphite electrode surfaces: a molecular dynamics study.
Q98564759Structure and dynamics of the active Gs-coupled human secretin receptor
Q50959391Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale
Q50641788Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example
Q92854572Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules
Q34547230Synthetic Studies of Neoclerodane Diterpenes from Salvia divinorum: Identification of a Potent and Centrally Acting μ Opioid Analgesic with Reduced Abuse Liability.
Q98177715T-Cell Receptor CDR3 Loop Conformations in Solution Shift the Relative Vα-Vβ Domain Distributions
Q90245783T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation
Q90051401TDP-43 α-helical structure tunes liquid-liquid phase separation and function
Q64972283Tau local structure shields an amyloid-forming motif and controls aggregation propensity.
Q40960149The Conformation of Interfacially Adsorbed Ranaspumin-2 Is an Arrested State on the Unfolding Pathway
Q57976357The G-Triplex DNA
Q47685725The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit
Q34611043The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions
Q24293505The Parkinson disease-linked LRRK2 protein mutation I2020T stabilizes an active state conformation leading to increased kinase activity
Q55411474The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.
Q35012592The adaptive biasing force method: everything you always wanted to know but were afraid to ask
Q37143502The allosteric communication pathways in KIX domain of CBP
Q41633843The cellular membrane as a mediator for small molecule interaction with membrane proteins
Q92224343The energetics of protein-lipid interactions as viewed by molecular simulations
Q38698755The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids
Q37438825The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state
Q50057309The liquid-liquid transition in supercooled ST2 water: a comparison between umbrella sampling and well-tempered metadynamics
Q57943293The role of water in host-guest interaction
Q40176435The structural impact of DNA mismatches
Q41353268Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations
Q48031360Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.
Q28551159Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics
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Q91707981Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale
Q38207562Tricks of light on helices: transformation of helical polymers by photoirradiation
Q50952303Triggering nanoparticle surface ligand rearrangement via external stimuli: light-based actuation of biointerfaces
Q27313495Two distinct states of the HAMP domain from sensory rhodopsin transducer observed in unbiased molecular dynamics simulations
Q38520438Type II kinase inhibitors show an unexpected inhibition mode against Parkinson's disease-linked LRRK2 mutant G2019S.
Q48048110Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study
Q92268977Understanding Ligand Binding Selectivity in a Prototypical GPCR Family
Q38959329Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
Q48286826Unraveling Mg2+-RNA binding with atomistic molecular dynamics
Q41455059Unrestrained computation of free energy along a path
Q57591553Use of Metadynamics in the Design of isoDGR-Based αvβ3 Antagonists To Fine-Tune the Conformational Ensemble
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Q34291803Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
Q57955149Using collective variables to drive molecular dynamics simulations
Q35887074Using sketch-map coordinates to analyze and bias molecular dynamics simulations
Q38685898Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking
Q26826746Visualizing functional motions of membrane transporters with molecular dynamics simulations
Q40221977Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study
Q51069984Well-tempered metadynamics converges asymptotically
Q48214486Zinc Complexes of Cyclodextrin-bearing 8-Hydroxyquinoline Ligands: A Comparative Study.
Q53239658μ-tempered metadynamics: Artifact independent convergence times for wide hills

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