Topic 91

biophysics simulations conformational dynamics molecular md structural energy binding conformations conformation protein states structures simulation free state atom structure ligand proteins atomic calculations allosteric ensemble atomistic sampling folding molecule transition residues nmr experimental interactions force flexibility ensembles equilibrium motions coupled mechanism coarse solvent pocket bound design experimentally hydrogen dynamic grained molecules ligands complex disordered site crystal thermodynamic residue experiments native agreement kinetic markov general closed microsecond active intrinsically all computational transitions idps coupling spectroscopy domain receptor dynamical open loop detailed insight electrostatic its kinetics docking small folded local description it energies flexible adopt switching helix can bond kcal carlo bonds

229 items. Top items listed below.

Mechanistic Picture for Monomeric Human Fibroblast Growth Factor 1 Stabilization by Heparin Binding 91 8 3

State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane 163 91 82 8 3

A kinetic ensemble of the Alzheimer's Aβ peptide 91 78 38 8 4

Discovering loop conformational flexibility in T4 lysozyme mutants through Artificial Intelligence aided Molecular Dynamics 91 8 4

Exploring Conformational Transition of 2019 Novel Coronavirus Spike Glycoprotein Between Its Closed and Open States Using Molecular Dynamics Simulations 36 1

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein 149 91 78 8

Data-guided Multi-Map variables for ensemble refinement of molecular movies 111 91 51 8 4

Conformational states of the cytoprotective protein Bcl-xL 91 78 63 8 3

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution 91 78 8

Refinement of protein structure via contact based potentials in replica exchange simulations 91 38 26 4

Protein dynamics enables phosphorylation of buried residues in Cdk2/Cyclin A-bound p27 149 91 8

Allosteric communications between domains modulate activity of matrix metalloprotease-1 91 63 8

A sodium-dependent communication pathway across class A G-protein coupled receptors 91 63 8 3

The relation between intrinsic protein conformational changes and ligand binding 91 8

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway 149 91 78 8

Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy calculations of peptide binding 91 8 4

Integrating NMR and Simulations Reveals Motions in the UUCG Tetraloop 91 8

Free Energy Landscape and Conformational Kinetics of Hoogsteen Base-Pairing in DNA vs RNA 91 8

Insulin-Induced Conformational Changes in the Full-Length Insulin Receptor: Structural Insights Gained from Molecular Modeling Analyses 91 8

Coupling of conformational switches in calcium sensor unraveled with local Markov models and transfer entropy 163 91 8

Molecular recognition and dynamics of linear poly-ubiquitins: integrating coarse-grain simulations and experiments 149 91 78 8

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

Cholesterol sensing by CD81 is important for hepatitis C virus entry 91 63 8 3

The Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor 163 91 78 63 8 3

Substrate Recognition by γ-Glutamyltransferase: A Molecular Dynamics Simulations Study 91 63 8

The flexibility of ACE2 in the context of SARS-CoV-2 infection 36 1

Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins 149 91 78 8

RNA-dependent structures of the RNA-binding loop in the flavivirus NS3 helicase 91 63 8

Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein 36 1

Markov State Models and NMR Uncover an Overlooked Allosteric Loop in p53 91 8

Characterizing receptor flexibility to predict mutations that lead to human adaptation of influenza hemagglutinin 91 63 8

GPCR Oligomerisation Modulation by Conformational State and Lipid Interactions Revealed by MD Simulations and Markov Models 91 78 8 3

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics 91 8

Cotranslational protein folding can promote the formation of correct folding intermediate 91 78 8

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR 78 8

Molecular mechanism of SARS-CoV-2 cell entry inhibition via TMPRSS2 by Camostat and Nafamostat mesylate 91 44 1

A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins 149 91 78 26 8 4

Coarse-grained molecular simulations of the binding of the SARS-CoV 2 spike protein RBD to the ACE2 receptor 36 1

Conformational state switching and pathways of chromosome dynamics in cell cycle 7

Ligand Modulation of the Conformational Dynamics of the A2A Adenosine Receptor Revealed by Single-Molecule Fluorescence 91 8

High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme 91 78 4

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling 91 63 8

Long-range coupled motions underlie ligand recognition by a chemokine receptor 91 63 8

Comparative effects of oncogenic mutations G12C, G12V, G13D, and Q61H on local conformations and dynamics of K-Ras 91 63 8

Membrane-mediated ligand unbinding of the PK-11195 ligand from the translocator protein (TSPO) 91 8

The intrinsically disordered N-terminus of the voltage-dependent anion channel 91 78 8

Molecular basis for SARS-CoV-2 spike affinity for human ACE2 receptor 91 36 1

Exploring Chromosomal Structural Heterogeneity AcrossMultiple Cell Lines 91 8

Information theoretics for the machine learning detection of functionally conserved and coordinated protein motions 91 8 4

Insights into actin polymerization and nucleation using a coarse grained model 111 51 8

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations 149 91 78 8

N-terminus of the third PDZ Domain of PSD-95 Orchestrates Allosteric Communication for Selective Ligand Binding 91 63 8

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations 78 8

Monomeric amyloid beta-peptide (1-42) significantly populates compact fibril-like conformations 78 8

Mg2+ Sensing by an RNA Fragment: Role of Mg2+ Coordinated Water Molecules 91 8

Structural Mechanism Underlying Ligand Binding and Activation of PPARγ 91 63 8 3

A Molecular View of Lipid-mediated Activation Process of Apolipoprotein E 91 8

Structural characterization of LsrK to target quorum sensing and comparison between X-ray and homology model 91 63 8

The electrostatic allostery could be the trigger for the changes in dynamics for the PDZ domain of PICK1 63 8 3

Extraction of Protein Dynamics Information Hidden in Cryo-EM Map Using Deep Learning 111 51 8 4

Molecular details of protein condensates probed by microsecond-long atomistic simulations 149 78 8

Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2 36 1

Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA 91 8

FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution 105 91 26 4

Wavelet coherence phases decode the universal switching mechanism of Ras GTPase superfamily 91 8

Molecular mechanism of SARS-CoV-2 inactivation by temperature 91 8 1

Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides 91 8

Extending the Martini coarse-grained forcefield to N-glycans 91 78 8

Static All-Atom Energetic Mappings of the SARS-Cov-2 Spike Protein with Potential Latch Identification of the Down State Protomer 91 63 1

Intrinsically disordered protein ensembles shape evolutionary rates revealing conformational patterns 149 91 21 8 5

Dynamics-driven allostery underlies pre-activation of the regulatory Ca2+-ATPase/phospholamban complex 91 8 3

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis 91 26 4

High-Speed AFM directly visualizes conformational dynamics of the HIV-Vif protein complex 91 8

The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array 91 8

Learning a force field from small-molecule crystal lattice predictions enables consistent sub-Angstrom protein-ligand docking 91 4

How and why plants and humans N-glycans are different: Insight from molecular dynamics into the "glycoblocks" architecture of complex carbohydrates 149 91 8

Physical Interactions Driving the Activation/Inhibition of Calcium/Calmodulin Dependent Protein Kinase II 91 8 3

An Accurate Free Energy Method for Solvation of Organic Compounds and Binding to Proteins 91 26 8 4

Dynamics of chromosomal target search by a membrane-integrated one-component receptor 127 8 3

Inchworm stepping of Myc-Max heterodimer protein diffusion along DNA 91 8

Charge Interactions in a Highly Charge-depleted Protein 149 91 8

Protein sequence design by explicit energy landscape optimization 91 26 4

Predicting substitutions to modulate disorder and stability in coiled-coils 149 91 8

Distance-based metrics for comparing conformational ensembles of intrinsically disordered proteins 149 91 8 4

How antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK 91 8

Order and disorder - an integrative structure of the full-length human growth hormone receptor 78 8

The high-energy transition state of a membrane transporter 91 8

RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding 119 91 8

Small Glycols Discover Cryptic Pockets on Proteins for Fragment-based Approaches 91 8

Reconciling conformational heterogeneity and Substrate Recognition in Cytochrome P450 91 63 8

DBFOLD: An efficient algorithm for computing folding pathways of complex proteins 91 38 4

Multiscale simulations examining glycan shield effects on drug binding to influenza neuraminidase 91 8

Mechanism of Dynamic Binding of Replication Protein A to ssDNA 91 8

Substrate binding modulates the conformational kinetics of the secondary multidrug transporter LmrP 91 8

Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding 91 8

Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein AssociationAssociation: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor 91 8

Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease 78 8

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State 1

A modified ACE2 peptide mimic to block SARS-CoV2 entry 91 36 8 1

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister Ribozyme 91 8