| Nome |
# |
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Using metadynamics to explore complex free-energy landscapes, file dd8a4bf8-bddf-20a0-e053-d805fe0a8cb0
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2.794
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Canonical sampling through velocity rescaling, file dd8a4bf7-109d-20a0-e053-d805fe0a8cb0
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304
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Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations, file dd8a4bf7-8922-20a0-e053-d805fe0a8cb0
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196
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Machine learning a model for RNA structure prediction, file dd8a4bf8-d196-20a0-e053-d805fe0a8cb0
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150
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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview, file dd8a4bf7-e863-20a0-e053-d805fe0a8cb0
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145
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Using the maximum entropy principle to combine simulations and solution experiments, file dd8a4bf7-db8d-20a0-e053-d805fe0a8cb0
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93
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The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models, file dd8a4bf8-59c7-20a0-e053-d805fe0a8cb0
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93
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Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides, file dd8a4bf8-c0fd-20a0-e053-d805fe0a8cb0
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85
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Fitting Corrections to an RNA Force Field Using Experimental Data, file dd8a4bf8-a390-20a0-e053-d805fe0a8cb0
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79
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Hamiltonian replica-exchange in GROMACS: a flexible implementation, file dd8a4bf7-1ced-20a0-e053-d805fe0a8cb0
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64
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Exploring RNA structure and dynamics through enhanced sampling simulations, file dd8a4bf8-a392-20a0-e053-d805fe0a8cb0
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63
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Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field, file 528fd374-0638-4043-bc50-3f9fc645b882
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58
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Molecular Simulations Matching Denaturation Experiments for N-6-Methyladenosine, file 7bb45f5b-4ac3-4205-b274-c7f3168f990d
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57
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Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility, file dd8a4bf8-19e3-20a0-e053-d805fe0a8cb0
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57
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Empirical corrections to the Amber RNA force field with Target Metadynamics, file dd8a4bf7-d8a6-20a0-e053-d805fe0a8cb0
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56
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Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles, file dd8a4bf9-03d3-20a0-e053-d805fe0a8cb0
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56
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1, file dd8a4bf7-e3b5-20a0-e053-d805fe0a8cb0
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52
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Understanding In-line Probing Experiments by Modeling Cleavage of Non-reactive RNA Nucleotides, file dd8a4bf7-547b-20a0-e053-d805fe0a8cb0
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51
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Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch, file dd8a4bf7-16ed-20a0-e053-d805fe0a8cb0
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49
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Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach, file dd8a4bf7-cc9f-20a0-e053-d805fe0a8cb0
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49
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Unravelling Mg2+-RNA binding with atomistic molecular dynamics, file dd8a4bf7-5478-20a0-e053-d805fe0a8cb0
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48
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Assessing the accuracy of direct-coupling analysis for RNA contact prediction, file dd8a4bf8-b5ef-20a0-e053-d805fe0a8cb0
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48
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Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations, file dd8a4bf8-3f8c-20a0-e053-d805fe0a8cb0
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45
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The Role of Nucleobase Interactions in RNA Structure and Dynamics, file dd8a4bf7-2145-20a0-e053-d805fe0a8cb0
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44
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Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations, file dd8a4bf7-1484-20a0-e053-d805fe0a8cb0
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42
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Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments, file dd8a4bf7-147e-20a0-e053-d805fe0a8cb0
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38
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ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations, file dd8a4bf7-1339-20a0-e053-d805fe0a8cb0
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36
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Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility, file dd8a4bf7-e9ec-20a0-e053-d805fe0a8cb0
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35
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Asymmetric base-pair opening drives helicase unwinding dynamics, file dd8a4bf8-86ab-20a0-e053-d805fe0a8cb0
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35
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The Role of Nucleobase Interactions in RNA Structure and Dynamics, file dd8a4bf8-96ab-20a0-e053-d805fe0a8cb0
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35
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RNA Folding Pathways in Stop Motion, file dd8a4bf7-1254-20a0-e053-d805fe0a8cb0
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33
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Barnaba: software for analysis of nucleic acid structures and trajectories, file dd8a4bf8-3fe9-20a0-e053-d805fe0a8cb0
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33
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Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data, file dd8a4bf8-a386-20a0-e053-d805fe0a8cb0
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33
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Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration, file dd8a4bf7-1d6e-20a0-e053-d805fe0a8cb0
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32
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Toward empirical force fields that match experimental observables, file dd8a4bf8-c344-20a0-e053-d805fe0a8cb0
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29
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Directional translocation resistance of Zika xrRNA, file dd8a4bf8-c82c-20a0-e053-d805fe0a8cb0
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29
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Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments, file 312fcc28-fd35-4335-97f4-a489a7307d30
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25
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Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations, file dd8a4bf7-13db-20a0-e053-d805fe0a8cb0
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24
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Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering, file dd8a4bf7-1e0c-20a0-e053-d805fe0a8cb0
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24
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Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1, file dd8a4bf7-e9bb-20a0-e053-d805fe0a8cb0
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24
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Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics, file dd8a4bf8-3ccf-20a0-e053-d805fe0a8cb0
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24
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Toward empirical force fields that match experimental observables, file dd8a4bf8-c345-20a0-e053-d805fe0a8cb0
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23
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A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs, file dd8a4bf7-e45b-20a0-e053-d805fe0a8cb0
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22
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A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs, file dd8a4bf7-e7b2-20a0-e053-d805fe0a8cb0
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21
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Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations, file dd8a4bf9-008c-20a0-e053-d805fe0a8cb0
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18
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Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions, file de2b3061-4df0-4cce-ba9e-57410a844f17
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17
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Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations, file 85aad84b-e83d-4357-8256-91ea8acefad8
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16
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Towards de novo RNA 3D Structure Prediction, file dd8a4bf7-12e8-20a0-e053-d805fe0a8cb0
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16
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Analyzing and Biasing Simulations with PLUMED, file dd8a4bf8-7963-20a0-e053-d805fe0a8cb0
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16
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Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling, file dd8a4bf9-0090-20a0-e053-d805fe0a8cb0
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14
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Accurate multiple time step in biased molecular simulations, file dd8a4bf7-13df-20a0-e053-d805fe0a8cb0
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12
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RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations, file dd8a4bf7-14cd-20a0-e053-d805fe0a8cb0
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11
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Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering, file 9e618271-c3b8-4a0b-be0f-bf8818c80c24
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10
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RNA Conformational Ensembles: Narrowing the GAP between Experiments and Simulations with Metadynamics, file dd8a4bf7-5f36-20a0-e053-d805fe0a8cb0
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10
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Using metadynamics to explore complex free-energy landscapes, file dd8a4bf8-ac5d-20a0-e053-d805fe0a8cb0
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10
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Machine learning a model for RNA structure prediction, file dd8a4bf8-cacf-20a0-e053-d805fe0a8cb0
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10
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Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface, file dd8a4bf7-2f3e-20a0-e053-d805fe0a8cb0
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7
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Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data, file dd8a4bf8-a387-20a0-e053-d805fe0a8cb0
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7
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Predicting the kinetics of RNA oligonucleotides using Markov state models, file dd8a4bf7-2791-20a0-e053-d805fe0a8cb0
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5
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Folding of guanine quadruplex molecules – funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies, file dd8a4bf7-8197-20a0-e053-d805fe0a8cb0
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5
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Exploring RNA structure and dynamics through enhanced sampling simulations, file dd8a4bf7-d5cb-20a0-e053-d805fe0a8cb0
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5
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Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics, file dd8a4bf7-2282-20a0-e053-d805fe0a8cb0
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4
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Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans, file 156e8b62-83d1-46cb-a128-55a80a85ad41
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3
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Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach, file dd8a4bf7-1457-20a0-e053-d805fe0a8cb0
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3
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Metadynamics with adaptive Gaussians, file dd8a4bf7-15e9-20a0-e053-d805fe0a8cb0
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3
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Effects of the electron-hole interaction on the optical properties of materials: the Bethe-Salpeter equation, file dd8a4bf7-1e2a-20a0-e053-d805fe0a8cb0
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3
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Using Reweighted Pulling Simulations to Characterize Conformational Changes in Riboswitches, file dd8a4bf7-23db-20a0-e053-d805fe0a8cb0
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3
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Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics, file dd8a4bf7-e45e-20a0-e053-d805fe0a8cb0
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3
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Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages, file dd8a4bf7-ebb9-20a0-e053-d805fe0a8cb0
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3
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Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution, file dd8a4bf8-6dfe-20a0-e053-d805fe0a8cb0
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3
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Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data, file 863efa01-58c2-424b-8416-0990ff55e1a4
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2
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Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations, file d170a804-7ed7-4a64-8df0-beb4dc8b8ed9
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2
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Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations, file dd8a4bf7-140b-20a0-e053-d805fe0a8cb0
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2
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Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations, file dd8a4bf7-16e5-20a0-e053-d805fe0a8cb0
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2
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First-principles approach for the calculation of optical properties of one-dimensional systems with helical symmetry: The case of carbon nanotubes, file dd8a4bf7-1af7-20a0-e053-d805fe0a8cb0
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2
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RNA Unwinding from Reweighted Pulling Simulations, file dd8a4bf7-1b86-20a0-e053-d805fe0a8cb0
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2
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Well-tempered metadynamics: A smoothly converging and tunable free-energy method, file dd8a4bf7-1c7a-20a0-e053-d805fe0a8cb0
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2
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Ab-initio study of excitonic effects in conventional and organic semiconductors, file dd8a4bf7-1c95-20a0-e053-d805fe0a8cb0
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2
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SiO2 in density functional theory and beyond, file dd8a4bf7-1d33-20a0-e053-d805fe0a8cb0
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2
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Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide, file dd8a4bf7-2011-20a0-e053-d805fe0a8cb0
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2
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Combining simulations and solution experiments as a paradigm for RNA force field refinement, file dd8a4bf7-213b-20a0-e053-d805fe0a8cb0
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2
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Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding, file dd8a4bf7-22ed-20a0-e053-d805fe0a8cb0
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2
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A Nucleobase-Centric Coarse-Grained Model for Structure Prediction of RNA Fragments, file dd8a4bf7-22f9-20a0-e053-d805fe0a8cb0
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2
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Free-energy calculations with metadynamics: theory and practice, file dd8a4bf7-237b-20a0-e053-d805fe0a8cb0
|
2
|
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Protein folding with combined parallel tempering and metadynamics, file dd8a4bf7-23ed-20a0-e053-d805fe0a8cb0
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2
|
|
RNA Conformational Fluctuations from Elastic Network Models: A Comparison with Molecular Dynamics and Shape Experiments, file dd8a4bf7-646e-20a0-e053-d805fe0a8cb0
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2
|
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Fitting Corrections to an RNA Force Field Using Experimental Data, file dd8a4bf8-6dfa-20a0-e053-d805fe0a8cb0
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2
|
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Promoting transparency and reproducibility in enhanced molecular simulations, file dd8a4bf8-7557-20a0-e053-d805fe0a8cb0
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2
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Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications, file dd8a4bf9-0ca5-20a0-e053-d805fe0a8cb0
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2
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Molecular Dynamics Simulations of Chemically Modified Ribonucleotides, file 0f288db6-a0fe-47fd-841d-8910b1e789bb
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1
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Integrating experimental data with molecular simulations to investigate RNA structural dynamics, file 18636c20-7bd7-4237-8ac0-2c0044f54546
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1
|
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Langevin Equation with Colored Noise for Constant-Temperature Molecular Dynamics Simulations, file dd8a4bf7-0ff8-20a0-e053-d805fe0a8cb0
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1
|
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Solid State Effects on Exciton States and Optical Properties of PPV, file dd8a4bf7-1206-20a0-e053-d805fe0a8cb0
|
1
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Ab initio complex band structure of conjugated polymers: Effects of hydrid density functional theory and GW schemes, file dd8a4bf7-1277-20a0-e053-d805fe0a8cb0
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1
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Bowl Inversion of Surface-Adsorbed Sumanene, file dd8a4bf7-13d9-20a0-e053-d805fe0a8cb0
|
1
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PLUMED: A portable plugin for free-energy calculations with molecular dynamics, file dd8a4bf7-1401-20a0-e053-d805fe0a8cb0
|
1
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Relationship between structural and optoelectronic properties in semiconducting polymers, file dd8a4bf7-145b-20a0-e053-d805fe0a8cb0
|
1
|
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Excitons in Carbon Nanotubes: An Ab Initio Symmetry-Based Approach, file dd8a4bf7-1461-20a0-e053-d805fe0a8cb0
|
1
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Nonkinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments, file dd8a4bf7-152a-20a0-e053-d805fe0a8cb0
|
1
|
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Stochastic thermostats: comparison of local and global schemes, file dd8a4bf7-15ab-20a0-e053-d805fe0a8cb0
|
1
|
| Totale |
5.599 |