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Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements
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inferred← citeshttps://doi.org/10.1042/bsr20203495openalex-snapshot
Remodeling hydrogen bond interactions results in relaxed specificity of Caspase-3
inferred← citeshttps://doi.org/10.1063/1.3273903openalex-snapshot
Kirkwood–Buff derived force field for alkali chlorides in simple point charge water
inferred← citeshttps://doi.org/10.1063/1.3360310openalex-snapshot
Dissociation of NaCl in water from ab initio molecular dynamics simulations
inferred← citeshttps://doi.org/10.1063/1.3454193openalex-snapshot
A statistical mechanical theory for a two-dimensional model of water
inferred← citeshttps://doi.org/10.1063/1.3693330openalex-snapshot
Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules
inferred← citeshttps://doi.org/10.1063/1.4937156openalex-snapshot
Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution
inferred← citeshttps://doi.org/10.1063/1.5001190openalex-snapshot
A potential model for sodium chloride solutions based on the TIP4P/2005 water model
inferred← citeshttps://doi.org/10.1063/1.5019939openalex-snapshot
Concentration-dependent and configuration-dependent interactions of monovalent ions with an RNA tetraloop
inferred← citeshttps://doi.org/10.1063/1.5144991openalex-snapshot
Dielectric constant and density of aqueous alkali halide solutions by molecular dynamics: A force field assessment
inferred← citeshttps://doi.org/10.1063/5.0321463openalex-snapshot
Deriving effective electrode–ion interactions from free-energy profiles at electrochemical interfaces
inferred← citeshttps://doi.org/10.1063/5.0343028openalex-snapshot
Scaled-charge ion force field optimized for individual ion partial molar volumes in water
inferred← citeshttps://doi.org/10.1073/pnas.1119552109openalex-snapshot
Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations
inferred← citeshttps://doi.org/10.1073/pnas.1603154113openalex-snapshot
Free-energy landscape of a hyperstable RNA tetraloop
inferred← citeshttps://doi.org/10.1073/pnas.1713027115openalex-snapshot
RNA force field with accuracy comparable to state-of-the-art protein force fields
inferred← citeshttps://doi.org/10.1074/jbc.m109.027011openalex-snapshot
N-terminal Domains of DELLA Proteins Are Intrinsically Unstructured in the Absence of Interaction with GID1/Gibberellic Acid Receptors
inferred← citeshttps://doi.org/10.1074/jbc.ra117.000728openalex-snapshot
Modifications to a common phosphorylation network provide individualized control in caspases
inferred← citeshttps://doi.org/10.1080/00268976.2016.1165296openalex-snapshot
Recent progress in molecular simulation of aqueous electrolytes: force fields, chemical potentials and solubility
inferred← citeshttps://doi.org/10.1080/07391102.2012.732344openalex-snapshot
Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/08927022.2011.566605openalex-snapshot
Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucanendo-transglycosylase
inferred← citeshttps://doi.org/10.1080/08927022.2017.1366656openalex-snapshot
Molecular dynamics simulation of the cyclotron motion of ions in a carbon nanotorus induced by gigahertz rotating electric field
inferred← citeshttps://doi.org/10.1080/14756366.2016.1210136openalex-snapshot
Development of the β-lactam type molecular scaffold for selective estrogen receptor α modulator action: synthesis and cytotoxic effects in MCF-7 breast cancer cells
inferred← citeshttps://doi.org/10.1093/nar/gkv830openalex-snapshot
Competitive interaction of monovalent cations with DNA from 3D-RISM
inferred← citeshttps://doi.org/10.1101/2025.05.13.653794openalex-snapshot
The Kink-Turn Motif: A Powerful Test for Revealing Weaknesses in RNA Force Fields
inferred← citeshttps://doi.org/10.1103/physrevlett.114.258105openalex-snapshot
Generalized Manning Condensation Model Captures the RNA Ion Atmosphere
inferred← citeshttps://doi.org/10.1134/s1068162022040057openalex-snapshot
Investigation of the Interaction between Nilotinib and Alpha-Lactalbumin by Spectroscopic Methods and Docking Studies
inferred← citeshttps://doi.org/10.1146/annurev-physchem-040412-110059openalex-snapshot
Advances in the Determination of Nucleic Acid Conformational Ensembles
inferred← citeshttps://doi.org/10.1261/rna.2543711openalex-snapshot
Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1002099openalex-snapshot
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
inferred← citeshttps://doi.org/10.17760/d20385577openalex-snapshot
SLIC (solvation-layer interface condition)
inferred← citeshttps://doi.org/10.21203/rs.3.rs-7098501/v1openalex-snapshot
Structure-Guided Discovery of 2-Phenylethanol as a Dual-Target Antifungal and Antiviral Agent: Integrative Docking, Dynamics, and ADMET Profiling Against Key Pathogenic Enzymes
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-88sqnopenalex-snapshot
Dissociation Rate Calculation via Constant Force Molecular Simulation
inferred← citeshttps://doi.org/10.26434/chemrxiv-2023-0j7p4openalex-snapshot
Benchmarking RNA all-atom force fields using hairpin motifs
inferred← citeshttps://doi.org/10.3389/fmolb.2022.1027223openalex-snapshot
Refinement of SARS-CoV-2 envelope protein structure in a native-like environment by molecular dynamics simulations
inferred← citeshttps://doi.org/10.3389/fphar.2022.825741openalex-snapshot
Combined Machine Learning and GRID-Independent Molecular Descriptor (GRIND) Models to Probe the Activity Profiles of 5-Lipoxygenase Activating Protein Inhibitors
inferred← citeshttps://doi.org/10.3390/ijms19113405openalex-snapshot
Enriched Conformational Sampling of DNA and Proteins with a Hybrid Hamiltonian Derived from the Protein Data Bank
inferred← citeshttps://doi.org/10.3390/ijms20143385openalex-snapshot
Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon
inferred← citeshttps://doi.org/10.3390/ijms23063337openalex-snapshot
A Study on the Effect of the Substituent against PAK4 Inhibition Using In Silico Methods
inferred← citeshttps://doi.org/10.3390/ijms27125246openalex-snapshot
Peculiarities of the Interaction of the Bacteriolytic Protease Blp from Lysobacter capsici XL1 with the Cell Wall of Staphylococcus aureus 209P
inferred← citeshttps://doi.org/10.3923/pjbs.2013.1836.1848openalex-snapshot
Screening of Commercial Cyclic Peptides as Inhibitor Envelope Protein Dengue Virus (DENV) Through Molecular Docking and Molecular Dynamics
inferred← citeshttps://doi.org/10.64898/2026.05.07.721674openalex-snapshot
The turn less taken: Investigating patterns in β -turn dynamics using large-scale molecular dynamics data
inferred← citeshttps://doi.org/10.70675/92fe029bzf85az4980z98e9z5928ec9bcf70openalex-snapshot
Nanofluidics : a theoretical and numerical investigation of fluid transport in nanochannels
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