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Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials?
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Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in Chemistry
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Synthesis and Encapsulation Behavior of New Redox‐Active Dimeric Assemblies
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Solvent effects on protein association and protein folding
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Representation of the molecular electrostatic potential by a net atomic charge model
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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An all atom force field for simulations of proteins and nucleic acids
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A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
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How transferable are hydrogen parameters in molecular mechanics calculations?
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Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules
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Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup
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A molecular mechanical model that reproduces the relative energies for chair and twist‐boat conformations of 1,3‐dioxanes
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Principles of protein folding — A perspective from simple exact models
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Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
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Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
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Free energy simulations: The meaning of the individual contributions from a component analysis
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LINUS: A hierarchic procedure to predict the fold of a protein
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Decomposition of the Free Energy of a System in Terms of Specific Interactions
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Observation of theA-DNA toB-DNA Transition During Unrestrained Molecular Dynamics in Aqueous Solution
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Solvent Effects and Chemical Reactivity
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Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results
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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
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Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
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Ligand-receptor interactions
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History of Intermolecular Forces
inferredcites →https://doi.org/10.1016/c2013-0-02436-xopenalex-snapshot
Theory of Intermolecular Forces
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Monte Carlo simulations yield absolute free energies of binding for guanine—cytosine and adenine—uracil base pairs in chloroform
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Structural and Dynamic Characterization of the Heterodimeric and Homodimeric Complexes of Distamycin and 1-Methylimidazole-2-carboxamide-netropsin Bound to the Minor Groove of DNA
inferredcites →https://doi.org/10.1021/bi00238a003openalex-snapshot
Computer simulation and analysis of the reaction pathway of triosephosphate isomerase
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Free energy calculations: Applications to chemical and biochemical phenomena
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Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N-Methylacetamide
inferredcites →https://doi.org/10.1021/j100025a006openalex-snapshot
Molecular Dynamics and Free Energy Perturbation Study of Spherand Complexation with Metal Ions Employing Additive and Nonadditive Force Fields
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Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential
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Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials
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Direct Measure of Hydrophilic Interaction
inferredcites →https://doi.org/10.1021/j100142a004openalex-snapshot
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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Free energy calculations on the relative solvation free energies of benzene, anisole, and 1,2,3-trimethoxybenzene: theoretical and experimental analysis of aromatic methoxy solvation
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Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions
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The missing term in effective pair potentials
inferredcites →https://doi.org/10.1021/j100494a019openalex-snapshot
Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid
inferredcites →https://doi.org/10.1021/j150653a049openalex-snapshot
Enthalpies, free energies, and entropies of transfer of phenols from nonpolar solvents to water
inferredcites →https://doi.org/10.1021/ja00001a043openalex-snapshot
Differential binding energy: a detailed evaluation of the influence of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorus-containing inhibitors
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Solvent effects on a Diels-Alder reaction from computer simulations
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Catalytic pathway of serine proteases: classical and quantum mechanical calculations
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Simulation of the solvation free energies for methane, ethane, and propane and corresponding amino acid dipeptides: a critical test of the bond-PMF correction, a new set of hydrocarbon parameters, and the gas phase-water hydrophobicity scale
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Atomic charges for variable molecular conformations
inferredcites →https://doi.org/10.1021/ja00053a046openalex-snapshot
Effects of hydration on the Claisen rearrangement of allyl vinyl ether from computer simulations
inferredcites →https://doi.org/10.1021/ja00081a034openalex-snapshot
Molecular dynamics and free energy calculations on the peculiar bimodal alkali ion selectivity of an 8-subunit cavitand
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Free Energy Perturbation Calculations of the Relative Binding Affinities of an 8-Subunit Cavitand for Alkali Ions in Methanol
inferredcites →https://doi.org/10.1021/ja00102a056openalex-snapshot
Geminal Dialkyl Substitution, Intramolecular Reactions, and Enzyme Efficiency
inferredcites →https://doi.org/10.1021/ja00105a060openalex-snapshot
Accurate Solvation Free Energies of Acetate and Methylammonium Ions Calculated with a Polarizable Water Model
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Quantitation and Nature of the Macrocyclic Effect: K+ Complexation with 18-Crown-6 and Pentaglyme
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Cation-.pi. Interactions: Nonadditive Effects Are Critical in Their Accurate Representation
inferredcites →https://doi.org/10.1021/ja00119a045openalex-snapshot
Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/ja00124a015openalex-snapshot
Investigation of Structure, Dynamics, and Solvation in 1-Octanol and Its Water-Saturated Solution: Molecular Dynamics and Free-Energy Perturbation Studies
inferredcites →https://doi.org/10.1021/ja00127a019openalex-snapshot
Solvation Free Energies of Amides and Amines: Disagreement between Free Energy Calculations and Experiment
inferredcites →https://doi.org/10.1021/ja00132a022openalex-snapshot
Insight into the specificity of thymidylate synthase from molecular dynamics and free energy perturbation calculations
inferredcites →https://doi.org/10.1021/ja00136a020openalex-snapshot
A Smart Monte Carlo Technique for Free Energy Simulations of Multiconformational Molecules. Direct Calculations of the Conformational Populations of Organic Molecules
inferredcites →https://doi.org/10.1021/ja00144a011openalex-snapshot
Do Enzymes Stabilize Transition States by Electrostatic Interactions or pKa Balance: The Case of Triose Phosphate Isomerase (TIM)?
inferredcites →https://doi.org/10.1021/ja00153a017openalex-snapshot
An all-atom empirical energy function for the simulation of nucleic acids
inferredcites →https://doi.org/10.1021/ja00197a022openalex-snapshot
Free energy perturbation simulations of the inhibition of thermolysin: prediction of the free energy of binding of a new inhibitor
inferredcites →https://doi.org/10.1021/ja00205a003openalex-snapshot
Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons
inferredcites →https://doi.org/10.1021/ja00214a001openalex-snapshot
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot
A new force field for molecular mechanical simulation of nucleic acids and proteins
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Theoretical studies of basicity. Proton affinities, lithium(1+) ion affinities, and hydrogen-bond affinities of some simple bases
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Theoretical study of the [chlorine] (Cl2)2 dimer
inferredcites →https://doi.org/10.1021/jo00071a040openalex-snapshot
Chair and twist-boat conformations of 1,3-dioxanes: limitations of molecular mechanics force fields
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Elucidating the Origin of Conformational Energy Differences in Substituted 1,3-Dioxanes: A Combined Theoretical and Experimental Study
inferredcites →https://doi.org/10.1021/jp950840dopenalex-snapshot
Are There Water-Bridge-Induced Hydrophilic Interactions?
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Investigating the Anomalous Solvation Free Energies of Amines with a Polarizable Potential
inferredcites →https://doi.org/10.1021/jp960256kopenalex-snapshot
Application of Free Energy Perturbation Calculations to the “Tennis Ball” Dimer: Why Is CF4 Not Encapsulated by This Host?
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Thermodynamics of cavity formation in water. A molecular dynamics study
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High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
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Statistical Mechanics of Fluid Mixtures
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Comparison of simple potential functions for simulating liquid water
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Monte Carlo simulation of differences in free energies of hydration
inferredcites →https://doi.org/10.1063/1.454895openalex-snapshot
Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
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Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
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Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase.
inferredcites →https://doi.org/10.1073/pnas.90.18.8402openalex-snapshot
What determines the strength of noncovalent association of ligands to proteins in aqueous solution?
inferredcites →https://doi.org/10.1073/pnas.91.16.7673openalex-snapshot
Relative binding affinities of distamycin and its analog to d(CGCAAGTTGGC).d(GCCAACTTGCG): comparison of simulation results with experiment.
inferredcites →https://doi.org/10.1073/pnas.91.18.8715openalex-snapshot
Atomic-level accuracy in simulations of large protein crystals.
inferredcites →https://doi.org/10.1073/pnas.92.5.1754openalex-snapshot
Site-directed mutagenesis studies of the high-affinity streptavidin-biotin complex: contributions of tryptophan residues 79, 108, and 120.
inferredcites →https://doi.org/10.1073/pnas.92.8.3190openalex-snapshot
Computer determination of peptide conformations in water: different roads to structure.
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Decisions in Force Field Development: An Alternative to Those Described by Rotermanet al.
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Decisions in Force Field Development Reply to Kollman and Dill
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Free energy calculations of the mutation of Ile96 → Ala in barnase: contributions to the difference in stability
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A Priori Evaluation of Aqueous Polarization Effects through Monte Carlo QM-MM Simulations
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Structural Origins of High-Affinity Biotin Binding to Streptavidin
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Encapsulation of Methane and Other Small Molecules in a Self-Assembling Superstructure
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Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data
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Some practical aspects of free energy calculations from molecular dynamics simulation
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Explicit and implicit water simulations of a ?-hairpin peptide
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AMBER : A Program for Simulation of Biological and Organic Molecules
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Protein flexibility: its role in structure and mechanism revealed by molecular simulations
inferred← citeshttps://doi.org/10.1007/s00214-005-0073-1openalex-snapshot
Direct calculation of Henry’s law constants from Gibbs ensemble Monte Carlo simulations: nitrogen, oxygen, carbon dioxide and methane in ethanol
inferred← citeshttps://doi.org/10.1007/s00726-012-1276-0openalex-snapshot
Design of a highly potent inhibitory peptide acting as a competitive inhibitor of HMG-CoA reductase
inferred← citeshttps://doi.org/10.1007/s10311-006-0065-yopenalex-snapshot
The estrogen receptor and polyphenols: molecular simulation studies of their interactions, a review
inferred← citeshttps://doi.org/10.1007/s10600-005-0176-xopenalex-snapshot
Structure—Activity Relationships of the Peptide Ile-Ala-Val-Pro and Its Derivatives Revealed Using the Semi-Empirical AM1 Method
inferred← citeshttps://doi.org/10.1007/s10600-012-0399-6openalex-snapshot
Conformational analysis of yvae peptide derivatives
inferred← citeshttps://doi.org/10.1007/s10723-015-9353-8openalex-snapshot
Scaling Ab Initio Predictions of 3D Protein Structures in Microsoft Azure Cloud
inferred← citeshttps://doi.org/10.1007/s10822-016-9971-7openalex-snapshot
Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge
inferred← citeshttps://doi.org/10.1007/s10822-020-00295-0openalex-snapshot
Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge
inferred← citeshttps://doi.org/10.1007/s10989-021-10221-zopenalex-snapshot
Design of Tripeptides as a Competitive Inhibitor for HMG-CoA Reductase
inferred← citeshttps://doi.org/10.1007/s10989-022-10455-5openalex-snapshot
Design of Tetrapeptides as a Competitive Inhibitor for HMG-CoA Reductase and Modeling Recognized Sequence as a β-Turn Structure
inferred← citeshttps://doi.org/10.1007/s11094-008-0107-9openalex-snapshot
Studies of the interaction between the hepatoprotective detoxifying activity of chemical compounds and their molecular structure using quantum chemical descriptors
inferred← citeshttps://doi.org/10.1007/s11433-018-9313-1openalex-snapshot
Enhanced sampling based on slow variables of trajectory mapping
inferred← citeshttps://doi.org/10.1007/s12257-026-00319-wopenalex-snapshot
Macroscopic joint-based analysis of protein ensembles generated by molecular dynamics simulation
inferred← citeshttps://doi.org/10.1007/s13361-014-0990-0openalex-snapshot
Combining Ion Mobility Spectrometry with Hydrogen-Deuterium Exchange and Top-Down MS for Peptide Ion Structure Analysis
inferred← citeshttps://doi.org/10.1007/s13738-026-03518-7openalex-snapshot
Synthesis and characterization of palladium complexes derived from 4-aminoantipyridine-based Schiff base: evaluation of antioxidant, antibacterial, and anticancer properties
inferred← citeshttps://doi.org/10.1016/j.abb.2014.01.002openalex-snapshot
Simulations of monomeric amyloid β-peptide (1–40) with varying solution conditions and oxidation state of Met35: Implications for aggregation
inferred← citeshttps://doi.org/10.1016/j.bbrc.2014.12.084openalex-snapshot
Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand
inferred← citeshttps://doi.org/10.1016/j.biochi.2006.06.011openalex-snapshot
Actinide speciation in relation to biological processes
inferred← citeshttps://doi.org/10.1016/j.bmc.2004.03.024openalex-snapshot
S1 subsite in snake venom thrombin-like enzymes: can S1 subsite lipophilicity be used to sort binding affinities of trypsin-like enzymes to small-molecule inhibitors?
inferred← citeshttps://doi.org/10.1016/j.bmc.2007.10.064openalex-snapshot
Binding effect and design of a competitive inhibitory peptide for HMG-CoA reductase through modeling of an active peptide backbone
inferred← citeshttps://doi.org/10.1016/j.bmc.2010.04.090openalex-snapshot
Peptide fragmentation as an approach in modeling of an active peptide and designing a competitive inhibitory peptide for HMG-CoA reductase
inferred← citeshttps://doi.org/10.1016/j.bpj.2014.02.009openalex-snapshot
Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles
inferred← citeshttps://doi.org/10.1016/j.bpj.2014.06.037openalex-snapshot
Complex Pathways in Folding of Protein G Explored by Simulation and Experiment
inferred← citeshttps://doi.org/10.1016/j.bpj.2017.07.009openalex-snapshot
Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models
inferred← citeshttps://doi.org/10.1016/j.cbpa.2016.08.004openalex-snapshot
Computational methods to design cyclic peptides
inferred← citeshttps://doi.org/10.1016/j.chemphys.2004.03.018openalex-snapshot
Influence of the solvation model and the solvent on the gauche-trans equilibrium of 1,1,2-trichloroethane
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.10.011openalex-snapshot
Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.05.044openalex-snapshot
CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform
inferred← citeshttps://doi.org/10.1016/j.fluid.2009.11.022openalex-snapshot
Molecular simulation of the hydration Gibbs energy of barbiturates
inferred← citeshttps://doi.org/10.1016/j.fluid.2010.02.041openalex-snapshot
Molecular simulation of absolute hydration Gibbs energies of polar compounds
inferred← citeshttps://doi.org/10.1016/j.gca.2006.04.023openalex-snapshot
Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces
inferred← citeshttps://doi.org/10.1016/j.gca.2007.08.030openalex-snapshot
Molecular models of a hydrated calcite mineral surface
inferred← citeshttps://doi.org/10.1016/j.jmb.2007.06.002openalex-snapshot
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
inferred← citeshttps://doi.org/10.1016/j.matpr.2021.03.024openalex-snapshot
Molecular modeling and molecular docking studies on the derivatives of 1,4-dihydropyridine towards Cytochrome P450 for structure based drug design
inferred← citeshttps://doi.org/10.1016/j.microc.2024.112016openalex-snapshot
Constructing a hollow-cage nanoenzyme sensor for dual detection of thiamine hydrochloride and hydrogen peroxide based on dielectric barrier discharge microplasma etching
inferred← citeshttps://doi.org/10.1016/j.molliq.2022.120260openalex-snapshot
Adsorption and accumulation mechanism of N2 on groove-type rough surfaces: A molecular simulation study
inferred← citeshttps://doi.org/10.1016/j.molstruc.2022.132909openalex-snapshot
Design of competitive inhibitory peptides for HMG-CoA reductase and modeling structural preference for short linear peptides
inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.136248openalex-snapshot
Modeling of hydrophobic tetrapeptides as a competitive inhibitor for HMG-CoA reductase
inferred← citeshttps://doi.org/10.1016/j.sbi.2012.11.002openalex-snapshot
To milliseconds and beyond: challenges in the simulation of protein folding
inferred← citeshttps://doi.org/10.1016/j.solidstatesciences.2006.02.016openalex-snapshot
Intermolecular potential for methane in zeolite A and Y: Adsorption isotherm and related properties
inferred← citeshttps://doi.org/10.1016/s0005-2736(00)00174-7openalex-snapshot
Molecular dynamics study on lipid A from Escherichia coli: insights into its mechanism of biological action
inferred← citeshttps://doi.org/10.1016/s0006-3495(01)75738-4openalex-snapshot
Free Energy Decomposition of Protein-Protein Interactions
inferred← citeshttps://doi.org/10.1016/s0006-3495(98)77501-0openalex-snapshot
Structural Equilibrium of DNA Represented with Different Force Fields
inferred← citeshttps://doi.org/10.1016/s0006-3495(99)76877-3openalex-snapshot
Change in Conformation by DNA-Peptide Association: Molecular Dynamics of the Hin-Recombinase– hixL Complex
inferred← citeshttps://doi.org/10.1016/s0021-9673(02)00171-1openalex-snapshot
Temperature effects on the retention of n-alkanes and arenes in helium–squalane gas–liquid chromatography
inferred← citeshttps://doi.org/10.1016/s0065-3233(03)66001-8openalex-snapshot
Assessment of the Role of Computations in Structural Biology
inferred← citeshttps://doi.org/10.1016/s0076-6879(01)40428-9openalex-snapshot
Molecular modeling of drug-DNA complexes: An update
inferred← citeshttps://doi.org/10.1016/s0166-1280(98)00184-5openalex-snapshot
Modelling of the CCK antagonist activity of benzodiazepines on cerebral receptors
inferred← citeshttps://doi.org/10.1016/s0166-1280(99)00314-0openalex-snapshot
Ewald summation and multiple time step methods for molecular dynamics simulation of biological molecules
inferred← citeshttps://doi.org/10.1016/s0167-8191(01)00079-5openalex-snapshot
Parallel molecular dynamics simulation of a protein
inferred← citeshttps://doi.org/10.1016/s0169-7439(98)00033-1openalex-snapshot
Modelling of the CCK antagonist activity of benzodiazepines on gastrin receptors
inferred← citeshttps://doi.org/10.1016/s0959-440x(98)80044-4openalex-snapshot
Simulations of the molecular dynamics of nucleic acids
inferred← citeshttps://doi.org/10.1016/s0959-440x(98)80046-8openalex-snapshot
Theory of biomolecular recognition
inferred← citeshttps://doi.org/10.1016/s0968-0896(01)00408-4openalex-snapshot
Binding of 1-Benzopyran-4-one Derivatives to Aldose Reductase: A Free Energy Perturbation Study
inferred← citeshttps://doi.org/10.1016/s1093-3263(01)00108-5openalex-snapshot
Fast prediction of hydration free energies from molecular interaction fields
inferred← citeshttps://doi.org/10.1016/s1367-5931(97)80038-5openalex-snapshot
Computational approaches to molecular recognition
inferred← citeshttps://doi.org/10.1016/s1380-7323(99)80086-7openalex-snapshot
Application of Reduced Models to Protein Structure Prediction
inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c01087openalex-snapshot
Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.1021/acs.jced.6c00404openalex-snapshot
Thermophysical Properties of [EMIM][BF4] and [EMIM][EtSO4] Mixtures with Molecular Solvents from a Charge-Transfer-Informed Force Field
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00651openalex-snapshot
Property Map Collective Variable as a Useful Tool for a Force Field Correction
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02787openalex-snapshot
Osimertinib’s Proton-Catalyzed, Pseudoconcerted EGFR Inhibition Guides Next-Generation Inhibitor Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00132openalex-snapshot
Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00375openalex-snapshot
Exhaustive Exploration of the Conformational Landscape of Small Cyclic Peptides Using a Robotics Approach
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00028openalex-snapshot
Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of PHF6 Peptide of Tau Protein
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00088openalex-snapshot
Kinetic Network Models of Tryptophan Mutations in β-Hairpins Reveal the Importance of Non-Native Interactions
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b00737openalex-snapshot
FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs
inferred← citeshttps://doi.org/10.1021/acs.jctc.5b01211openalex-snapshot
An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides
inferred← citeshttps://doi.org/10.1021/acs.jctc.5c01123openalex-snapshot
Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00626openalex-snapshot
OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics
inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01107openalex-snapshot
Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ 16–22 Dimer
inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c08183openalex-snapshot
Knowledge-Based Atomic Polarizabilities Used to Model Circular Dichroism Spectra of Proteins
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c05645openalex-snapshot
Protein–Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c06231openalex-snapshot
Recent Advances in Simulation Software and Force Fields: Their Importance in Theoretical and Computational Chemistry and Biophysics
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b00087openalex-snapshot
Altruistic Metadynamics: Multisystem Biased Simulation
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b05611openalex-snapshot
Kirkwood–Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies
inferred← citeshttps://doi.org/10.1021/acs.jpcb.6b12888openalex-snapshot
Impact of Mutations at C-Terminus on Structures and Dynamics of Aβ40 and Aβ42: A Molecular Simulation Study
inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b11871openalex-snapshot
Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.4c00859openalex-snapshot
Predictive Model Building for Aggregation Kinetics Based on Molecular Dynamics Simulations of an Antibody Fragment
inferred← citeshttps://doi.org/10.1021/ar970146bopenalex-snapshot
From Knowledge-Based Potentials to Combinatorial Lead Design in Silico
inferred← citeshttps://doi.org/10.1021/bk-2010-1052.ch008openalex-snapshot
Molecular Simulation Methods
inferred← citeshttps://doi.org/10.1021/ci500102yopenalex-snapshot
Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models
inferred← citeshttps://doi.org/10.1021/ci500768uopenalex-snapshot
Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides
inferred← citeshttps://doi.org/10.1021/ci980154mopenalex-snapshot
Prediction of Solvation Free Energies of Small Organic Molecules: Additive-Constitutive Models Based on Molecular Fingerprints and Atomic Constants
inferred← citeshttps://doi.org/10.1021/cr500628bopenalex-snapshot
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
inferred← citeshttps://doi.org/10.1021/cr960370zopenalex-snapshot
Molecular Recognition of Protein−Ligand Complexes: Applications to Drug Design
inferred← citeshttps://doi.org/10.1021/cr990052aopenalex-snapshot
Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems
inferred← citeshttps://doi.org/10.1021/ct2007814openalex-snapshot
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
inferred← citeshttps://doi.org/10.1021/ct4007162openalex-snapshot
RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins
inferred← citeshttps://doi.org/10.1021/ct800468hopenalex-snapshot
Dynamically Polarizable Water Potential Based on Multipole Moments Trained by Machine Learning
inferred← citeshttps://doi.org/10.1021/ct900214yopenalex-snapshot
1-Octanol/Water Partition Coefficients of n-Alkanes from Molecular Simulations of Absolute Solvation Free Energies
inferred← citeshttps://doi.org/10.1021/ic020040zopenalex-snapshot
Deprotonation of Zinc(II)−Water and Zinc(II)−Alcohol and Nucleophilicity of the Resultant Zinc(II) Hydroxide and Zinc(II) Alkoxide in Double-Functionalized Complexes: Theoretical Studies on Models for Hydrolytic Zinc Enzymes
inferred← citeshttps://doi.org/10.1021/ja037274hopenalex-snapshot
Adsorption Isotherm and Other Properties of Methane in Zeolite A from an Intermolecular Potential Derived from ab Initio Calculations
inferred← citeshttps://doi.org/10.1021/ja970601zopenalex-snapshot
Molecular Dynamics Simulations of the d(T·A·T) Triple Helix
inferred← citeshttps://doi.org/10.1021/ja972457nopenalex-snapshot
Use of Locally Enhanced Sampling in Free Energy Calculations: Testing and Application to the α → β Anomerization of Glucose
inferred← citeshttps://doi.org/10.1021/ja9837349openalex-snapshot
Theoretical Study of Base-Catalyzed Amide Hydrolysis: Gas- and Aqueous-Phase Hydrolysis of Formamide
inferred← citeshttps://doi.org/10.1021/je100535popenalex-snapshot
Quantitative Structure−Property Relationship (QSPR) Prediction of Solvation Gibbs Energy of Bifunctional Compounds by Recursive Neural Networks
inferred← citeshttps://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferred← citeshttps://doi.org/10.1021/jm0105833openalex-snapshot
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferred← citeshttps://doi.org/10.1021/jm030161oopenalex-snapshot
Multiple Active Site Corrections for Docking and Virtual Screening
inferred← citeshttps://doi.org/10.1021/jm9910775openalex-snapshot
Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins
inferred← citeshttps://doi.org/10.1021/jo0355956openalex-snapshot
Impact of the Solvent on the Conformational Isomerism of Calix[4]arenes: A Study Based on Continuum Solvation Models
inferred← citeshttps://doi.org/10.1021/jo9907437openalex-snapshot
Selective Anion Complexation by a Calix[4]pyrrole Investigated by Monte Carlo Simulations
inferred← citeshttps://doi.org/10.1021/jp0041252openalex-snapshot
Free Energy Simulations of d -Xylose in Water and Methyl d -Xylopyranoside in Methanol
inferred← citeshttps://doi.org/10.1021/jp013773yopenalex-snapshot
Molecular Dynamics Simulation with the Charge Response Kernel: Vibrational Spectra of Liquid Water and N-Methylacetamide in Aqueous Solution
inferred← citeshttps://doi.org/10.1021/jp0217839openalex-snapshot
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
inferred← citeshttps://doi.org/10.1021/jp0373797openalex-snapshot
Accurate Calculations of Ligand Binding Free Energies: Chiral Separation with Enantioselective Receptors
inferred← citeshttps://doi.org/10.1021/jp037821lopenalex-snapshot
First-Shell Solvation of Ion Pairs: Correction of Systematic Errors in Implicit Solvent Models
inferred← citeshttps://doi.org/10.1021/jp0735987openalex-snapshot
Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations
inferred← citeshttps://doi.org/10.1021/jp2097263openalex-snapshot
Coarse-Grained Modeling of Simple Molecules at Different Resolutions in the Absence of Good Sampling
inferred← citeshttps://doi.org/10.1021/jp401911hopenalex-snapshot
Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics
inferred← citeshttps://doi.org/10.1021/jp403802copenalex-snapshot
Systematic Improvement of a Classical Molecular Model of Water
inferred← citeshttps://doi.org/10.1021/jp4105823openalex-snapshot
Extensive Conformational Heterogeneity within Protein Cores
inferred← citeshttps://doi.org/10.1021/jp500193wopenalex-snapshot
How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study
inferred← citeshttps://doi.org/10.1021/jp901540topenalex-snapshot
Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides
inferred← citeshttps://doi.org/10.1021/jp972593eopenalex-snapshot
Investigation of the Anomalous Solvation Free Energies of Amides and Amines: FEP Calculations in Cyclohexane and PS-GVB Calculations on Amide−Water Complexes
inferred← citeshttps://doi.org/10.1021/jp9801065openalex-snapshot
Thermodynamic Properties of the Williams, OPLS-AA, and MMFF94 All-Atom Force Fields for Normal Alkanes
inferred← citeshttps://doi.org/10.1021/jp984215vopenalex-snapshot
Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations
inferred← citeshttps://doi.org/10.1021/jp984271wopenalex-snapshot
Prediction of Aqueous Solvation Free Energies from Properties of Solute Molecular Surface Electrostatic Potentials
inferred← citeshttps://doi.org/10.1021/jp990822mopenalex-snapshot
Transferable Potentials for Phase Equilibria. 3. Explicit-Hydrogen Description of Normal Alkanes
inferred← citeshttps://doi.org/10.1021/jp994359popenalex-snapshot
Influence of Protonation on Internal Rotation of Dimethyl Ether
inferred← citeshttps://doi.org/10.1023/a:1008781006867openalex-snapshot
Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function
inferred← citeshttps://doi.org/10.1023/a:1017037831628openalex-snapshot
3D QSAR: current state, scope, and limitations
inferred← citeshttps://doi.org/10.1023/a:1027268223451openalex-snapshot
Molecular dynamics simulations: a tool for drug design
inferred← citeshttps://doi.org/10.1038/s41467-024-46446-xopenalex-snapshot
Hairpin trimer transition state of amyloid fibril
inferred← citeshttps://doi.org/10.1038/srep44116openalex-snapshot
Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY
inferred← citeshttps://doi.org/10.1039/a900442dopenalex-snapshot
About the TATB hypothesis: solvation of the Asϕ4+ and Bϕ4- ions and their tetrahedral and spherical analogues in aqueous/nonaqueous solvents and at a water–chloroform interface
inferred← citeshttps://doi.org/10.1039/b100159kopenalex-snapshot
Elucidation of the mechanism of carboxy ester cleavage promoted by a Cu(ii) alkoxide complex of a tripodal ligand (N3OX)
inferred← citeshttps://doi.org/10.1039/b306954kopenalex-snapshot
Continuum solvation models: Dissecting the free energy of solvation
inferred← citeshttps://doi.org/10.1039/b905748jopenalex-snapshot
Optimal construction of a fast and accurate polarisable water potential based on multipole moments trained by machine learning
inferred← citeshttps://doi.org/10.1039/c0cp02037kopenalex-snapshot
Conjugation of organic-metallic hybrid polymers and calf-thymus DNA
inferred← citeshttps://doi.org/10.1039/c3cp55251aopenalex-snapshot
A hybrid MD-kMC algorithm for folding proteins in explicit solvent
inferred← citeshttps://doi.org/10.1039/c4cp04580gopenalex-snapshot
Toward structure prediction of cyclic peptides
inferred← citeshttps://doi.org/10.1039/c5cp01939gopenalex-snapshot
Impacts of retinal polyene (de)methylation on the photoisomerization mechanism and photon energy storage of rhodopsin
inferred← citeshttps://doi.org/10.1039/c5cp03479eopenalex-snapshot
A polarizable coarse-grained protein model for dissipative particle dynamics
inferred← citeshttps://doi.org/10.1039/c5cp06867copenalex-snapshot
Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent
inferred← citeshttps://doi.org/10.1039/c6cp05322jopenalex-snapshot
Conformational sampling of metastable states: Tq-REM as a novel replica exchange method
inferred← citeshttps://doi.org/10.1039/c7cp03035eopenalex-snapshot
An adaptive bias – hybrid MD/kMC algorithm for protein folding and aggregation
inferred← citeshttps://doi.org/10.1039/c8ob00534fopenalex-snapshot
Stereodivergent synthesis of 5-aminopipecolic acids and application in the preparation of a cyclic RGD peptidomimetic as a nanomolar α V β 3 integrin ligand
inferred← citeshttps://doi.org/10.1039/d5ob01798jopenalex-snapshot
Sustainable electrochemical synthesis of a new isoxazoline scaffold as turn inducer to build parallel β-hairpins
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