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Molecular dynamics simulations of macromolecular crystals
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Calculation and Measurement of Terahertz Active Normal Modes in Crystalline PETN
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CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields
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Robustness in the fitting of molecular mechanics parameters
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Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics
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Structural heterogeneity in microcrystalline ubiquitin studied by solid‐state NMR
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Molecular dynamics simulation of triclinic lysozyme in a crystal lattice
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Urease activity in the crystalline state
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Comparison of different schemes to treat long‐range electrostatic interactions in molecular dynamics simulations of a protein crystal
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Making optimal use of empirical energy functions: Force‐field parameterization in crystal space
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
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Protein dynamics from X‐ray crystallography: Anisotropic, global motion in diffuse scattering patterns
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Improved side‐chain torsion potentials for the Amber ff99SB protein force field
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Exploration of disorder in protein structures by X‐ray restrained molecular dynamics
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Automatic identification of discrete substates in proteins: Singular value decomposition analysis of time‐averaged crystallographic refinements
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X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation 1 1Edited by R. Huber
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Refinement of Three-dimensional Structures of Proteins and Nucleic Acids
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Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin
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Monte Carlo Modeling of Diffuse Scattering from Single Crystals: The Program ZMC
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Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals
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Time-dependent distance restraints in molecular dynamics simulations
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X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 Å resolution
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An NMR study of the backbone dynamics of staphylococcal nuclease in the crystalline state
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All-atom crystal simulations of DNA and RNA duplexes
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Application of Elastic Network Models to Proteins in the Crystalline State
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Evaluating Elastic Network Models of Crystalline Biological Molecules with Temperature Factors, Correlated Motions, and Diffuse X-Ray Scattering
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Moving in the Right Direction: Protein Vibrations Steering Function
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Terahertz vibrations of crystalline α-D-glucose and the spectral change in mutual transitions between the anhydride and monohydrate
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The molecular conformation of Ibuprofen, C13H18O2, through X-ray diffuse scattering
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NMR studies of dynamic biomolecular conformational ensembles
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Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules
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Effect of Crystal Packing Environment on Conformation of the DNA Duplex
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On the Role of the Crystal Environment in Determining Protein Side-chain Conformations
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Diffuse scattering in protein crystallography
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X-ray Scattering Studies of Protein Structural Dynamics
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Improved Estimation of Density of States for Monte Carlo Sampling via MBAR
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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins
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Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water
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Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1ρ NMR Measurements: Application to Protein Backbone Dynamics Measurements
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Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water
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Biomolecular Simulations under Realistic Macroscopic Salt Conditions
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Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A
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Protein dynamics in solution and in a crystalline environment: a molecular dynamics study
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Protein Conformational Relaxation and Ligand Migration in Myoglobin: A Nanosecond to Millisecond Molecular Movie from Time-Resolved Laue X-ray Diffraction
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Simulations of a Protein Crystal: Explicit Treatment of Crystallization Conditions Links Theory and Experiment in the Streptavidin−Biotin Complex
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Time-Resolved Biochemical Crystallography: A Mechanistic Perspective
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Efficient Free Energy Calculation of Biomolecules from Diffusion-Biased Molecular Dynamics
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Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles
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Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
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Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
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Practical Aspects of Free-Energy Calculations: A Review
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Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
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Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
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Conformational polymorphism. The influence of crystal structure on molecular conformation
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Energy functions for peptides and proteins. II. Amide hydrogen bond and calculation of amide crystal properties
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Protein Structure Determination by High-Resolution Solid-State NMR Spectroscopy: Application to Microcrystalline Ubiquitin
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Quantitative Analysis of Backbone Dynamics in a Crystalline Protein from Nitrogen-15 Spin−Lattice Relaxation
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Conformational Flexibility of a Microcrystalline Globular Protein: Order Parameters by Solid-State NMR Spectroscopy
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Chemical-Shift Anisotropy Measurements of Amide and Carbonyl Resonances in a Microcrystalline Protein with Slow Magic-Angle Spinning NMR Spectroscopy
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Peptide Crystal Simulations Reveal Hidden Dynamics
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New Insights into the Role of Water in Biological Function: Studying Solvated Biomolecules Using Terahertz Absorption Spectroscopy in Conjunction with Molecular Dynamics Simulations
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Anisotropic Collective Motion Contributes to Nuclear Spin Relaxation in Crystalline Proteins
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Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements
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Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models
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Thermodynamic, Diffusional, and Structural Anomalies in Rigid-Body Water Models
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Hydration-Dependent Protein Dynamics Revealed by Molecular Dynamics Simulation of Crystalline Staphylococcal Nuclease
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Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
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Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules
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Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation
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Building Force Fields: An Automatic, Systematic, and Reproducible Approach
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On using time-averaging restraints in molecular dynamics simulation
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Millisecond X-ray diffraction and the first electron density map from Laue photographs of a protein crystal
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The conformation of the DNA double helix in the crystal is dependent on its environment
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De novo protein crystal structure determination from X-ray free-electron laser data
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Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser
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Macromolecular diffractive imaging using imperfect crystals
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X-ray refinement significantly underestimates the level of microscopic heterogeneity in biomolecular crystals
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Observing the overall rocking motion of a protein in a crystal
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Slow conformational exchange and overall rocking motion in ubiquitin protein crystals
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Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity
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Fixed-target protein serial microcrystallography with an x-ray free electron laser
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Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics
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State-resolved THz spectroscopy and dynamics of crystalline peptide–water systems
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Lattice-sum methods for computing electrostatic interactions in molecular simulations
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Flexible simple point-charge water model with improved liquid-state properties
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Water dynamics in small reverse micelles in two solvents: Two-dimensional infrared vibrational echoes with two-dimensional background subtraction
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The nuclear magnetic resonance relaxation data analysis in solids: General R1/R1ρ equations and the model-free approach
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Solvation structures of protons and hydroxide ions in water
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Structural enzymology using X-ray free electron lasers
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Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering
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Measuring and modeling diffuse scattering in protein X-ray crystallography
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Structure of fully protonated proteins by proton-detected magic-angle spinning NMR
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"...the tyranny of the lattice...".
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A sampling problem in molecular dynamics simulations of macromolecules.
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Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease
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Diffuse x-ray scattering and models of disorder
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Lattice and continuum theories of Huang scattering
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Lattice Dynamics of a Protein Crystal
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Screening and optimization of protein crystallization conditions through gradual evaporation using a novel crystallization platform
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A refinement strategy for Monte Carlo modelling of diffuse scattering from molecular crystal systems
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Diffuse scattering study of aspirin forms (I) and (II)
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Polarizable atomic multipole X-ray refinement: application to peptide crystals
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Towards automated crystallographic structure refinement with phenix.refine
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Refinement of Triclinic Hen Egg-White Lysozyme at Atomic Resolution
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Acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals
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Cheetah : software for high-throughput reduction and analysis of serial femtosecond X-ray diffraction data
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Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering
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Multichannel FPGA-Based Data-Acquisition-System for Time-Resolved Synchrotron Radiation Experiments
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Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography
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Inclusion of Thermal Motion in Crystallographic Structures by Restrained Molecular Dynamics
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Direct observation of hierarchical protein dynamics
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Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser
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Biostructural Science Inspired by Next-Generation X-Ray Sources
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MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects
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Computer Simulation Using Particles
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Nuclear Spin Relaxation in Liquids
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Time-resolved protein nanocrystallography using an X-ray free-electron laser
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Evidence of Functional Protein Dynamics from X-Ray Crystallographic Ensembles
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Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations
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Fluctuations and Correlations in Crystalline Protein Dynamics: A Simulation Analysis of Staphylococcal Nuclease
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Hydration Effect on Low-Frequency Protein Dynamics Observed in Simulated Neutron Scattering Spectra
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Modelling dynamics in protein crystal structures by ensemble refinement
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Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis
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Noncovalent Interactions in Solvated Proteins and Protein Crystals Studied with the Fragment Molecular Orbital Method
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01487openalex-snapshot
Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c00566openalex-snapshot
Novel Medicinal Chemistry Strategies Targeting CDK5 for Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jpclett.2c03398openalex-snapshot
Integrated Assessment of the Structure and Dynamics of Solid Proteins
inferred← citeshttps://doi.org/10.1021/acs.nanolett.6c02166openalex-snapshot
In Situ Probing of Early Stage Phase Transformation of KCl in Aqueous Solutions via Liquid-Cell TEM
inferred← citeshttps://doi.org/10.1021/acsomega.5c13251openalex-snapshot
Interactions of Cyclic Peptides Ribifolin and Gramicidin S with Montmorillonite Surface by Molecular Modeling
inferred← citeshttps://doi.org/10.1038/s41467-020-14933-6openalex-snapshot
Diffuse X-ray scattering from correlated motions in a protein crystal
inferred← citeshttps://doi.org/10.1038/s41467-024-47473-4openalex-snapshot
Functional protein dynamics in a crystal
inferred← citeshttps://doi.org/10.1038/s41557-026-02194-7openalex-snapshot
Molecular neighbours reshape protein dynamics
inferred← citeshttps://doi.org/10.1063/4.0000779openalex-snapshot
Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations
inferred← citeshttps://doi.org/10.1080/02331888.2025.2478203openalex-snapshot
GENEOnet: statistical analysis supporting explainability and trustworthiness
inferred← citeshttps://doi.org/10.1101/2022.08.04.502807openalex-snapshot
Torsion angles to map and visualize the conformational space of a protein
inferred← citeshttps://doi.org/10.1101/2023.07.06.548023openalex-snapshot
Functional Protein Dynamics in a Crystal
inferred← citeshttps://doi.org/10.1101/805424openalex-snapshot
Diffuse X-ray Scattering from Correlated Motions in a Protein Crystal
inferred← citeshttps://doi.org/10.1107/s2052252522011198openalex-snapshot
Simulating diffraction photographs based on molecular dynamics trajectories of a protein crystal: a new option to examine structure-solving strategies in protein crystallography
inferred← citeshttps://doi.org/10.1146/annurev-biophys-111622-091155openalex-snapshot
Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics
inferred← citeshttps://doi.org/10.1186/s12906-024-04372-xopenalex-snapshot
Network pharmacology and in vitro experimental verification unveil glycyrrhizin from glycyrrhiza glabra alleviates acute pancreatitis via modulation of MAPK and STAT3 signaling pathways
inferred← citeshttps://doi.org/10.12688/f1000research.25097.1openalex-snapshot
Advances in methods for atomic resolution macromolecular structure determination
inferred← citeshttps://doi.org/10.3389/fchem.2021.738077openalex-snapshot
Hydration and its Hydrogen Bonding State on a Protein Surface in the Crystalline State as Revealed by Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.3389/fimmu.2022.887759openalex-snapshot
Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes
inferred← citeshttps://doi.org/10.3390/en17143591openalex-snapshot
Crystal Structure Prediction and Performance Assessment of Hydrogen Storage Materials: Insights from Computational Materials Science
inferred← citeshttps://doi.org/10.3390/ijms27156553openalex-snapshot
AI-Predicted Model-Guided Rebuilding of the Experimental Structure of Mouse δ-Aminolevulinic Acid Dehydratase
inferred← citeshttps://doi.org/10.6084/m9.figshare.26673564openalex-snapshot
Additional file 1 of Network pharmacology and in vitro experimental verification unveil glycyrrhizin from glycyrrhiza glabra alleviates acute pancreatitis via modulation of MAPK and STAT3 signaling pathways
inferred← citeshttps://doi.org/10.62292/10.62292/njp.v34i2.2025.254openalex-snapshot
Analysis and Exploration of Kronig and Penney Potential Models in Crystal Lattice Structures
inferred← citeshttps://doi.org/10.82153/2me0-hd96openalex-snapshot
Supplying a user-defined bulk solvent map for refinement
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