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From whispering gallery mode resonators to biochemical sensors
Optical biosensors are frontrunners for the rapid and real-time detection of analytes,
particularly for low concentrations. Among them, whispering gallery mode (WGM) resonators …
particularly for low concentrations. Among them, whispering gallery mode (WGM) resonators …
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …
Autodock vina adopts more accurate binding poses but autodock4 forms better binding affinity
The binding pose and affinity between a ligand and enzyme are very important pieces of
information for computer-aided drug design. In the initial stage of a drug discovery project …
information for computer-aided drug design. In the initial stage of a drug discovery project …
New machine learning and physics-based scoring functions for drug discovery
Scoring functions are essential for modern in silico drug discovery. However, the accurate
prediction of binding affinity by scoring functions remains a challenging task. The …
prediction of binding affinity by scoring functions remains a challenging task. The …
g_mmpbsaA GROMACS Tool for High-Throughput MM-PBSA Calculations
Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate
interaction free energies, has been increasingly used in the study of biomolecular …
interaction free energies, has been increasingly used in the study of biomolecular …
Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols …
By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
The Molecular Mechanics/Poisson− Boltzmann Surface Area (MM/PBSA) and the Molecular
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free …
Free energy calculations by the molecular mechanics Poisson− Boltzmann surface area method
N Homeyer, H Gohlke - Molecular informatics, 2012 - Wiley Online Library
Detailed knowledge of how molecules recognize interaction partners and of the
conformational preferences of biomacromolecules is pivotal for understanding biochemical …
conformational preferences of biomacromolecules is pivotal for understanding biochemical …
Using AMBER18 for relative free energy calculations
With renewed interest in free energy methods in contemporary structure-based drug design,
there is a pressing need to validate against multiple targets and force fields to assess the …
there is a pressing need to validate against multiple targets and force fields to assess the …
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
PA Kollman, I Massova, C Reyes, B Kuhn… - Accounts of chemical …, 2000 - ACS Publications
A historical perspective on the application of molecular dynamics (MD) to biological
macromolecules is presented. Recent developments combining state-of-the-art force fields …
macromolecules is presented. Recent developments combining state-of-the-art force fields …