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Relative binding free energy calculations in drug discovery: recent advances and practical considerations
Accurate in silico prediction of protein–ligand binding affinities has been a primary objective
of structure-based drug design for decades due to the putative value it would bring to the …
of structure-based drug design for decades due to the putative value it would bring to the …
Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states
The quantum nature of electrons and nuclei is manifested in countless biological events
including the rearrangements of electrons in biochemical reactions, electron and proton …
including the rearrangements of electrons in biochemical reactions, electron and proton …
Three-dimensional convolutional neural networks and a cross-docked data set for structure-based drug design
One of the main challenges in drug discovery is predicting protein–ligand binding affinity.
Recently, machine learning approaches have made substantial progress on this task …
Recently, machine learning approaches have made substantial progress on this task …
CHARMM: the biomolecular simulation program
Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and
widely used molecular simulation program. It has been developed over the last three …
widely used molecular simulation program. It has been developed over the last three …
Docking and scoring in virtual screening for drug discovery: methods and applications
Computational approaches that'dock'small molecules into the structures of macromolecular
targets and'score'their potential complementarity to binding sites are widely used in hit …
targets and'score'their potential complementarity to binding sites are widely used in hit …
Molecular dynamics simulations of biomolecules
Molecular dynamics simulations are important tools for understanding the physical basis of
the structure and function of biological macromolecules. The early view of proteins as …
the structure and function of biological macromolecules. The early view of proteins as …
The many roles of computation in drug discovery
The Many Roles of Computation in Drug Discovery | Science Skip to main content news
careers commentary Journals Science Log in Become A Member journal-menu-img science …
careers commentary Journals Science Log in Become A Member journal-menu-img science …
Molecular dynamics: survey of methods for simulating the activity of proteins
The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …
Hot spots—A review of the protein–protein interface determinant amino‐acid residues
Proteins tendency to bind to one another in a highly specific manner forming stable
complexes is fundamental to all biological processes. A better understanding of complex …
complexes is fundamental to all biological processes. A better understanding of complex …