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Electrostatic interactions in protein structure, folding, binding, and condensation
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
specific electrostatic interactions, impart important properties to proteins. Modulation of the …
How water's properties are encoded in its molecular structure and energies
How are water's material properties encoded within the structure of the water molecule? This
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
is pertinent to understanding Earth's living systems, its materials, its geochemistry and …
FreeSolv: a database of experimental and calculated hydration free energies, with input files
This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …
energies for small neutral molecules in water, along with molecular structures, input files …
Water models for biomolecular simulations
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …
function rely heavily on a variety of methods—water models—to approximate the influence …
Super-resolution in solution X-ray scattering and its applications to structural systems biology
Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural
characterizations of biological macromolecular complexes in solution. Here, we present a …
characterizations of biological macromolecular complexes in solution. Here, we present a …
Structural and dynamic characterizations highlight the deleterious role of SULT1A1 R213H polymorphism in substrate binding
Sulfotransferase 1A1 (SULT1A1) is responsible for catalyzing various types of endogenous
and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 …
and exogenous compounds. Accumulating data indicates that the polymorphism rs9282861 …
[HTML][HTML] Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation
Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG)
models for simulations at extended length and time scales but are often limited by a …
models for simulations at extended length and time scales but are often limited by a …
Testing inhomogeneous solvation theory in structure-based ligand discovery
Binding-site water is often displaced upon ligand recognition, but is commonly neglected in
structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become …
structure-based ligand discovery. Inhomogeneous solvation theory (IST) has become …
A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration
We present a simple optimization strategy for incorporating experimental dielectric response
information on neat liquids in classical molecular models of alcohol. Using this strategy, we …
information on neat liquids in classical molecular models of alcohol. Using this strategy, we …
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains
The current practical “workhorses” of the atomistic implicit solvation─ the Poisson–
Boltzmann (PB) and generalized Born (GB) models─ face fundamental accuracy limitations …
Boltzmann (PB) and generalized Born (GB) models─ face fundamental accuracy limitations …