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How water's properties are encoded in its molecular structure and energies
E Brini, CJ Fennell, M Fernandez-Serra… - Chemical …, 2017 - ACS Publications
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 …
Practical aspects of free-energy calculations: a review
N Hansen, WF Van Gunsteren - Journal of chemical theory and …, 2014 - ACS Publications
Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …
nowadays used in a wide range of research areas including solvation thermodynamics …
FreeSolv: a database of experimental and calculated hydration free energies, with input files
DL Mobley, JP Guthrie - Journal of computer-aided molecular design, 2014 - Springer
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
AV Onufriev, S Izadi - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
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 …
Adaptive supramolecular nanomaterials based on strong noncovalent interactions
B Rybtchinski - ACS nano, 2011 - ACS Publications
Noncovalent systems are adaptive and allow facile processing and recycling. Can they be at
the same time robust? How can one rationally design such systems? Can they compete with …
the same time robust? How can one rationally design such systems? Can they compete with …
Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
Y Cao, L Li - Bioinformatics, 2014 - academic.oup.com
Motivation: Hydrophobic effect plays a pivotal role in most protein–ligand binding. State-of-
the-art protein–ligand scoring methods usually treat hydrophobic free energy as surface …
the-art protein–ligand scoring methods usually treat hydrophobic free energy as surface …
A cavity corrected 3D-RISM functional for accurate solvation free energies
JF Truchon, BM Pettitt, P Labute - Journal of Chemical Theory and …, 2014 - ACS Publications
We show that an Ng bridge function modified version of the three-dimensional reference
interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict …
interaction site model (3D-RISM-NgB) solvation free energy method can accurately predict …
[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 …
A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration
CJ Fennell, KL Wymer, DL Mobley - The Journal of Physical …, 2014 - ACS Publications
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
IS Tolokh, DE Folescu, AV Onufriev - The Journal of Physical …, 2024 - ACS Publications
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 …