energy perturbation, since its successful implementation requires finding a transformation M for which the secondary ensemble A ′ comes reasonably close to “hitting” the target ensemble, B. Several potential extensions of targeted free energy perturbation, to be developed more ...
EED and valemetostat. Binding affinities predicted using the free-energy perturbation algorithm showed that the EZH2–EED interface provides a favourable platform for valemetostat. Substitution of the amino acids would significantly
On the drug-like molecules in the HiPen dataset, the method accelerates the calculation of the free energy difference of switching from an FF to a DFTB3 potential by three orders of magnitude compared to standard free energy perturbation and by a factor of eight compared to previously published...
Recently, precise computational approaches including free energy calculation methods like molecular mechanics/Poisson–Boltzmann surface area (MM/PB(GB)SA),227,228 free energy perturbation (FEP),229 quantum mechanical/MM calculations,230 and fragment molecular orbital231,232 have been employed with ...
et al. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J. Chem. Theory Comput. 6, 1509–1519 (2010). Article CAS PubMed Google Scholar Tian, W., Chen, C., Lei, X., Zhao, J., Liang, J. CASTp 3.0: Computed...
Transforming growth factor-β (TGF-β) signaling has a paradoxical role in cancer progression, and it acts as a tumor suppressor in the early stages but a tumor promoter in the late stages of cancer. Once cancer cells are generated, TGF-β signaling is r
Transforming growth factor-β (TGF-β) signaling has a paradoxical role in cancer progression, and it acts as a tumor suppressor in the early stages but a tumor promoter in the late stages of cancer. Once cancer cells are generated, TGF-β signaling is r
H Prediction of the association between YTHDF1 and STAT3 binding and perturbation using the m6A2Target tool, and analysis of potential m6A sites on STAT3 mRNA using the m6Avar tool. I Western blot analysis of the expression of YTHDF1, STAT1, P-STAT1, STAT3, P-STAT3, NOS2, ARG-1 and ...
R346K mutation in the Mu variant of SARS-CoV-2 alters the interactions with monoclonal antibodies from class 2: a free energy perturbation study. J. Chem. Inf. Model 62, 627–631 (2022). Article CAS PubMed Google Scholar Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations ...
The histidine protonation states were obtained using a protocol based on free energy perturbation calculations, as described in ref.67. Except for histidines, all amino acids were built in their standard protonation states, as were the N- and C-termini of the kinase (NH3+ and COO−, respecti...