scholarly journals Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes

2017 ◽  
Vol 13 (12) ◽  
pp. 6275-6289 ◽  
Author(s):  
Vytautas Gapsys ◽  
Bert L. de Groot
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Dna Complexes ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

scholarly journals Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Kevin Hauser ◽  
Christopher Negron ◽  
Steven K. Albanese ◽  
Soumya Ray ◽  
Thomas Steinbrecher ◽  
...  
Keyword(s):  
Free Energy ◽  
Kinase Inhibitors ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

Thermodynamic Stability of Human γD-Crystallin Mutants Using Alchemical Free-Energy Calculations

2019 ◽  
Vol 123 (27) ◽  
pp. 5671-5677 ◽  
Author(s):  
Rodrigo Aguayo-Ortiz ◽  
Augusto González-Navejas ◽  
Giovanni Palomino-Vizcaino ◽  
Oscar Rodriguez-Meza ◽  
Miguel Costas ◽  
...  
Keyword(s):  
Free Energy ◽  
Thermodynamic Stability ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

scholarly journals An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling

2020 ◽  
Vol 60 (11) ◽  
pp. 5407-5423 ◽  
Author(s):  
Gerhard König ◽  
Nina Glaser ◽  
Benjamin Schroeder ◽  
Alžbeta Kubincová ◽  
Philippe H. Hünenberger ◽  
...  
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Intermediate States ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations
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