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PypKa: A Flexible Python Module for Poisson–Boltzmann-Based pKa Calculations

2020 ◽  
Vol 60 (10) ◽  
pp. 4442-4448
Author(s):  
Pedro B. P. S. Reis ◽  
Diogo Vila-Viçosa ◽  
Walter Rocchia ◽  
Miguel Machuqueiro
Keyword(s):  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals pKa Calculations with the Polarizable Drude Force Field and Poisson–Boltzmann Solvation Model

2020 ◽  
Vol 16 (7) ◽  
pp. 4655-4668 ◽  
Author(s):  
Alexey Aleksandrov ◽  
Benoît Roux ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Solvation Model ◽  
Pka Calculations ◽  
Poisson Boltzmann

pKa calculations for tautomerizable and conformationally flexible molecules: partition function vs. state transition approach

2019 ◽  
Vol 25 (5) ◽  
Author(s):  
Nicolas Tielker ◽  
Lukas Eberlein ◽  
Christian Chodun ◽  
Stefan Güssregen ◽  
Stefan M. Kast
Keyword(s):  
Partition Function ◽  
State Transition ◽  
Flexible Molecules ◽  
Pka Calculations ◽  
Transition Approach

Antioxidant activity and pKa calculations of 4‑mercaptostilbene and some derivatives: A theoretical approach

2019 ◽  
Vol 275 ◽  
pp. 221-231 ◽  
Author(s):  
Ali Benayahoum ◽  
Samia Bouakkaz ◽  
Tarik Bordjiba ◽  
Mohamed Abdaoui
Keyword(s):  
Antioxidant Activity ◽  
Theoretical Approach ◽  
Pka Calculations

scholarly journals PypKa: a python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism

2018 ◽  
Author(s):  
Miguel Machuqueiro ◽  
Pedro Reis ◽  
Diogo Vila-Viçosa ◽  
Walter Rocchia
Keyword(s):  
Pka Calculations ◽  
Poisson Boltzmann

scholarly journals Improving pKa calculations of membrane inserting amino acids using replica exchange CpHMD simulations

2017 ◽  
Author(s):  
Miguel Machuqueiro ◽  
Pedro Reis ◽  
Diogo Vila-Viçosa
Keyword(s):  
Amino Acids ◽  
Replica Exchange ◽  
Pka Calculations

Investigation of Ionization Pattern of the Adjacent Acidic Residues in the DXDXE Motif of GH-18 Chitinases Using Theoretical pKa Calculations

2017 ◽  
Vol 57 (3) ◽  
pp. 572-583 ◽  
Author(s):  
Piyanat Meekrathok ◽  
Predrag Kukic ◽  
Jens Erik Nielsen ◽  
Wipa Suginta
Keyword(s):  
Pka Calculations ◽  
Acidic Residues

scholarly journals Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations

2016 ◽  
Vol 13 (1) ◽  
pp. 147-160 ◽  
Author(s):  
Plamen Dobrev ◽  
Serena Donnini ◽  
Gerrit Groenhof ◽  
Helmut Grubmüller
Keyword(s):  
Amino Acids ◽  
Pka Calculations ◽  
Constant Ph ◽  
Explicit Solvent

Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides

2016 ◽  
Vol 18 (16) ◽  
pp. 11202-11212 ◽  
Author(s):  
S. Sastre ◽  
R. Casasnovas ◽  
F. Muñoz ◽  
J. Frau
Keyword(s):  
Amino Acids ◽  
Computational Chemistry ◽  
Computational Cost ◽  
Quantitative Prediction ◽  
Isodesmic Reaction ◽  
Pka Calculations ◽  
Current Challenge ◽  
Low Computational Cost ◽  
A Current

Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry.

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