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 …
Dielectric continuum methods for quantum chemistry
JM Herbert - Wiley Interdisciplinary Reviews: Computational …, 2021 - Wiley Online Library
This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
continuum electrostatics. Within quantum chemistry this formalism is sometimes …
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
The accuracy of atomistic biomolecular modeling and simulation studies depend on the
accuracy of the input structures. Preparing these structures for an atomistic modeling task …
accuracy of the input structures. Preparing these structures for an atomistic modeling task …
On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi
Implicit methods for modeling protein electrostatics require dielectric properties of the system
to be known, in particular, the value of the dielectric constant of protein. While numerous …
to be known, in particular, the value of the dielectric constant of protein. While numerous …
Quantum mechanical continuum solvation models
This review on continuum solvation models has been preceded in Chemical Reviews by
others addressing the same subject. They are due to Tomasi and Persico1 (published in …
others addressing the same subject. They are due to Tomasi and Persico1 (published in …
H++: a server for estimating p Ka s and adding missing hydrogens to macromolecules
JC Gordon, JB Myers, T Folta, V Shoja… - Nucleic acids …, 2005 - academic.oup.com
The structure and function of macromolecules depend critically on the ionization
(protonation) states of their acidic and basic groups. A number of existing practical methods …
(protonation) states of their acidic and basic groups. A number of existing practical methods …
Very fast empirical prediction and rationalization of protein pKa values
A very fast empirical method is presented for structure‐based protein pKa prediction and
rationalization. The desolvation effects and intra‐protein interactions, which cause variations …
rationalization. The desolvation effects and intra‐protein interactions, which cause variations …
Molecular dynamics: survey of methods for simulating the activity of proteins
The term molecular mechanics (MM) refers to the use of simple potential-energy functions
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
(eg, harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular …
Quantitative correlation of physical and chemical properties with chemical structure: utility for prediction
AR Katritzky, M Kuanar, S Slavov, CD Hall… - Chemical …, 2010 - ACS Publications
All properties of organic moleculessphysical, chemical, biological, and
technologicalsdepend on their chemical structure and vary with it in a systematic way. The …
technologicalsdepend on their chemical structure and vary with it in a systematic way. The …
Very fast prediction and rationalization of pKa values for protein–ligand complexes
The PROPKA method for the prediction of the pKa values of ionizable residues in proteins is
extended to include the effect of non-proteinaceous ligands on protein pKa values as well as …
extended to include the effect of non-proteinaceous ligands on protein pKa values as well as …