Computation of pH-dependent binding free energies-Reference-Cited by-同舟云学术

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Computation of pH-dependent binding free energies

Published:2015-10-26 Issue:1 Volume:105 Page:43-49
ISSN:0006-3525
Container-title:Biopolymers
language:en
Short-container-title:Biopolymers

Author:

Kim M. Olivia¹,McCammon J. Andrew¹²³⁴

Affiliation:

1. Department of Pharmacology; University of California San Diego; La Jolla CA 92093

2. Department of Chemistry and Biochemistry; University of California San Diego; La Jolla CA 92093

3. Howard Hughes Medical Institute; University of California San Diego; La Jolla CA 92093

4. National Biomedical Computation Resource; University of California San Diego; La Jolla CA 92093

Funder

NSF

NIH

Howard Hughes Medical Institute, National Biomedical Computation Resource (NBCR), and NSF supercomputer centers

Publisher

Wiley

Subject

Organic Chemistry,Biomaterials,Biochemistry,General Medicine,Biophysics

Link

http://onlinelibrary.wiley.com/wol1/doi/10.1002/bip.22702/fullpdf

Reference82 articles.

1. Protonation and pK changes in protein–ligand binding

2. Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”

3. Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein-inhibitor association: Application to plasmepsin, cathepsin D and endothiapepsin-pepstatin complexes

4. Combining Conformational Flexibility and Continuum Electrostatics for Calculating pKas in Proteins

5. Electrostatic Properties of Protein-Protein Complexes

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1. Constant-pH Simulation Methods for Biomolecular Systems;Comprehensive Computational Chemistry;2024

2. Accurately Predicting Protein pK_a Values Using Nonequilibrium Alchemy;Journal of Chemical Theory and Computation;2023-10-11

3. Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2;Computer Physics Communications;2023-06

4. Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin;Journal of Chemical Theory and Computation;2022-02-16

5. The Molecular Effects of Dietary Acid Load on Metabolic Disease (The Cellular PasaDoble: The Fast-Paced Dance of pH Regulation);Frontiers in Molecular Medicine;2021-11-16

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