Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. (Q52064388)

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7 November 2019

title

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations (English)

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1

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author name string

G Vriend

series ordinal

2

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language of work or name

English

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publication date

1 June 2001

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7 November 2019

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:11340657%20AND%20SRC:MED&resulttype=core&format=json

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volume

43

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issue

4

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page(s)

403-412

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pKa calculations for class A beta-lactamases: influence of substrate binding

7 November 2019

cites work

1 reference

pKa calculations for class A beta-lactamases: methodological and mechanistic implications

21 January 2018

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A fast and simple method to calculate protonation states in proteins.

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Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.

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Prediction of pH-dependent properties of proteins

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Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

21 January 2018

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The determinants of pKas in proteins

21 January 2018

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Explicit solvent models in protein pKa calculations.

21 January 2018

1 reference

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility

21 January 2018

1 reference

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

21 January 2018

1 reference

The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

21 January 2018

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The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagine, glutamine and histidine side chains

21 January 2018

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A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding

21 January 2018

1 reference

Self-consistent field approach to protein structure and stability. I: pH dependence of electrostatic contribution

21 January 2018

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Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries.

21 January 2018

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A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

21 January 2018

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Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.

21 January 2018

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Tanford-Kirkwood electrostatics for protein modeling.

21 January 2018

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WHAT IF: a molecular modeling and drug design program

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides

21 January 2018

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21 January 2018

The Protein Data Bank

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Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase

21 January 2018

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Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR

21 January 2018

1 reference

Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution

21 January 2018

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Molecular structure of a new family of ribonucleases

21 January 2018

1 reference

Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model

21 January 2018

1 reference

Modeling of protein conformational fluctuations in pKa predictions

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/PROT.1053

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7 November 2019

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