Primary Citation PubMed: 19533744
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Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study.
(2011) Proteins 79
PubMed: 22072520 | PubMedCentral: PMC3227005 | DOI: 10.1002/prot.23136
31 – 37 Along with other computational groups, we have computed blind p K a predictions for residues of wild-type SNase (PDB ID: 1STN or 1SNC), the SNase mutant Δ+PHS (PDB ID: 3bdc), a... d various mutants from the Δ+PHS parent protein (referred to as calculated results in this study).
Publication Year: 2011
On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi.
(2013) J Chem Theory Comput 9
PubMed: 23585741 | PubMedCentral: PMC3622359 | DOI: 10.1021/ct400065j
In 19 of the cases, the p K a calculations were based on the structure of wild type (PDB ID: 1stn) 48 SNase and its hyperstable variant (PDB ID: 3bdc), 46 which is called Δ+PHS.
In 20 of the cases, p K a calculations were based on the X-ray structures of SNase with mutations, and in 50 of the cases, the p K a calculations were based on the in silico generated mutant from the wild type SNase (PDB ID: 3bdc; list of the amino acids, structure used, and experimental p K a ’s are available from the p K a Cooperative web page, http://pkacoop.org/wordpress/ ).
Publication Year: 2013
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