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Proteins: Structure, Function and Bioinformatics, ISSN 0887-3585, 12/2011, Volume 79, Issue 12, pp. 3333 - 3345
In this study, we validate and probe the description of electrostatic interactions within proteins by predicting and comparing pK(a) values of ionizable groups... 
Validation | PROPKA | Null-model | Homology modeling | Reorganization | Staphylococcal nuclease | Relative rmsd | DIELECTRIC-CONSTANTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | relative rmsd | homology modeling | BIOPHYSICS | staphylococcal nuclease | INTERIOR | RATIONALIZATION | VALUES | reorganization | IONIZATION | validation | ASP
Journal Article
Journal of Molecular Modeling, ISSN 1610-2940, 03/2012, Volume 18, Issue 3, pp. 1097 - 1106
Unlike atomistic and continuum models, empirical pk(a) predicting methods need to include desolvation contributions explicitly. This study describes a new... 
Protein modeling | Solvation | PROPKA | Desolvation | ENERGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | PKA | CHEMISTRY, MULTIDISCIPLINARY | MOLECULAR-MECHANICS | PREDICTION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | RATIONALIZATION | pK(a) | VALUES
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 08/2001, Volume 123, Issue 32, pp. 7866 - 7876
The dimeric CuA site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the... 
Cytochrome c | Density functionals | Usage | Research | Naturvetenskap | Natural Sciences | Kemi | Theoretical Chemistry | Teoretisk kemi | Chemical Sciences
Journal Article
Journal Article
Chemical Reviews, ISSN 0009-2665, 05/2006, Volume 106, Issue 5, p. 1737
Journal Article
Proceedings of the National Academy of Sciences of the United States, ISSN 0027-8424, 06/2007, Volume 104, Issue 23, p. 9661
The catalytic power of enzymes containing coenzyme [B.sub.12] cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present... 
Vitamin B complex | Vitamin B | Research | Enzyme kinetics | Electrostatics | Simulation methods
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 6/2007, Volume 104, Issue 23, pp. 9661 - 9666
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 06/2001, Volume 105, Issue 23, pp. 5546 - 5552
Inner-sphere reorganization energies have been calculated for a number of models of six-coordinate iron porphyrins (with varying axial ligands), using the... 
POLYPEPTIDE-CHAIN | REDOX POTENTIALS | HEME | ENZYMES | ELECTRONIC-STRUCTURE CONTRIBUTIONS | COMPLEXES | LIGATION | CHEMISTRY, PHYSICAL | REDUCTION POTENTIALS | C-OXIDASE | METAL SITES | Cytochromes | Ligands | Structure | Analysis | Naturvetenskap | Natural Sciences | Kemi | Theoretical Chemistry | Teoretisk kemi | Chemical Sciences
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 11/2004, Volume 126, Issue 46, p. 15167
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 03/2004, Volume 126, Issue 9, p. 2820
Journal Article
Computational and Structural Biotechnology Journal, ISSN 2001-0370, 2015, Volume 13, Issue C, pp. 256 - 264
New variants of β-1,4-galactanase from the mesophilic organism were designed using the structure of β-1,4-galactanase from the thermophile organism as a... 
Thermostability | β-1,4-galactanase | Computational prediction | Protein design | GH53 | HYDROLASES | PROTEIN STABILITY | PK(A) VALUES | BIOCHEMISTRY & MOLECULAR BIOLOGY | BACILLUS-LICHENIFORMIS | ENERGETICS | DIFFERENTIAL SCANNING CALORIMETRY | PREDICTION | MODELS | IRREVERSIBLE THERMAL-DENATURATION | ENDO-BETA-1,4-GALACTANASE | beta-1,4-galactanase
Journal Article
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