Donald S. Berkholz, Ph.D.
Affiliations: | 2009 | Oregon State University, Corvallis, OR |
Area:
Biochemistry, Bioinformatics BiologyGoogle:
"Donald Berkholz"Mean distance: (not calculated yet)
Parents
Sign in to add mentorP. Andrew (Andy) Karplus | grad student | 2009 | Oregon State | |
(Modeling protein structure at atomic resolution.) |
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Publications
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Berkholz DS, Driggers CM, Shapovalov MV, et al. (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proceedings of the National Academy of Sciences of the United States of America. 109: 449-53 |
Hollingsworth SA, Lewis MC, Berkholz DS, et al. (2012) (φ,ψ)₂ motifs: a purely conformation-based fine-grained enumeration of protein parts at the two-residue level. Journal of Molecular Biology. 416: 78-93 |
Tronrud DE, Berkholz DS, Karplus PA. (2010) Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Crystallographica. Section D, Biological Crystallography. 66: 834-42 |
Berkholz DS, Krenesky PB, Davidson JR, et al. (2010) Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Nucleic Acids Research. 38: D320-5 |
Berkholz DS, Shapovalov MV, Dunbrack RL, et al. (2009) Conformation dependence of backbone geometry in proteins. Structure (London, England : 1993). 17: 1316-25 |
Hollingsworth SA, Berkholz DS, Karplus PA. (2009) On the occurrence of linear groups in proteins. Protein Science : a Publication of the Protein Society. 18: 1321-5 |
Berkholz DS, Faber HR, Savvides SN, et al. (2008) Catalytic cycle of human glutathione reductase near 1 A resolution. Journal of Molecular Biology. 382: 371-84 |
Karplus PA, Shapovalov MV, Dunbrack RL, et al. (2008) A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallographica. Section D, Biological Crystallography. 64: 335-6 |
Benison G, Berkholz DS, Barbar E. (2007) Protein assignments without peak lists using higher-order spectra. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 189: 173-81 |