Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix

Autor: Nigel W. Moriarty, Jane S. Richardson, Hai Nguyen, Pawel A. Janowski, Jason M. Swails, Paul D. Adams, David A. Case

Publikováno v: Acta crystallographica. Section D, Structural biology, vol 76, iss Pt 1

The refinement of biomolecular crystallographic models relies on geometric restraints to help address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic model

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::80b48ad6314df372ab7e911df8230138

A/B Testing at Scale: Accelerating Software Innovation

Autor: Alex Deng, Jeff Omhover, Pawel A. Janowski, Somit Gupta, Ron Kohavi

Publikováno v: WWW (Companion Volume)

The Internet and the general digitalization of products and operations provides an unprecedented opportunity to accelerate innovation while applying a rigorous and trustworthy methodology for supporting key product decisions. Developers of connected

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::986b94df6283c709ddfaba2ae78eec8d
https://doi.org/10.1145/3308560.3320093

All-atom crystal simulations of DNA and RNA duplexes

Autor: Pawel A. Janowski, David A. Case, Chunmei Liu

Publikováno v: Biochimica et Biophysica Acta (BBA) - General Subjects. 1850:1059-1071

Molecular dynamics simulations can complement experimental measures of structure and dynamics of biomolecules. The quality of such simulations can be tested by comparisons to models refined against experimental crystallographic data.We report simulat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b872179104f11e1b29692fb6600da9d
https://doi.org/10.1016/j.bbagen.2014.09.018

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

Autor: Nigel W. Moriarty, Darrin M. York, Gregory L. Warren, Paul D. Adams, Pawel A. Janowski, David A. Case, Brian Kelley

Publikováno v: Acta crystallographica. Section D, Structural biology, vol 72, iss Pt 9
Acta Crystallographica. Section D, Structural Biology
Janowski, PA; Moriarty, NW; Kelley, BP; Case, DA; York, DM; Adams, PD; et al.(2016). Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. Acta Crystallographica Section D: Structural Biology, 72(9), 1062-1072. doi: 10.1107/S2059798316012225. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/8pz8w0vj

A method for the more accurate refinement of small molecules and ligands in biomolecular structures is provided. Improved ligand geometry is obtained via an all-atom molecular-mechanics force field.
Modern crystal structure refinement programs r

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72bb8f35d793975cac8718d3cf70e061
https://escholarship.org/uc/item/8pz8w0vj

Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path

Autor: Darrin M. York, Timothy J. Giese, George M. Giambaşu, Pawel A. Janowski, Hugh Heldenbrand, Joseph E. Wedekind

Publikováno v: Journal of the American Chemical Society

The hairpin ribozyme accelerates a phosphoryl transfer reaction without catalytic participation of divalent metal ions. Residues A38 and G8 have been implicated as playing roles in general acid and base catalysis, respectively. Here we explore the st

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::25a1436996744f73180abdc01f161407
https://pubmed.ncbi.nlm.nih.gov/24842535