Zobrazeno 1 - 10
of 31
pro vyhledávání: '"Oleg V. Sobolev"'
Autor:
Malgorzata Biczysko, Pavel V. Afonine, Oleg V. Sobolev, Lum Wang, Mark P. Waller, Nigel W. Moriarty, Holger Kruse
Publikováno v:
Acta Crystallographica Section D Structural Biology. 76:1184-1191
Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to signi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f3d3bb3365d6c43a529a2d7e9b494d4
https://doi.org/10.1107/s2059798320013194
https://doi.org/10.1107/s2059798320013194
Publikováno v:
Acta Crystallographica. Section D, Structural Biology
Acta crystallographica. Section D, Structural biology, vol 76, iss Pt 10
Acta crystallographica. Section D, Structural biology, vol 76, iss Pt 10
The prerequisites for density modification of maps from electron cryomicroscopy are examined and a procedure for incorporating model-based information is presented.
Density modification uses expectations about features of a map such as a flat so
Density modification uses expectations about features of a map such as a flat so
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::217b90792cc2d49645121df43aaf13b0
http://europepmc.org/articles/PMC7543659
http://europepmc.org/articles/PMC7543659
Bulk solvent is a major component of bio-macromolecular crystals and therefore contributes significantly to diffraction intensities. Accurate modeling of the bulk-solvent region has been recognized as important for many crystallographic calculations,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f5844ff3f7ae3bdaffb8df2714af33da
https://doi.org/10.1101/2021.12.09.471976
https://doi.org/10.1101/2021.12.09.471976
Autor:
John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang Feng, Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M Berrisford, Gerard Bricogne, Kay Diederichs, Robbie P. Joosten, Peter Keller, Nigel W. Moriarty, Oleg V. Sobolev, Sameer Velankar, Clemens Vonrhein, David G. Waterman, Genji Kurisu, Helen M. Berman, Stephen K. Burley, Ezra Peisach
Publikováno v:
Journal of molecular biology, vol 434, iss 11
PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provide
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9054c5675bbed4d1a40c7a38f5ad581d
https://pubmed.ncbi.nlm.nih.gov/35460671
https://pubmed.ncbi.nlm.nih.gov/35460671
Publikováno v:
Protein Science : A Publication of the Protein Society
A procedure for building protein chains into maps produced by single‐particle electron cryo‐microscopy (cryo‐EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on second
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ee458b639233f3a952ec3c8c08af08e2
http://europepmc.org/articles/PMC6933853
http://europepmc.org/articles/PMC6933853
Autor:
Paul D. Adams, Doo Nam Kim, Pavel V. Afonine, Serdal Kirmizialtin, Karissa Y. Sanbonmatsu, Oleg V. Sobolev, Nigel W. Moriarty, Billy K. Poon
Publikováno v:
Journal of Structural Biology. 208:1-6
Cryo-electron microscopy (cryo-EM) is becoming a method of choice for describing native conformations of biomolecular complexes at high resolution. The rapid growth of cryo-EM in recent years has created a high demand for automated solutions, both in
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4704096717b7e1006d898b4141171b71
https://doi.org/10.1016/j.jsb.2019.05.012
https://doi.org/10.1016/j.jsb.2019.05.012
Autor:
Marcin Wojdyr, Paul D. Adams, David G. Brown, Zukang Feng, Yasuyo Ikegawa, Lora Mak, Minyu Chen, Billy K. Poon, John D. Westbrook, Ezra Peisach, Jasmine Young, Helen M. Berman, Masashi Yokochi, Nigel W. Moriarty, Yu-He Liang, Stephen K. Burley, John L. Markley, Garib N. Murshudov, John M. Berrisford, Eldon L. Ulrich, Sameer Velankar, Yumiko Kengaku, Aleksandras Gutmanas, Dorothee Liebschner, C. Flensburg, Pavel V. Afonine, Kumaran Baskaran, Clemens Vonrhein, Jeffrey C. Hoch, Eugene Krissinel, Irina Persikova, Genji Kurisu, Oleg V. Sobolev, Martin E.M. Noble, Gérard Bricogne
Publikováno v:
Acta crystallographica. Section D, Structural biology, vol 75, iss Pt 4
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::88e593a136cedb0a65b4e5c2e32df2a6
https://doi.org/10.1107/s2059798319004522
https://doi.org/10.1107/s2059798319004522
Autor:
Z. Hong Zhou, Oleg V. Sobolev, Chi-Min Ho, Xiaorun Li, Paul D. Adams, Thomas C. Terwilliger, Pavel V. Afonine
Publikováno v:
Acta crystallographica. Section D, Structural biology, vol 77, iss Pt 4
Acta Crystallographica. Section D, Structural Biology
Acta Crystallographica. Section D, Structural Biology
A procedure for the identification of a protein in a map from electron cryomicroscopy based on automated model building and sequence assignment is presented.
Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain mult
Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain mult
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a12c291843597712b23a653c807f3473
https://escholarship.org/uc/item/67k783vf
https://escholarship.org/uc/item/67k783vf
Autor:
Nigel W. Moriarty, Oleg V. Sobolev, Lum Wang, Malgorzata Biczysko, Holger Kruse, Pavel V. Afonine, Mark P. Waller
Electron cryo-microscopy (cryo-EM) is fast becoming a major competitor to X-ray crystallography especially for large structures that are difficult or impossible to crystallize. While recent spectacular technology improvements are leading to significa
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9345eb8645373b5880f669487b02348c
https://doi.org/10.1101/2020.05.25.115386
https://doi.org/10.1101/2020.05.25.115386
Autor:
Pavel V. Afonine, Nigel W. Moriarty, Paul D. Adams, Maarten L. Hekkelman, Anastassis Perrakis, Oleg V. Sobolev, Robbie P. Joosten
Publikováno v:
Structure (London, England : 1993), vol 28, iss 11
Structure
Structure
SummaryRamachandran plots report the distribution of the (φ, Ψ) torsion angles of the protein backbone and are one of the best quality metrics of experimental structure models. Typically, validation software reports the number of residues belonging
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7744d413070a2a51b354d17c0ee6b053