Data-driven challenges and opportunities in crystallography

被引：2

作者：

Glynn, Calina ^{[1
]}

Rodriguez, Jose A. ^{[1
]}

机构：

[1] Univ Calif Los Angeles, DOE Inst Genom & Prote, Dept Chem & Biochem, Los Angeles, CA 90095 USA

来源：

EMERGING TOPICS IN LIFE SCIENCES | 2019年 / 3卷 / 04期

关键词：

SERIAL FEMTOSECOND CRYSTALLOGRAPHY; PROTEIN-STRUCTURE DETERMINATION; INITIO STRUCTURE DETERMINATION; ELECTRON-DIFFRACTION; ATOMIC-RESOLUTION; DATA-COLLECTION; CRYOELECTRON MICROSCOPY; STRUCTURAL BIOLOGY; ENZYME CATALYSIS; MICROED DATA;

D O I：

10.1042/ETLS20180177

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.

引用

页码：423 / 432

页数：10

共 89 条

[1] CRYO-ELECTRON MICROSCOPY OF VIRUSES [J].

ADRIAN, M ;

DUBOCHET, J ;

LEPAULT, J ;

MCDOWALL, AW .

NATURE, 1984, 308 (5954) :32-36

[2] The Adaptive Gain Integrating Pixel Detector at theEuropean XFEL [J].

Allahgholi, Aschkan ;

Becker, Julian ;

Delfs, Annette ;

Dinapoli, Roberto ;

Goettlicher, Peter ;

Greiffenberg, Dominic ;

Henrich, Beat ;

Hirsemann, Helmut ;

Kuhn, Manuela ;

Klanner, Robert ;

Klyuev, Alexander ;

Krueger, Hans ;

Lange, Sabine ;

Laurus, Torsten ;

Marras, Alessandro ;

Mezza, Davide ;

Mozzanica, Aldo ;

Niemann, Magdalena ;

Poehlsen, Jennifer ;

Schwandt, Joern ;

Sheviakov, Igor ;

Shi, Xintian ;

Smoljanin, Sergej ;

Steffen, Lothar ;

Sztuk-Dambietz, Jolanta ;

Trunk, Ulrich ;

Xia, Qingqing ;

Zeribi, Mourad ;

Zhang, Jiaguo ;

Zimmer, Manfred ;

Schmitt, Bernd ;

Graafsma, Heinz .

JOURNAL OF SYNCHROTRON RADIATION, 2019, 26 (01) :74-82

[3] Cryo-EM of macromolecular assemblies at near-atomic resolution [J].

Baker, Matthew L. ;

Zhang, Junjie ;

Ludtke, Steven J. ;

Chiu, Wah .

NATURE PROTOCOLS, 2010, 5 (10) :1697-1708

[4] Big data in cryoEM: automated collection, processing and accessibility of EM data [J].

Baldwin, Philip R. ;

Tan, Yong Zi ;

Eng, Edward T. ;

Rice, William J. ;

Noble, Alex J. ;

Negro, Carl J. ;

Cianfrocco, Michael A. ;

Pottert, Clinton S. ;

Carraghert, Bridget .

CURRENT OPINION IN MICROBIOLOGY, 2018, 43 :1-8

[5]

Barty A, 2012, NAT PHOTONICS, V6, P35, DOI [10.1038/nphoton.2011.297, 10.1038/NPHOTON.2011.297]

[6] The Protein Data Bank [J].

Berman, HM ;

Westbrook, J ;

Feng, Z ;

Gilliland, G ;

Bhat, TN ;

Weissig, H ;

Shindyalov, IN ;

Bourne, PE .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242

[7] Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams [J].

Botha, Sabine ;

Nass, Karol ;

Barends, Thomas R. M. ;

Kabsch, Wolfgang ;

Latz, Beatrice ;

Dworkowski, Florian ;

Foucar, Lutz ;

Panepucci, Ezequiel ;

Wang, Meitian ;

Shoeman, Robert L. ;

Schlichting, Ilme ;

Doak, R. Bruce .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2015, 71 :387-397

[8] High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography [J].

Boutet, Sebastien ;

Lomb, Lukas ;

Williams, Garth J. ;

Barends, Thomas R. M. ;

Aquila, Andrew ;

Doak, R. Bruce ;

Weierstall, Uwe ;

DePonte, Daniel P. ;

Steinbrener, Jan ;

Shoeman, Robert L. ;

Messerschmidt, Marc ;

Barty, Anton ;

White, Thomas A. ;

Kassemeyer, Stephan ;

Kirian, Richard A. ;

Seibert, M. Marvin ;

Montanez, Paul A. ;

Kenney, Chris ;

Herbst, Ryan ;

Hart, Philip ;

Pines, Jack ;

Haller, Gunther ;

Gruner, Sol M. ;

Philipp, Hugh T. ;

Tate, Mark W. ;

Hromalik, Marianne ;

Koerner, Lucas J. ;

van Bakel, Niels ;

Morse, John ;

Ghonsalves, Wilfred ;

Arnlund, David ;

Bogan, Michael J. ;

Caleman, Carl ;

Fromme, Raimund ;

Hampton, Christina Y. ;

Hunter, Mark S. ;

Johansson, Linda C. ;

Katona, Gergely ;

Kupitz, Christopher ;

Liang, Mengning ;

Martin, Andrew V. ;

Nass, Karol ;

Redecke, Lars ;

Stellato, Francesco ;

Timneanu, Nicusor ;

Wang, Dingjie ;

Zatsepin, Nadia A. ;

Schafer, Donald ;

Defever, James ;

Neutze, Richard .

SCIENCE, 2012, 337 (6092) :362-364

[9] Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns [J].

Brewster, Aaron S. ;

Sawaya, Michael R. ;

Rodriguez, Jose ;

Hattne, Johan ;

Echols, Nathaniel ;

McFarlane, Heather T. ;

Cascio, Duilio ;

Adams, Paul D. ;

Eisenberg, David S. ;

Sauter, Nicholas K. .

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2015, 71 :357-366

[10]

Bustillo K.C., 2017, Microscopy and Microanalysis, V23, P1782, DOI DOI 10.1017/S1431927617009576

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