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Title: Target highlights from the first post-PSI CASP experiment (CASP12, May–August 2016)

Abstract

In this paper, the functional and biological significance of the selected CASP12 targets are described by the authors of the structures. Finally, the crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.

Authors:
ORCiD logo [1];  [2];  [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6];  [7];  [8]; ORCiD logo [1]; ORCiD logo [4];  [9]; ORCiD logo [3];  [10]; ORCiD logo [2];  [11];  [12];  [5];  [13];  [14]; ORCiD logo [15] more »; ORCiD logo [9]; ORCiD logo [16];  [17]; ORCiD logo [18]; ORCiD logo [4]; ORCiD logo [19]; ORCiD logo [19];  [3]; ORCiD logo [20];  [21]; ORCiD logo [22]; ORCiD logo [20]; ORCiD logo [23];  [8]; ORCiD logo [24]; ORCiD logo [25];  [26];  [5]; ORCiD logo [27] « less
  1. Univ. of California, Davis, CA (United States). Genome Center
  2. Max Planck Inst. for Developmental Biology, Tübingen (Germany). Dept. of Protein Evolution
  3. Newcastle Univ., Newcastle upon Tyne (United Kingdom). Inst. for Cell and Molecular Biosciences
  4. Univ. of Lisbon (Portugal). Faculty of Veterinary Medicine. Centre for Interdisciplinary Research in Animal Health (CIISA)
  5. Univ. of Oxford (United Kingdom). Oxford Glycobiology Inst. Dept. of Biochemistry
  6. New Univ. of Lisbon (Portugal). Chemistry Dept. UCIBIO. Chemistry and Technology Network (REQUIMTE)
  7. Univ. of Maryland, Rockville, MD (United States). Inst. for Bioscience and Biotechnology Research
  8. Weizmann Inst. of Science, Rehovot (Israel). Dept. of Structural Biology
  9. Univ. of Copenhagen (Denmark). Dept. of Chemistry
  10. Univ. of California, Irvine, CA (United States). Dept. of Molecular Biology and Biochemistry/Pharmaceutical Sciences
  11. Univ. of California, Santa Barbara, CA (United States). Dept. of Molecular, Cellular and Developmental Biology. Biomolecular Science and Engineering Program
  12. Univ. of Maryland, Rockville, MD (United States). Inst. for Bioscience and Biotechnology Research; Univ. of Maryland, College Park, MD (United States). Dept. of Chemistry and Biochemistry
  13. Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics. Structural Biology Center. Biosciences Division; Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology
  14. Saarland Univ., Saarbrücken (Germany). Microbiology
  15. Leiden Univ. (Netherlands). Netherlands Centre for Electron Nanoscopy. Inst. of Biology Leiden; Leiden Univ. Medical Center (Netherlands). Dept. of Molecular Cell Biology
  16. Univ. of Milano-Bicocca, Milan (Italy). Dept. of Biotechnology and Biosciences
  17. Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics. Structural Biology Center. Biosciences Division
  18. Univ. of Maryland, Rockville, MD (United States). Dept. of Cell Biology and Molecular Genetics. Inst. for Bioscience and Biotechnology Research
  19. Univ. of Milan (Italy). Dept. of Biosciences
  20. CSIC National Center for Biotechnology (CNB), Madrid (Spain). Dept. of Macromolecular Structures
  21. Univ. of Lyon (France). Center for High Field NMR (CRMN). Inst. of Analytical Sciences
  22. Univ. of Maryland School of Medicine, Baltimore, MD (United States). Inst. of Human Virology
  23. Univ. of Oxford (United Kingdom). Oxford Glycobiology Inst. Dept. of Biochemistry; Univ. of Leicester (United Kingdom). Leicester Inst. of Structural and Chemical Biology. Dept. of Molecular and Cell Biology
  24. Univ. of Kent, Canterbury (United Kingdom). School of Biosciences
  25. Univ. of Maryland School of Medicine, Baltimore, MD (United States). Dept. of Medicine. Dept. of Microbiology and Immunology. Inst. of Human Virology
  26. Latvian Biomedical Research and Study Center, Riga (Latvia); Univ. of Latvia, Riga (Latvia). Faculty of Biology. Dept. of Molecular Biology
  27. SIB Swiss Inst. of Bioinformatics, Basel (Switzerland)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of California, Davis, CA (United States); Univ. of Maryland, Rockville, MD (United States); Univ. of Latvia, Riga (Latvia); Max Planck Inst. for Developmental Biology, Tübingen (Germany); Weizmann Inst. of Science, Rehovot (Israel); Newcastle Univ., Newcastle upon Tyne (United Kingdom); Univ. of Oxford (United Kingdom); CSIC National Center for Biotechnology (CNB), Madrid (Spain); Univ. of Lisbon (Portugal)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Inst. of Health (NIH) (United States); Latvian Council of Sciences; European Regional Development Fund (ERDF); European Union (EU); Israel Science Foundation (ISF); Wellcome Trust (United Kingdom); Ministry of Economy and Competitiveness (MINECO) (Spain); Foundation for Science and Technology (FCT) (Portugal)
OSTI Identifier:
1461425
Alternate Identifier(s):
OSTI ID: 1399794
Grant/Contract Number:  
AC02-06CH11357; GM100482; GM102318; GM094585; GM115586; R01GM102810; 12.094; 2010/0314/2DP/2.1.1.1.0/10/APIA/VIAA/052; NMP3-SL-2008-213487; 682/16; 097300/Z/11/Z; 106272/Z/14/Z; BFU2014-53425-P; PTDC/BIA-MIC/5947/2014; RECI/BBB-BEP/0124/2012; SFRH/BD/86821/2012
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Proteins
Additional Journal Information:
Journal Volume: 86; Journal Issue: S1; Journal ID: ISSN 0887-3585
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CASP; NMR; protein structure prediction; X-ray crystallography

Citation Formats

Kryshtafovych, Andriy, Albrecht, Reinhard, Basle, Arnaud, Bule, Pedro, Caputo, Alessandro T., Carvalho, Ana Luisa, Chao, Kinlin L., Diskin, Ron, Fidelis, Krzysztof, Fontes, Carlos M. G. A., Fredslund, Folmer, Gilbert, Harry J., Goulding, Celia W., Hartmann, Marcus D., Hayes, Christopher S., Herzberg, Osnat, Hill, Johan C., Joachimiak, Andrzej, Kohring, Gert-Wieland, Koning, Roman I., Lo Leggio, Leila, Mangiagalli, Marco, Michalska, Karolina, Moult, John, Najmudin, Shabir, Nardini, Marco, Nardone, Valentina, Ndeh, Didier, Nguyen, Thanh-Hong, Pintacuda, Guido, Postel, Sandra, van Raaij, Mark J., Roversi, Pietro, Shimon, Amir, Singh, Abhimanyu K., Sundberg, Eric J., Tars, Kaspars, Zitzmann, Nicole, and Schwede, Torsten. Target highlights from the first post-PSI CASP experiment (CASP12, May–August 2016). United States: N. p., 2017. Web. doi:10.1002/prot.25392.
Kryshtafovych, Andriy, Albrecht, Reinhard, Basle, Arnaud, Bule, Pedro, Caputo, Alessandro T., Carvalho, Ana Luisa, Chao, Kinlin L., Diskin, Ron, Fidelis, Krzysztof, Fontes, Carlos M. G. A., Fredslund, Folmer, Gilbert, Harry J., Goulding, Celia W., Hartmann, Marcus D., Hayes, Christopher S., Herzberg, Osnat, Hill, Johan C., Joachimiak, Andrzej, Kohring, Gert-Wieland, Koning, Roman I., Lo Leggio, Leila, Mangiagalli, Marco, Michalska, Karolina, Moult, John, Najmudin, Shabir, Nardini, Marco, Nardone, Valentina, Ndeh, Didier, Nguyen, Thanh-Hong, Pintacuda, Guido, Postel, Sandra, van Raaij, Mark J., Roversi, Pietro, Shimon, Amir, Singh, Abhimanyu K., Sundberg, Eric J., Tars, Kaspars, Zitzmann, Nicole, & Schwede, Torsten. Target highlights from the first post-PSI CASP experiment (CASP12, May–August 2016). United States. doi:10.1002/prot.25392.
Kryshtafovych, Andriy, Albrecht, Reinhard, Basle, Arnaud, Bule, Pedro, Caputo, Alessandro T., Carvalho, Ana Luisa, Chao, Kinlin L., Diskin, Ron, Fidelis, Krzysztof, Fontes, Carlos M. G. A., Fredslund, Folmer, Gilbert, Harry J., Goulding, Celia W., Hartmann, Marcus D., Hayes, Christopher S., Herzberg, Osnat, Hill, Johan C., Joachimiak, Andrzej, Kohring, Gert-Wieland, Koning, Roman I., Lo Leggio, Leila, Mangiagalli, Marco, Michalska, Karolina, Moult, John, Najmudin, Shabir, Nardini, Marco, Nardone, Valentina, Ndeh, Didier, Nguyen, Thanh-Hong, Pintacuda, Guido, Postel, Sandra, van Raaij, Mark J., Roversi, Pietro, Shimon, Amir, Singh, Abhimanyu K., Sundberg, Eric J., Tars, Kaspars, Zitzmann, Nicole, and Schwede, Torsten. Thu . "Target highlights from the first post-PSI CASP experiment (CASP12, May–August 2016)". United States. doi:10.1002/prot.25392. https://www.osti.gov/servlets/purl/1461425.
@article{osti_1461425,
title = {Target highlights from the first post-PSI CASP experiment (CASP12, May–August 2016)},
author = {Kryshtafovych, Andriy and Albrecht, Reinhard and Basle, Arnaud and Bule, Pedro and Caputo, Alessandro T. and Carvalho, Ana Luisa and Chao, Kinlin L. and Diskin, Ron and Fidelis, Krzysztof and Fontes, Carlos M. G. A. and Fredslund, Folmer and Gilbert, Harry J. and Goulding, Celia W. and Hartmann, Marcus D. and Hayes, Christopher S. and Herzberg, Osnat and Hill, Johan C. and Joachimiak, Andrzej and Kohring, Gert-Wieland and Koning, Roman I. and Lo Leggio, Leila and Mangiagalli, Marco and Michalska, Karolina and Moult, John and Najmudin, Shabir and Nardini, Marco and Nardone, Valentina and Ndeh, Didier and Nguyen, Thanh-Hong and Pintacuda, Guido and Postel, Sandra and van Raaij, Mark J. and Roversi, Pietro and Shimon, Amir and Singh, Abhimanyu K. and Sundberg, Eric J. and Tars, Kaspars and Zitzmann, Nicole and Schwede, Torsten},
abstractNote = {In this paper, the functional and biological significance of the selected CASP12 targets are described by the authors of the structures. Finally, the crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.},
doi = {10.1002/prot.25392},
journal = {Proteins},
number = S1,
volume = 86,
place = {United States},
year = {Thu Sep 28 00:00:00 EDT 2017},
month = {Thu Sep 28 00:00:00 EDT 2017}
}

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Works referenced in this record:

Structural characterization of the thermostable Bradyrhizobium japonicum D-sorbitol dehydrogenase
journal, October 2016

  • Fredslund, Folmer; Otten, Harm; Gemperlein, Sabrina
  • Acta Crystallographica Section F Structural Biology Communications, Vol. 72, Issue 11, p. 846-852
  • DOI: 10.1107/S2053230X16016927