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

Andriy Kryshtafovych; Reinhard Albrecht; Arnaud Baslé; Pedro Bule; Alessandro T Caputo; Ana Luisa Carvalho; Kinlin L Chao; Ron Diskin; Krzysztof Fidelis; Carlos M G A Fontes; Folmer Fredslund; Harry J Gilbert; Celia W Goulding; Marcus D Hartmann; Christopher S Hayes; Osnat Herzberg; Johan C Hill; Andrzej Joachimiak; Gert-Wieland Kohring; Roman I Koning; Leila Lo Leggio; Marco Mangiagalli; Karolina Michalska; John Moult; Shabir Najmudin; Marco Nardini; Valentina Nardone; Didier Ndeh; Thanh-Hong Nguyen; Guido Pintacuda; Sandra Postel; Mark J van Raaij; Pietro Roversi; Amir Shimon; Abhimanyu K Singh; Eric J Sundberg; Kaspars Tars; Nicole Zitzmann; Torsten Schwede

doi:10.1002/prot.25392

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

Proteins. 2018 Mar;86 Suppl 1(Suppl 1):27-50. doi: 10.1002/prot.25392. Epub 2017 Oct 16.

Authors

Andriy Kryshtafovych¹, Reinhard Albrecht², Arnaud Baslé³, Pedro Bule⁴, Alessandro T Caputo⁵, Ana Luisa Carvalho⁶, Kinlin L Chao⁷, Ron Diskin⁸, Krzysztof Fidelis¹, Carlos M G A Fontes⁴, Folmer Fredslund⁹, Harry J Gilbert³, Celia W Goulding¹⁰, Marcus D Hartmann², Christopher S Hayes¹¹, Osnat Herzberg^{7

12}, Johan C Hill⁵, Andrzej Joachimiak^{13

14}, Gert-Wieland Kohring¹⁵, Roman I Koning^{16

17}, Leila Lo Leggio⁹, Marco Mangiagalli¹⁸, Karolina Michalska¹³, John Moult¹⁹, Shabir Najmudin⁴, Marco Nardini²⁰, Valentina Nardone²⁰, Didier Ndeh³, Thanh-Hong Nguyen²¹, Guido Pintacuda²², Sandra Postel²³, Mark J van Raaij²¹, Pietro Roversi^{5

24}, Amir Shimon⁸, Abhimanyu K Singh²⁵, Eric J Sundberg²⁶, Kaspars Tars^{27

28}, Nicole Zitzmann⁵, Torsten Schwede²⁹

Affiliations

¹ Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616.
² Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
³ Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom.
⁴ CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa.
⁵ Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom.
⁶ UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.
⁷ Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850.
⁸ Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
⁹ Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
¹⁰ Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697.
¹¹ Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106.
¹² Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742.
¹³ Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439.
¹⁴ Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637.
¹⁵ Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany.
¹⁶ Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands.
¹⁷ Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
¹⁸ Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy.
¹⁹ Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850.
²⁰ Department of Biosciences, University of Milano, Milano, 20133, Italy.
²¹ Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain.
²² Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France.
²³ University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201.
²⁴ Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK.
²⁵ School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom.
²⁶ Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201.
²⁷ Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia.
²⁸ Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia.
²⁹ Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland.

Abstract

The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. 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.

Keywords: CASP; NMR; X-ray crystallography; protein structure prediction.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Bacteria / chemistry
Computational Biology / methods*
Crystallography, X-Ray
Humans
Models, Molecular*
Protein Conformation*
Protein Folding
Proteins / chemistry*
Software

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding