13
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Adams PD, Afonine PV, Baskaran K, Berman HM, Berrisford J, Bricogne G, Brown DG, Burley SK, Chen M, Feng Z, Flensburg C, Gutmanas A, Hoch JC, Ikegawa Y, Kengaku Y, Krissinel E, Kurisu G, Liang Y, Liebschner D, Mak L, Markley JL, Moriarty NW, Murshudov GN, Noble M, Peisach E, Persikova I, Poon BK, Sobolev OV, Ulrich EL, Velankar S, Vonrhein C, Westbrook J, Wojdyr M, Yokochi M, Young JY. Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB). Acta Crystallogr D Struct Biol 2019; 75:451-454. [PMID: 30988261 PMCID: PMC6465986 DOI: 10.1107/s2059798319004522] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/03/2019] [Indexed: 11/10/2022] Open
Abstract
This letter announces that PDBx/mmCIF format files will become mandatory for crystallographic depositions to the Protein Data Bank (PDB).
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Affiliation(s)
- Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kumaran Baskaran
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Gerard Bricogne
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - David G. Brown
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Minyu Chen
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Claus Flensburg
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Jeffrey C. Hoch
- BioMagResBank (BMRB), UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Yasuyo Ikegawa
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yumiko Kengaku
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Eugene Krissinel
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Yuhe Liang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - John L. Markley
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Martin Noble
- Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Irina Persikova
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eldon L. Ulrich
- BioMagResBank (BMRB), University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Clemens Vonrhein
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge, CB3 0AX, UK
- CCP4, Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
| | - Masashi Yokochi
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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33
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Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM. Remediation of the protein data bank archive. Nucleic Acids Res 2008; 36:D426-33. [PMID: 18073189 PMCID: PMC2238854 DOI: 10.1093/nar/gkm937] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 10/08/2007] [Accepted: 10/11/2007] [Indexed: 11/13/2022] Open
Abstract
The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB-RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)-have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.
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Affiliation(s)
- Kim Henrick
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zukang Feng
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wolfgang F. Bluhm
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Dimitris Dimitropoulos
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jurgen F. Doreleijers
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuchismita Dutta
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Judith L. Flippen-Anderson
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John Ionides
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chisa Kamada
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eugene Krissinel
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Catherine L. Lawson
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John L. Markley
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruki Nakamura
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Richard Newman
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yukiko Shimizu
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jawahar Swaminathan
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sameer Velankar
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jeramia Ory
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eldon L. Ulrich
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wim Vranken
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - John Westbrook
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Reiko Yamashita
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Huanwang Yang
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Jasmine Young
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Muhammed Yousufuddin
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Helen M. Berman
- MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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