NOTE: Hyperlinks within the text may have been deactivated because they no longer link to active sites and/or e-mail addresses.

Agreed Principles

Coordination of International Programs in Structural Genomics

This document reports the principles agreed at the April 4-6, 2000 meeting of representatives of the structural genomics community. Its purpose is to generate further co-operation in the structural biology and general scientific communities. The document may serve as a basis for an appropriately timed announcement to the international public on the initiation of a worldwide effort in structural genomics.

I. Introduction

Success of the genome sequencing projects and major advances in methods of protein structure determination have led the structural biology community to propose the large scale mapping of protein structure space. This structural genomics initiative aims at the discovery, analysis and dissemination of three-dimensional structures of protein, RNA and other biological macromolecules representing the entire range of structural diversity found in nature. Such a complete knowledge will facilitate fundamental understanding and applications in biology, agriculture and medicine. The three-dimensional structures will be crucial for rational drug design, for advancing catalysis in chemistry and biotechnology, and for diagnosis and treatment of disease, as well as for advancing basic principles of biology.

This opportunity is made possible by rapid recent progress in several related key technologies. These include the construction of synchrotrons and high-field NMR instruments, the MAD method of phase determination, high throughput cloning and recombinant expression, a flood of information from genome sequencing projects, and new bioinformatic methods for fold assignment, model building, and prediction of function.

The following document outlines issues related to achieving this expansion of knowledge. The goal is to encourage harmonious cooperation among a broad range of public and private sector institutions in the international effort to characterize macromolecular structures in living organisms on a pan-genomic scale.

II. Goals

A.  Specific goals

1. Large scale determination and analysis of three-dimensional structures. 
    

   1. To determine by experimental methods a representative set of macromolecular structures, including medically important human proteins and proteins from important pathogens and model organisms.
   2. To provide models based on sequence homology to significantly extend the coverage of structure space.
   3. To derive functional information from these structures by experimental and computational methods.

   
    

2. Development of methods for Structural Genomics. 
    
   1. Methods of selecting representatives of protein families based on enhancement of structure space coverage, or functional significance.
   2. High-throughput methods for production of target proteins suitable for structure determination.
   3. Methods for high throughput data collection.
   4. Methods for automated determination, validation, and analysis of 3D structures.
   5. Methods for homology-based modeling, related methods and validation of modeled structures.
   6. Informatics systems to optimize and support the process of structure determination.
   7. Bioinformatics methods for assessing biological function based on structure and other linked biological information sources.
   8. Methods for more challenging problems of production and structure determination such as those involving membrane proteins and multimolecular complexes.

B.  Programs needed

1. Financial and organizational support for structural genomics projects.
2. Establish an international coordinating network to promote efficient application of resources and rapid dissemination of methods and results; to coordinate policies, standards, and formats; and to promote access to unique resources such as synchrotron and high field NMR facilities.
3. Support for the collection, archiving and dissemination of atomic information, experimental data, protocols, and materials.

III. Cooperation

A.  Public funding agencies can cooperate:

1. By agreeing and implementing uniform policies for deposition, quality standards, and formats.
2. By providing sustainable support for public domain programs in structural genomics.
3. By encouraging and supporting appropriate international collaborative programs.

B.  Information and Material Release in the National Structural Genomics Programs

1. The primary impetus for structural genomics is to obtain a base of freely available structural information and tools that will support advancements in wide areas of biology and medicine. Free exchange of data and materials is essential to the success of this effort, including the timely deposition of coordinates, data, and protocols.
2. For the public structural genomics programs, the following guidelines for release of structural data should be supported: 
    
   1. Timely release of coordinates and associated data. Release should follow immediately upon completion of refinement. For the time being, the decision regarding 'completion' will be made by the investigator. A longer-term goal is the automatic triggering of data release using numerical criteria.
   2. Public information on progress of projects. A primary mechanism for encouraging compliance with the guideline of timely release will be openness of progress tracking for projects. Members of the programs should maintain a public web site, showing progress status on determining the structure of each target. This information will be updated frequently.
   3. Short scientific papers. Ensuring high quality of released structures is a priority. In order to help achieve this, structures released by members of the public programs may be accompanied by a short, peer-reviewed paper. These papers could be similar in format and content to the publications of small molecule crystal structures in Acta Cryst. C. The key requirement is that reviews are rapid, and the whole process of preparing the release completed in about three weeks. Normal full-length publication is of course also possible, but should not delay the release of data.
3. To promote communication and prevent unintended duplication of effort, it is desirable to openly share information on targeting of proteins for structure determination.
4. At the time of coordinate deposition and data deposition, protocols for cloning, expression, crystallization and structure determination should also be deposited, enabling re-determination of all structures in the database from time to time.
5. Material deposition of clones, cell lines, and protein samples is also encouraged, provided that satisfactory procedures can be put in place for collection, storage, and dissemination.

C.  Relationship to industrial activities

1. The structural genomics community should explore formation of an international consortium involving industrial partners to further the goals of structural genomics.
2. International efforts should be made to facilitate the eventual deposition of structures determined in the private sector, and to promote harmonious cooperation and exchange between the public and private sectors.

IV. Intellectual property rights

Raw fundamental data on the shape of natural protein molecules, including 3D positional coordinates, should be made freely available to researchers everywhere. However, intellectual property protection for inventions based on these can play an important role in stimulating the development of important new health care projects. Policies should be established to permit an appropriate balance between these goals.

V. Future Meetings

Annual meetings of representatives of the structural genomics community are anticipated for the continued discussion of these issues. The Second International Structural Genomics Meeting is being planned for April 4-6, 2001, in Virginia, USA.

These principles were supported by the participants in the First International Structural Genomics Meeting in Cambridge, UK, April 4-6, 2000.

Roster

Dr Sherin Abdel-Meguid 
Suntory Pharmaceutical Research Laboratories 
One Kendall Square 
Building 1400W 
Cambridge, MA 02139 
USA 
Phone: 00 1 617 621 0222 
Fax: 00 1 617 621 0555 
sherin2@aol.com 

Dr Geoff Barton 
EMBL-EBI 
The Wellcome Trust Genome Campus 
Hinxton 
Cambridgeshire, UK 
CB10 1SD 
Phone: 01223 494414 
Fax: 01223 494496 
geoff@ebi.ac.uk 

Professor Helen Berman 
Protein Data Bank 
Rutgers University 
Chemistry Department 
610 Taylor Road 
Piscataway, NJ 08854 
USA 
Phone: 00 1 732 445 4667 
Fax: 00 1 732 445 4320 
berman@rcsb.rutgers.edu 

Professor Ivano Bertini 
Director, Magnetic Resonance Center 
University of Florence 
Via L. Sacconi 6 
50019 Sesto 
Fiorentino 
Italy 
Phone: 00 39 055 4209 270 
Fax: 00 39 055 4209 271 
bertini@cerm.unifi.it 

Professor Sir Tom Blundell 
Department of Biochemistry 
University of Cambridge 
Tennis Court Road 
Cambridge, UK 
CB2 1GA 
Phone: 01223 333628 
Fax: 01223 766082 
tom@cryst.bioc.cam.ac.uk 

Professor Stephen K Burley 
The Rockefeller University 
1230 York Avenue 
Box 55 
New York, NY 10021-6399 
USA 
Phone: 00 1 212 327 7240 
Fax: 00 1 327 7240 
burley@rockvax.rockefeller.edu 

Dr Christian Cambillau 
AFMB-CNRS 
31 Ch. J. Aiguier 
13402 Marseille 
Cedex 20 
France 
Phone: 00 33 491 16 45 02 
Fax: 00 33 491 16 45 36 
cambillau@afmb.cnrs-mrs.fr 

Mr. David Carr 
Policy Unit 
The Wellcome Trust 
210 Euston Road 
London, UK 
NW1 2BE 
Phone: 0171 611 8220 
Fax: 0171 611 8742 
d.carr@wellcome.ac.uk 

Dr Marvin Cassman 
Director, NIGMS NIH 
45 Center Drive 
MSC-6200 
Bethesda, MD 20892-6200 
USA 
Phone: 00 1 301 594 2172 
Fax: 00 1 301 402 0156 
cassmanm@nigms.nih.gov 

Dr Cyrus Chothia 
MRC Laboratory of Molecular Biology 
University of Cambridge 
Hills Road 
Cambridge, UK 
CB2 2QH 
Phone: 01223 402221 
Fax: 01223 213556 
chc1@mrc-lmb.cam.ac.uk 

Miss Nicky Clarkson 
Conference & Meetings Administrator 
Hinxton Hall Conference Centre 
The Wellcome Trust Genome Campus 
Hinxton 
Cambridgeshire, UK 
CB10 1RQ 
Phone: 01223 495002 
Fax: 01223 495114 
nicky.clarkson@hinxton.wellcome.ac.uk 

Dr Robert Cooke 
Head of Molecular Recognition 
Medicines Research Centre 
GlaxoWellcome Research & Development 
Gunnelswood Road 
Stevenage 
Herts, UK 
SG1 2NY 
Phone: 01438 763367 
Fax: 01438 764865 
rc8817@GlaxoWellcome.co.uk 

Ms Anna Curson 
Project Analyst 
The Wellcome Trust 
183 Euston Road 
London, UK 
NW1 2BE 
Phone: 0171 611 8773 
Fax: 0171 611 0708 
a.curson@wellcome.ac.uk 

Professor Christopher Dobson 
New Chemistry Laboratory 
University of Oxford 
South Parks Road 
Oxford, UK 
OX1 3QT 
Phone: 01865 275916 
Fax: 01865 275921 
chris.dobson@icl.ox.ac.uk 

Professor Guy Dodson 
Department of Chemistry 
University of York 
York, UK 
YO10 5DD 
Phone: 01904 432519 
Fax: 01904 410519 
ggd@ysbl.york.ac.uk 

Dr Richard Durbin 
Head of Informatics Division 
The Sanger Centre 
The Wellcome Trust Genome Campus 
Hinxton 
Cambridgeshire, UK CB10 1SA 
Phone: 01223 494978 
Fax: 01223 494919 
rd@sanger.ac.uk 

Dr Charles Edmonds 
Program Director 
Division of Cell Biology & Biophysics 
NIGMS/NIH 
45 Center Drive RM 2AN18B 
Bethesda, MD 20892-6200 
USA 
Phone: 00 1 301 594 4428 
Fax: 00 1 301 480 2004 
edmondsc@nigms.nih.gov 

Professor Aled Edwards 
Associate Professor 
Banting and Best Department Of Medical Research 
C.H Best Institute Room 402 
University of Toronto 112 College Street 
Toronto, Ontario 
M5G 1L6 
Canada 
Phone: 00 1 416 946 3436 
Fax: 00 1 416 978 8528 
aled.edwards@utoronto.ca 

Professor Roger Fourme 
LURE Universite Paris-Sud 
Bât 209 D 
Université Paris.Sud 
91898 
Orsay Cedex 
France 
Phone: 00 33 1 64 46 81 26 
Fax: 00 33 1 64 46 41 02 
fourme@lure.u-psud.fr 

Professor Paul Freemont 
Centre for Structural Biology 
Imperial College of Science, Technology and Medicine 
South Kensington 
London, UK 
Phone: 0171 269 3291/594 5324 
Fax: 0171 269 3671 
p.freemont@ic.ac.uk 

Dr Michael Geisow 
16 The Banks 
Bingham 
Nottinghamshire, UK 
NG13 8BL 
Phone: 01949 876 156 
Fax: 01949 876156 
mike@biodigm1.u-net.com 

Professor Paul Gilna 
Program Director 
Biological Databases & Informatics 
National Science Foundation 
4201 Wilson Blvd 
Arlington, VA 22230 
USA 
Phone: 00 1 703 306 1469 
Fax: 00 1 703 306 0356 
pgilna@nsf.gov 

Professor Udo Heinemann 
Kristallographie 
Max-Delbrück-Centrum für Molekulare Medicin 
Robert-Rössle-Strasse 10 
D-13125 Berlin 
Germany 
Phone: 00 49 30 9406 3420 
Fax: 00 49 30 9406 2548 
heinemann@mdc-berlin.de 

Professor Wayne Hendrickson 
Department of Biochemistry and Molecular Biology 
Columbia University 
630 West 168th Street 
BB-2-202 
New York, NY 10032 
USA 
Phone: 00 1 212 305 3456 
Fax: 00 1 212 305 7379 
wayne@convex.hhmi.columbia.edu 

Dr Nobuo Kamiya 
Senior Scientist 
Division of Bio-Crystallography Technology 
RIKEN Harima Institute/Spring 8 
Kocuto 
Mikazuki 
Myogo 679-5148 
Japan 
Phone: 00 81 791 58 2839 
Fax: 00 81 791 58 2834 
nkamiya@sp8sun.spring8.or.jp 

Professor Robert Kaptein 
Bijvoet Centre for Biomolecular Research 
University of Utrecht 
Padualaan 8 
NL-CH-3584 
Utrecht 
The Netherlands 
Phone: 00 31 30 253 3787 
Fax: 00 31 30 253 7623 
kaptein@nmr.chem.uu.nl 

Professor Sung-Hou Kim 
Calvin Laboratory 
University of California 
Berkeley, CA 94720 
USA 
Phone: 00 1 510 486 4333 
Fax: 00 1 510 486 5272 
shkim@cchem.berkley.edu 

Dr Richard Kramer 
Novartis Pharmaceuticals Corp 
556 Morris Avenue 
Summit, NJ 07901 
USA 
Phone: 00 1 908 277 4687 
Fax: 00 1 908 277 5035 
richard.kramer@pharma.novartis.com 

Dr Victor Lamzin 
EMBL C/O Desy 
Notkerstr 74 
22603 Hamburg 
Germany 
Phone: 00 49 40 89 902 121 
Fax: 00 49 40 89902 149 
victor@embl-hamburg.de 

Professor Michael Levitt 
Department of Structural Biology 
Stanford Medical School 
Stanford, CA 94305 
USA 
Phone: 00 1 650 723 6800 
Fax: 00 1 650 723 8464 
michael.levitt@stanford.edu 

Professor Peter Lindley 
European Synchrotron Radiation Facility 
ESRF, BP 220 
F-38043 Grenoble 
Cedex 
France 
Phone: 00 33 4 7688 2014 
Fax: 00 33 4 7688 2160 
lindley@esrf.fr 

Dr Michal Linial 
Department of Biological Chemistry 
Life Science Institute 
The Hebrew University 
Givat Ram 
Jerusalem 91904 
Israel 
Phone: 00 972 2 658 5425 
Fax: 00 972 2 658 6448 
michall@leonardo.ls.huji.ac.il 

Dr Albrecht Messerschmidt 
Max-Planck-Institute for Biochemistry 
AM Klopferspitz 18A 
Germany 
Phone: 00 49 89 8578 2669 
Fax: 00 49 89 8578 3516 
messersc@biochem.mpg.de 

Dr Stefan Michalowski 
Head, Megascience Unit 
OECD 
2 rue André-Pascal 
75016 Paris 
France 
Phone: 00 33 1 45 24 92 89 
Fax: 00 33 1 45 24 96 44 
michalowski@oecd.org 

Dr Colin Miles 
BBSRC 
Polaris House 
North Star Avenue 
Swindon 
SN2 1UH 
Phone: 01793 413359 
Fax: 01793 413234 
colin.miles@bbsrc.ac.uk 

Dr Gaetano Montelione 
CABM - Rutgers University 
679 Hoes Lane 
Piscataway, NJ 08854 
USA 
Phone: 00 1 732 235 5321 
Fax: 00 1 732 235 4850 
guy@cabm.rutgers.edu 

Dr Michael Morgan 
Chief Executive of The Wellcome Trust Genome Campus 
The Wellcome Trust 
183 Euston Road 
London, UK 
NW1 2BE 
Phone: 020 7611 8691 
Fax: 020 7611 8688 
m.morgan@wellcome.ac.uk 

Professor John Moult 
CARB 
University of Maryland 
9600 Gudelsky Drive 
Rockville, MD 20850 
USA 
Phone: 00 1 301 738 6241 
Fax: 00 1 202 738 6255 
jmoult@tunc.org 

Dr John Norvell 
Program Director 
Division of Cell Biology & Biophysics 
NIGMS/NIH 
45 Center Drive Room 2AS13B 
Bethesda, MD 20892-6200 
USA 
Phone: 00 1 301 594 0533 
Fax: 00 1 301 480 2004 
norvellj@nigms.nih.gov

Dr Mark Palmer 
Medical Research Council 
20 Park Crescent 
London, UK 
W1N 4AL 
Phone: 0171 7670 5360 
Fax: 0171 7637 2856 
palmer@headoffice.mrc.ac.uk 

Dr Ari Patrinos 
Associate Director for Biological & Environmental Research 
US Department of Energy 
19901 Germantown Road 
Germantown, MD 20874-1290 
USA 
Phone: 00 1 301 903 3251 
Fax: 00 1 903 5051 
ari.patrinos@science.doe.gov 

Professor Simon Phillips 
Astbury Centre for Structural Molecular Biology 
School of Biochemistry and Molecular Biology 
University of Leeds 
Leeds, UK 
LS2 9JT 
Phone: 0113 233 3027 
Fax: 0113 233 1407 
s.e.v.phillips@leeds.ac.uk 

Dr Debbie Poole 
Programme Manager 
The Wellcome Trust Genome Campus 
Hinxton 
Cambridgeshire, UK 
CB10 1RQ 
Phone: 01223 495006 
Fax: 01223 495114 
d.poole@hinxton.wellcome.ac.uk 

Professor Randy Read 
Wellcome Trust/MRC Building 
Hills Road 
Cambridge, UK 
CB2 2XY 
Phone: 01223 336500 
Fax: 01223 336827 
rjr27@cam.ac.uk 

Professor David Rice 
Department of Molecular Biology and Biotechnology 
University of Sheffield 
Firth Court 
Western Bank 
Sheffield, UK 
S10 2TN 
Phone: 0114 222 2750 
Fax: 0114 222 2850 
d.rice@sheffield.ac.uk 

Dr Ajay Royyuru 
Computational Biology Center 
IBM T J Watson Research Center 
PO Box 704 
Yorktown Heights, NY 10598 
USA 
Phone: 00 1 914 784 7813 
Fax: 00 1 914 784 7455 
ajayr@us.ibm.com 

Professor Chris Sander 
CISO 
Millennium Predictive Medicine 
700 One Kendall Square 
Cambridge, MA 02139 
USA 
Phone: 00 1 617 577 3534/7245 
Fax: 00 1 617 249 0169 
sander@mpi.com 

Mr. David Seemungal 
Policy Unit 
The Wellcome Trust 
210 Euston Road 
London, UK 
NW1 2BE 
Phone: 0171 611 8290 
Fax: 0171 611 8742 
d.seemungal@wellcome.ac.uk 

Dr Barbara Skene 
Scientific Programme Manager 
Wellcome Trust 
183 Euston Road 
London, UK 
NW1 2BE 
Phone: 0171 611 8677 
Fax: 0171 611 0708 
b.skene@wellcome.ac.uk 

Dr Sharon Spencer 
Catalyst Biomedica Ltd. 
183 Euston Road 
London, UK 
NW1 2BE 
Phone: 0171 611 8310 
Fax: 0171 611 8857 
spencer@wellcome.ac.uk 

Professor Joel Sussman 
Department of Structural Biology 
Weizmann Institute of Science 
Rehovot 76100 
Israel 
Phone: 00 972 8 934 2638 
Fax: 00 972 8 934 4159 
joel.sussman@weizmann.ac.il 

Dr William Taylor 
Division of Mathematical Biology 
National Institute for Medical Research 
The Ridgeway, Mill Hill 
London, UK 
NW7 1AA 
Phone: 0181 959 3666 
Fax: 0181 913 8545 
Wtaylor@nimr.mrc.ac.uk 

Dr Tom Terwilliger 
Los Alamos National Laboratory 
Mail Stamp M888 
Los Alamos, NM 87545 
USA 
Phone: 00 1 505 667 0072 
Fax: 00 1 505 665 3024 
terwilliger@lanl.gov 

Dr Jean-Claude Thierry 
CNRS 
IGBMC - 1 rue Laurent Fries 
67400 Illkirch 
France 
Phone: 00 33 3 88 65 33 06 
Fax: 00 33 3 88 65 32 76 
jct@igbmc.u-strasbg.fr 

Professor Janet Thornton 
Biomolecular & Molecular Biology 
University College London 
Gower Street 
London WC1E 6BT 
Phone: 0171 3807048 
Fax: 0171 9618499 
thornton@biochem.ucl.ac.uk 

Dr Tony Wilkinson 
AstraZeneca 
Mereside, Room 8AF4 
Alderley Park 
Macclesfield 
Cheshire 
SK10 4TG 
Phone: 01625 515167 
Fax: 01625 517692 
tony.wilkinson@astrazeneca.com 

Dr Shigeyuki Yokoyama 
Genomic Sciences Centre 
RIKEN 
2-1 Hirosawa 
Wako 
Saitama 351-0198 
Japan 
Phone: 00 81 48 467 9427 
Fax: 00 81 48 462 4675 
yokoyama@biochem.s.u-tokyo.ac.jp 

​