SBNet - Annual Report 2000

Dr. Björn O. Nilsson, Amersham Pharmacia Biotech, Chair
Prof. T. Alwyn Jones, Uppsala University, Programme Director

Dr. Gerard J. Kleywegt, Uppsala University, Coordinator

Uppsala, March 2001

1. Board
The composition of the Board underwent one change during the year 2000: due to a change of job for Dr Hoflack which took him to Belgium, he had to resign from the Board. By co-optation, the Board decided to recommend Dr Martin Norin as his replacement. This was later confirmed by the principal of Uppsala University, Prof. Bo Sundqvist. Hence, during the year 2000 the SBNet Board consisted of:
* Dr. Björn O. Nilsson, Amersham Pharmacia Biotech, Chair
* Dr. Jan Hoflack, AstraZeneca SCL (until Summer, 2000)
* Dr. Martin Norin, Pharmacia (from Autumn, 2000)
* Prof. Guy G.Dodson, University of York
* Prof. Iain D. Campbell, University of Oxford
* Prof. T. Alwyn Jones, UU, Programme Director
* Dr. Gerard J. Kleywegt, UU, Network Coordinator (not a member of the Board)
The Board met once during the year, namely at the Fourth Annual SBNet Conference in Tällberg. At the same meeting, the Board also met with the Network Council (all PIs), in particular to discuss a proposal to the SSF for a five-year continuation of the networking activities of SBNet (annual conference, workshops, courses, travel support, web site, mailing list, mentor system, coordinator, etc.). Also, the Board decided that the current Network will be continued until 31 December 2001.

2. Allocations
All available positions were allocated in 1996 and 1997. Allocations for supporting student travel, organisation of courses, etc. are made jointly by the Chair and the Programme Director on a case-by-case basis.

3. Graduate training
During the year 2000, the Network organised the following courses and workshops:

* "CNS". This was a two-day workshop (0.5 credit), held at the Biomedical Centre in Uppsala on 7 and 8 February, 2000. The workshop was organised by Gerard Kleywegt (SBNet coordinator, Uppsala University) with the help of local post-docs and students. The main speakers were Paul D Adams (Lawrence Berkeley Laboratory, USA), Ralf W Grosse-Kunstleve (Lawrence Berkeley Laboratory, USA), and John Kuszewski (NIDDK/NIH, USA). The object of the workshop was to acquaint both crystallographers and NMR spectroscopists with some of the basics of the structure solution, generation and refinement program CNS ("Crystallography and NMR System", developed by Axel T. Brünger and co-workers at Yale University, USA). The morning sessions consisted of lectures of interest to all users, whereas the afternoons were targeted (through lectures and computer practicals) to crystallographers and NMR spectroscopists separately. A total of 92 participants attended the workshop (72 from Swedish universities, 4 from Swedish industry, 13 from other Nordic countries, and the 3 speakers from the USA). Nineteen academic Swedish participants were awarded travel and accommodation grants.

* "NMR structure calculations using ARIA/CNS" (workshop). On March 29-30, 2000, in Göteborg, we organised the "ARIA workshop" on automated assignment and structure calculation of NMR data. The workshop attracted the attention of 19 participants, distributed over the NMR groups in Umeå, Stockholm (3), Linköping, Göteborg and Lund, and including one participant each from AstraZeneca and Pharmacia & Upjohn. Participants were encouraged to send relevant questions in advance, and to bring their own data to the workshop.
The workshop was held at Medicinareberget and practicals were organised in the computer lab of the Centre for Structural Biology. Invited lecturers were Michael Nilges and Jens Linge, both from EMBL Heidelberg, Germany, and Martin Billeter, Göteborg University.
The topics of the lectures included: CNS command language, structure calculations with ARIA/CNS, the ARIA protocols, data format and data conversion, automation of spectral analysis, the structure analysis scripts and installation notes for ARIA. The practicals focused on the setting up of structure calculations and structural analysis.
The workshop was concluded with a general discussion, and all participants were invited to the web-based ARIA discussion group.
The workshop was organised by Tineke Papavoine, Department of Chemistry, Göteborg University, and Göran Karlsson, Department of Molecular Biotechnology, Chalmers University of Technology.

* "Practical Protein Crystallisation" (course 1). The current bottlenecks in structure determination are the expression, purification, and crystallisation of the proteins. In this course, crystallisation was presented such that even beginners in the field could participate but the most up-to-date developments in the area were also included. Emphasis was on the practical, hands-on application of the current knowledge about crystallisation to problems in the laboratory. Expression and purification as they relate to crystallisation were also covered during one of the days.
The course includes extensive laboratory work. Invited guests of international repute present lectures in addition to leading the laboratory exercises. The course is one week (1.0 credit). It was held from 16 - 22 February 2000, at Uppsala University, Uppsala. There were 21 participants, of which 13 came from Swedish universities, 6 from Swedish industry and two from other Nordic universities.
The course was organised by Terese Bergfors, Uppsala University. In 1996, she organised the first "Practical Protein Crystallisation" course at Uppsala University. Thanks to funding by SBNet, this course now hosts guest speakers and crystallisation experts from abroad, and the course is currently held twice a year. The September 2000 course is the fifth such course. Terese Bergfors has edited the book used in the course, specifically because no such practical manual existed for teaching crystallisation.
Invited lecturers were Jan-Christer Jansson (Deputy Director at Centre for Surface Biotechnology, Uppsala University, and Principal Scientist at Amersham Pharmacia Biotech), George DeTitta (executive vice president of Hauptman-Woodward Medical Research Institute, whose most recent work is on high throughput approaches to crystallisation as will be needed for the Structural Proteomics post-genomic era), and Patrick Shaw Stewart (who founded Douglas Instruments, a company that specialises in automatic crystallisation systems). Lecturers are carefully selected not only on the basis of their expertise in the field and for their demonstrated teaching ability. The participants' written course evaluations were very positive.

* "Practical Protein Crystallisation" (course 2). For general information, see above. The course was held from 25 - 29 September 2000, at Uppsala University, Uppsala. There were 20 participants, of which 14 came from Swedish Universities, 3 from Swedish Industry and 3 from Denmark. The course was organised by Terese Bergfors, Research Engineer, Uppsala University. Invited lecturers were Naomi Chayen (principal research fellow in Biomedical Sciences at Imperial College where she specialises in the crystallisation of biological macromolecules), Bernadette Byrne (Uppsala University/Imperial College London; a molecular biologist working with so Iwata, specialising in the modification and over-expression of membrane proteins for structural analysis), and Thomas Urbig (Senior scientist at Stockholm University, Dept. of Biochemistry, who since 1997 has specialised in the over-expression and purification of membrane proteins for structural studies). The popularity and need of the course is reflected in the fact that the number of applications always exceeds the number of available places. For example, for this course 47 qualified applications were received. Again, the course evaluation was very positive.

* "Structure-assisted drug design" (course). From June 13 to 16, a course in Structure-assisted drug design was held at the Department of Medical Biochemistry & Biophysics, Karolinska Institute, Stockholm with support from SBNet. The course (corresponding to one point credit) gave an overview of the drug-design process by a combination of lectures on the various aspects of the design process and computer-based practicals. Emphasis was laid on the industrial side of the process, and all the teachers/lecturers were therefore recruited from industry.
Course organisers: Martin Norin and Mats Kihlén, Pharmacia & Upjohn, Tomas Lundqvist, AstraZeneca, and Gunter Schneider, Karolinska Institute. The course was limited to 20 participants due to limitations for the computer practicals. Sixteen of the participants were PhD students (12 were SBNet students) and four were post-docs. One of the post-docs, Thomas Hansson, was a former SBNet student.
The course was very well received by the students (based on 13 evaluations which were sent back by the participants). The mean overall rating on a scale from 1 to 10 was 9.

4. New PhDs
During the year 2000, two of the SBNet-funded students obtained their PhD:

* Patrik Andersson (PI Gottfried Otting; October 2000; Karolinska Institute). "Development of new NMR techniques and Structural characterization of complexes between the N-terminal domain of the E. coli arginine repressor and operator DNA."

* Andreas Muranyi (PIs Sture Forsén, Torbjörn Drakenberg; May 2000; Lund University). "EGF-like Modules in Blood Coagulation Proteins. Ca2+ binding, module interactions, structure and dynamics as studied by NMR spectroscopy."

5. Scientific output
Detailed research reports for the year 2000 are provided in Appendix I. A total of 21 papers were published by SBNet-funded scientists (compared to 21 in 1999, 22 in 1998, and 3 in 1997). In addition, a large number of talks and posters were presented by these scientists. Details are given in the research reports.

6. Fourth Annual Conference
The Fourth Annual SBNet Conference (Tällberg, 9-12 June) was again an eagerly awaited event with more than 170 participants (including 27 from Swedish industry and 13 foreign speakers and Board members). The format of the Conference was similar to that employed previously, with morning and evening lecture sessions. Each session included two renowned foreign speakers and several talks by Swedish students and post-docs. This year, the sessions were on "New horizons in NMR spectroscopy" (organised by Mikael Akke and Torleif Härd), "-Omics" (Sherry Mowbray), "Structures and Methods in EM and X-ray (Uwe Sauer), "Drug design" (Karl Hård), and "Complexes and other hot structures (Stefan Knight).
More than 80 posters were presented in a high-quality poster session. The Pharmacia Poster Award for the best poster went to Magnus Wolf-Watz (KTH), for his poster "Solution structure and Runt binding of CBFB". The lectures (both by the invited speakers and by the young persons) were generally of high quality. The Astra Structural Chemistry Laboratory Award for the best presentation by a young person went to Doreen Dobritzsch, KI ("Crystallographic studies on dihydropyrimidine dehydrogenase"). The traditional football match on Saturday afternoon ended in an equally traditional victory for the X-ray/EM team over the NMR/Modelling team (4-2).
More information about the Conference (including the programme, list of participants, abstracts of talks and posters, and many photos of the meeting) can be found on the SBNet website (

7. Internal and external communication
For the intra-Network communication, two major instruments are used. The first is the SBNet mailing list (, through which the Swedish structural biology community is regularly informed about Network matters (e.g., calls for proposals by related SSF-funded networks, annual conference), scientific matters (e.g., upcoming conferences, new software), educational matters (e.g., upcoming courses), new positions in academic and industrial structural biology labs in Sweden, and more. The current mailing list contains addresses of more than 270 Swedish structural biologists (PIs, researchers, post-docs, students).
The second instrument, which is also the Network's "face" to the outside world, is the SBNet site on the World-Wide Web (URL: This site is updated continuously (typically, two or three times a week) and contains a large amount of information about and related to the Network. to foster interactions between structural biologists and other biomedical scientists, a "Who is Who ?" page is maintained. The site also contains an archive of the history, activities and results of the Network. During 2000, the SBNet web site was visited ~29,000 times, and served ~80,000 HTML pages (these counts do not include images, visits by robots, etc.). For comparison: during 1999 the website was visited ~17,000 times, serving ~61,000 HTML pages).

8. Travel grants
The SBNet Board has allocated funds to support various types of travel for participants in the Network, including:
* Data-collection at SNC and MAX;
* Lab-rotation visits (Sweden);
* Student-mentor visits;
* Travel and accommodation for SBNet courses;
* Incidental support for travel to other relevant workshops;
* Foreign travel awards for PhD students. These awards are intended to fund travel and subsistence for a trip (1-4 weeks) to a foreign centre-of-excellence in any of the areas of (or related to) structural biology. The purpose of the trip must be to acquire expertise or know-how that is not readily available within Sweden itself. Candidates who receive an award must write a short report of their trip (that is published on the SBNet web-site), and be prepared to travel to other interested laboratories in Sweden to give a presentation about the results of their trip. During 2000, foreign travel awards were awarded to Jeff Abramson, Karl Edman, Jenny Sandmark, and Gergely Katona. Their travel reports have been or will be published on the SBNet website.

9. SBNet Lecturer
A few years ago, the SBNet Board decided to allocate funds to support foreign travel (see above) and an annual "SBNet Lecturer". This was envisaged to be a foreign structural biologist who has made seminal contributions to the field, and who is invited to tour all the structural biology laboratories in Sweden for a period of 10-14 days. In 1999, the first SBNet lecturer was Dr. Ad Bax (NIH), one of the world's foremost experts on NMR spectroscopy. For the year 2000, the SBNet Lectureship was awarded to Prof. Michael Rossmann (Purdue University), one of the real pioneers in structural biology. Prof. Rossmann participated in the early work to determine the structure of haemoglobin and has subsequently solved numerous structures of enzymes but primarily of viruses. All along he has developed new methods to extend the possibility to determine macromolecular structures. In recent years he has incorporated electron microscopy into his field of methods to tackle problems not accessible to crystallography. His name is associated with numerous major achievements. Prof. Rossmann visited the Swedish structural biology laboratories from 8 to 18 January, 2001.

10. Collaborations with industry
The structural biologists from the industrial laboratories at Pharmacia, AstraZeneca, Amersham Pharmacia Biotech, Biovitrum, Karo Bio and Active Biotech Research are active and valued participants in the Network (e.g., annual conference, mentor system). Some of the positions sponsored by SBNet involve close collaboration between industry and academia. The Network also involves the industrial participants more closely in its educational activities (e.g., the workshop on drug design was organised jointly by academic and industrial scientists). Such initiatives are beneficial to both students (who get to know leading scientists in Swedish industry) and the industrial scientists (who get to know students interested in their line of research).

11. International collaborations
Essentially all groups that participate in the Network have national and international collaborations, and many participate in one or more EU-funded programmes. Since these collaborations usually arise from personal networking, merits, and research interests, the Network does not play a significant role in their establishment. The "Who is Who ?" page on the SBNet website is intended to help biomedical scientists to identify and contact structural biologists who share some of their research interests.
It should also be noted that SBNet has functioned as a role model for a similar network that was set up in Finland last year.

12. Abbreviations
GU, Gothenburg University
KI, Karolinska Institute
KTH, Royal Institute of Technology
KVA, Royal Swedish Academy of Sciences
LU, Lund University
PI, Principal Investigator
SBNet, Structural Biology Network
SLU, Swedish University of Agricultural Sciences
SNC, Swedish NMR Centre
SSF, Swedish Foundation for Strategic Research
SU, Stockholm University
UmU, Umeå University
UU, Uppsala University

SBNet Latest update at 2 April, 2001.