Sesame Workshop/School on Bioinformatics and Structural Modelling; Sabanci University, Istanbul Turkey; September 3-8, 2001  

Irit Sagi, Metaxia Vlassi, Zehra Sayers

During the Sesame (Synchrotron-light Experimental Science and Applications in the Middle-East) Structural Molecular Biology (SMB) meeting in Cyprus in December 2000 (see the SESAME web site www.sesame.org.jo for a report) ideas for future projects were explored, keeping in mind the importance of developing a local user base for SESAME and establishing strong collaborations among scientists from the region. The idea for a bioinformatics workshop was conceived not only because bioinformatics is a fast developing field which can be used to complement structural studies carried out on synchrotrons, but also because bioinformatics tools are on the World Wide Web and hence accessible to people even in parts of the world where other facilities may not be present. People located in different countries can share data and analysis skills, establish collaborations and develop projects together in the electronic medium at a relatively low cost.

Dr. Zehra Sayers offered to host the 'Bioinformatics and Structural  Modelling' workshop/school at Sabanci University (SU) near Istanbul and Drs. Irit Sagi (Weizmann Institute, Israel) and Metaxia Vlassi (NCSR "Demokritos", Greece) offered their help as co-organisers. These three scientists met for the first time at the Cyprus SMB workshop.  With help from Dr. H. Winick, who is one of the driving forces behind the SESAME project, it was possible to get sponsorship from UNESCO. TUBITAK (Turkish National Scientific and Technical Research Council), Sabanci University and the Israeli Synchrotron Radiation Fund also provided funds which  made it possible to cover local expenses and also to provide travel allowances  for all participants.

The workshop/school was at post-graduate level, and the twenty-four students from different countries (including Armenia, Bosnia and Herzegovina, Egypt, Greece, Israel, Jordan, Morocco, Poland, Turkey and the USA) came from diverse disciplines such as medicine, computer science, physics and biology.

The lecturers included C. Baysal (Sabanci University, Turkey), I. Berezovsky (Weizmann Institute, Israel), E. Eliopoulos (University of Athens, Greece), A. Gürsoy (Bilkent University, Turkey), D. Lancet (Weizmann Institute, Israel), S. Mobashery (Wayne State University, USA), R. Najmanovich (Weizmann Institute, Israel), P. Rizkallah (Daresbury Laboratory, UK) I. Sagi (Weizmann Institute, Israel), Z. Sayers (Sabanci University, Turkey), U. Sezerman (Sabanci University, Turkey), M. Vlassi (NCSR "Demokritos", Greece), S. Wakatsuki (Photon Facotry, Japan), H. Winick (Stanford University,USA), A. Yonath (Weizmann Institute, Israel), and P. Zielenkiewicz (Polish Academy of Sciences, Poland).

The workshop/school was designed to have lectures in the morning and practical sessions in the afternoon. Lectures covered introduction to experimental techniques for structure determination based on synchrotron radiation, e.g. X-ray crystallography (M. Vlassi, P. Rizkallah), small angle scattering (Z. Sayers) and EXAFS (I. Sagi). Complementarity of results obtained with different techniques (Z. Sayers)   as well as emergence of novel methods for dynamic studies (I. Sagi) was emphasised.  Analysis of the crystallographicaly determined structures of bacterial ribosome and ribosome-antibiotics complexes (A. Yonath) highlighted possibilities for drug design. Structure based modelling and molecular dynamics simulations of biological systems at scales from those of catalytic sites of enzymes to large structures such as surface components of bacteria (S. Mobashary) provided examples for how 3D modelling tools may be used for bridging experimental data and developing alternative strategies  for rational drug design. A survey of a target oriented structural genomics project using synchrotron X-ray protein Crystallography was also given (S. Wakatzuki). These lectures focused on results obtained using various synchrotron radiation sources around the world e.g. APS, Photon Factory, ESRF, DESY, Daresbury, SSRl and Brookhaven. 

Talks on tools for utilisation of data from the Human Genome project (D. Lancet) and new strategies for structural motif recognition (I. Berezovsky) introduced different aspects of analysis of DNA and protein sequence data bases. Secondary structure predictions (E. Eliopoulos), molecular dynamics simulations (C. Baysal), homology modelling U. Sezerman), threading (P. Zielenkiewcz) and docking methods (R. Najmanovich) were presented both in lectures as well as used as topics for practical exercises.

Practical sessions were carried out in a computer lab at SU equipped with 15 PCs and the necessary peripherals (e.g. printers, multimedia facilities etc.). Each PC was used by a workgroup of two students, that allowed everybody to gain direct experience.

Practical sessions were computer based exercises in the form of tutorials prepared as web pages that were accessed through the local website developed for the purposes of the workshop.  The topics of each day's tutorial were related to the morning lectures and covered use of web-based resources related to macromolecular structure: search and retrieval (e.g. ENTREZ, SRS) of data from various databases (such as PFAM, PROSITE, MIME, SwissProt and the PDB structural database), sequence similarity searches (e.g.BLAST), sequence alignments (CLUSTALW, t-COFFEE), secondary structure predictions (PHD, GOR-IV and Joint prediction: by Eliopoulos), sequence-prototype based prediction of the closed loops (developed by I. Berezovsky),  homology modelling (SwissModel and 3D-PSSM), threading (developed by P. Zielenkiewicz) and ligand-protein contact analysis (developed by R. Najmanovich). Students were also introduced to 3D visualisation programs (e.g. rasmol and Swiss-pdb viewer) which were used to display, compare and analyse known 3D structures and models. One protein with unknown 3D structure belonging to a well-studied protein family served as a test case for all practical sessions.

Availability and rapid accumulation of DNA sequence data necessitate heavy use of electronic means for storage, transmission and analyses. Effective use of sequence-based information reveals previously unknown relationships - ranging from the identification of unknown genes to the prediction of protein structures. Parallel to improvements in experimental methodologies for faster structural data collection and analysis, computational tools are now being developed aimed at predicting structures and elucidation of structure-function relationships as well as for drug design. Today Web-based facilities such Entrez at NCBI or Biology Workbench at SDSC, worldwide accessible databases e.g. Swiss Prot, PDB as well as web-based tools (BLAST, CLUSTAL W), and servers for secondary structure predictions (e.g. PHD, JOINT, GOR-IV) and 3D modelling (e.g. SwissModel, 3d-pssm) are at the disposal of scientists from many countries. The ease of access to data and facilities provide opportunities for competitive research regardless of the location of the scientist.

The workshop/school confirmed that bioinformatics and computational biology are emerging fields which could be developed in SESAME countries as a prelude to the synchrotron activities. This would help to build a user base with background in structural analysis and encourage establishing collaborations in the region. A proposal, for a computational facility that will be based in Jordan at the SESAME site, to be taken to representatives of respective countries and to the SESAME Council, is being prepared.

The great success of the workshop has opened a window of new opportunities to expose young scientists to cutting edge scientific projects and to train them in these fields. The nice and relaxed scientific atmosphere has promoted scientific interactions and new hope for the future of the Middle East region.

Irit Sagi, Metaxia Vlassi, Zehra Sayers

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