SESAME WorkShop Bioinformatics and Structural Modeling

Publish Date
03 September, 2001

Organizers

Z. Sayers (Turkey), I. Sagi (Israel) and M. Vlassi (Greece)

Sponsored by

Sabanci University,TUBITAK, UNESCO, Israeli Synchrotron Fund

Background and Objectives

Following Sesame Workshops on Structural Molecular Biology (Athens, April 6-7, 2000 & Cyprus, December 6-8, 2000; see www.sesame.org.jo on experimental techniques for structure determination using synchrotron radiation, this workshop/school will focus on a complementary area - computational tools used in structure analysis. Lectures and practical sessions will offer students the opportunity to gain hands-on experience in using web-based tools for sequence and structural analysis and modelling.

In its broadest sense bioinformatics deals with the creation and development of information and computational technologies for problems in molecular biology, biochemistry and biophysics. Availability and rapid accumulation of DNA sequence data have resulted in coordinated efforts to enhance the capacity to critically evaluate and utilize this data. 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. Particular emphasis will be given to computational tools for determining sequence homologies, phylogenetic trees and prediction of 3-D structure of biological molecules.

Specifictopics for practical sessions

  • Introduction to primary, secondary and tertiary structure and related databases
  • Introduction to graphics programs for visualization of 3D structure of proteins
  • Secondary structure prediction and related databases and software
  • Homology searches and alignment strategies
  • Homology modeling of 3D structure of proteins and related databases and software

List of lecturers/working group leaders (some not yet confirmed)

C. Baysal (Turkey), M. Edelman (Israel), E. Eliopolos (Greece), D. Lancet (Israel), S. Mobashery (USA), I. Sagi (Israel), Z. Sayers (Turkey), U. Sezerman (Turkey), M. Vlassi (Greece), A. Yonath (Israel), P.Zielenkiewicz (Poland)

Information for Student Applicants

A maximum of 20 students will be accepted.To be considered please fill out the attached application form and send it by August 3, 2002 to Professor Zehra Sayers by fax [90-(0)216-483-9550] or Email:zehra@sabanciuniv.edu Students must arrive by the evening of September 2 and stay at least until the evening of September 7.An excursion is planned for Sept. 8.
Lodging and meals will be provided for all participants. Reimbursement for travel by students, up to a maximum of $500, is available with advance request and presentation of tickets upon arrival in Istanbul. Information about the exact location and other details will be sent to those applicants who are accepted.
(June 16, 2001)

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

Application Form (Deadline for is August 3,2001)

Family Name: Given Name:
Date of birth: Present Nationality:
Present or most recent position or student status:
Institution/Department/Country:
Highest Degree/University:
Your mailing address:
Phone (office): Phone (home):
Fax: E-mail:
Estimated cost of your air travel:
Please use the rest of this page, or one additional page, to tell us about your background, research interests and how you think this workshop/school will be useful for you.

Send by August 3, 2001 to Prof. Zehra Sayers by fax [90-(0)216-483-9550] or Email:zehra@sabanciuniv.edu

PRELIMINARY SCHEDULE; Workshop/School on Bioinformatics & Structural Modelling / (June 16, 2001)

Monday, September 3, 2001

09:00-09:15 Welcome and Introduction Z.Sayers
09:15-10:00 Introduction to SESAME activities H. Winick
10:00-10:30 Coffee break  
10:30-11:15 SR methods for 3D structure determination Z. Sayers
11:15-12:00 Introduction to protein structure M. Vlassi
12:00-13:00 Lunch Break  
13:00-17:30 Exercises  
Introduction to primary, secondary and tertiary structure and related databases

Tuesday, September 4, 2001

09:15-10:00 3D structure and structure/function relationships C. Baysal
10:00-10:30 Coffee break  
10:30-11:15 3D structure of bacterial ribosome A. Yonath
11:15-12:00 Secondary structure prediction software I. Eliopoulos
12:00-13:00 Lunch Break  
13:00-17-30 Exercises  
Introduction to graphics program for visualization of 3D structure of proteins

Wednesday, September 5, 2001

09:15-10:00 Human genome project D. Lancet
10:00-10:30 Coffee break  
10:30-11:15 Homology modelling U. Sezerman
11:15-12:00 Threading P. Zielenkiewicz
12:00-13:00 Lunch Break  
13:00-17:30 Exercises  
Secondary structure prediction and related databases and software

Thursday, September 6, 2001

09:15-10:00 Ligand - Protein Docking M. Edelman
10:00-10:30 Coffee break  
10:30-11:15 Modelling of RNA Helicases I. Sagi
11:15-12:00 Title to be announced P. Zielenkiewicz
12:00-13:00 Lunch Break S. Wakatzuki
13:00-17:30 Exercises  
Homology searches and alignment strategies

Friday, September 7, 2001

09:15-10:00 ioinformatics/drug design of Acetyl-cholinesterase J. Sussman
10:00-10:30 Coffee break  
10:30-11:15 Drug design for cancer S. Mobashary
11:15-12:00 Title to be announced A. Wlodawer
12:00-13:00 Lunch Break S. Wakatzuki
13:00-17:30 Exercises and general discussion  
Homology modelling of 3D structure of proteins and related databases and software

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