Structural Bioinformatics and Protein Modelling

Aim

This 4 days intensive hands-on course aims at providing the participants with basic understanding in the areas of modern structural bioinformatics and homology-based protein modelling. An overview of the crystallography techniques used in structure determination of proteins and protein-ligand complexes will be presented as well as general principles of protein structure, function and dynamics together with the basic requirements for three-dimensional structure prediction and homology-based modelling. After finishing the course the participants should be able to build own homology models of proteins of interest for use in projects with relation to biochemistry/molecular biology and other areas in biotechnology.

Location & Organization

Organizer

Lund University Commissioned Education

Co-organizers

Department of Molecular Biophysics, Lund University

Course Director

Professor Salam Al-Karadaghi

Faculty / Teachers

Professor Salam Al-Karadaghi is the head of the Department of Molecular Biophysics, Lund University, and is responsible for organizing the course. He is also one of lecturers. Professor Al-Karadaghi has published more than 60 scientific papers in the field of protein structure and function and has contributed to 41 entries in the Protein Data Bank, PDB. Outside the university Al-Karadaghi has been involved in structure-guided design projects with several companies such as Active Biotech, Biovitrum, Leo Pharma, ALK-Abelló.

Dr. Björn Walse is a founder and CEO of SARomics AB offering R&D support to pharmaceutical and biotechnology industries within the areas of structural biology and in silico drug discovery. Previously Björn was responsible for managing structural chemistry activities in drug discovery projects in the therapeutic areas of cancer, autoimmunity and inflammatory diseases at Active Biotech in Lund.

Location / venue

October 12 – October 15, 2009
The course will take place at the Chemistry Centre, Lund University. Course fee is 16.500 SEK, VAT exclusive. The fee comprises diploma, course literature, coffee, lunch and course dinner.

Costs

16.500 SEK

Timing & Workload

Duration 4 days
ECTS points 3 ECTS Credits
Frequency 1
 

Teaching methods used

Course program
Day 1
Morning: Overview of X-ray crystallography and protein crystallization. Basics of protein structure, classification of structures.
Afternoon: Structural databases (PDB, PDBSUM, CATH, SCOP, DALI); Graphics tools for analysis of structures: JalView, SwissPDB Viewer. Structure-based sequence alignment; Symmetry and the biological unit in PDB. How to view electron density; criteria for structure quality.
19.00 Course dinner
Day 2
Morning: Secondary structure prediction; homology modelling; quality of a homology model.
Afternoon: Simple modelling; effect of mistakes in sequence alignment; model optimisation and quality check.
Day 3
Morning: Advanced modelling: difficult cases. Overview of Discovery Studio and DS Modeller.
Afternoon: Modelling and model analysis using DS Visualiser & Modeller.
Day 4
Morning: General discussion. Overview of software alternatives, future trends in homology modelling. Visit to MAX-lab and lunch.
Afternoon: Private discussion of own projects with course tutors. Modelling of complexes. Evolutionary trace method.

Examination no

Criteria

Is the course taught in English? yes
Is documentation available? (book, syllabus)? yes
Is the course open for external researchers? yes

What quality assurance system is in place?

The course is monitored and approved by The Office of Evaluation at Lund University. Participants is asked to fill out an evaluation etc.

More Information

http://www.education.lu.se/o.o.i.s/20700