Structural Bioinformatics and Protein Modelling

Structural Bioinformatics and Protein Modelling

3  days intensive hands-on course, 3 ECTS Credits

Course Overview

Advances in high-throughput techniques in structural biology have resulted in thousands of three-dimensional structures of proteins and their complexes with various ligands, including substrate analogues and inhibitors. The technical developments and the wealth of information generated within these projects have radically transformed the way in which homology-based protein modelling and drug discovery projects can be run.

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. After finishing the course the participants will be able to:

• Use Internet-based structural bioinformatics tools and analyse the three-dimensional structure of a protein and a protein-ligand complex and perform homology-based modelling.

• Understand the general principles behind protein crystallisation and X-ray crystallography, assess the requirements and take active part in the planning and the subsequent development of this type of projects.

The course will also serve as a meeting point and will provide networking opportunities with people from Sweden and Denmark.

Scientists from industry and academia and persons responsible for R & D or persons just looking for new ideas for product development will benefit from the course.

There are no formal requirements on academic qualifications, however in order to be able to absorb as much as possible from the course content it is advisable that the participants have a background in chemistry/biochemistry/molecular biology or are involved in R & D work with the area. Participants with other backgrounds can expect to get a broad overview of principles and tools in proteins structure, modelling and design, which can inspire to new understanding and insights.

• An overview of the crystallography techniques used in structure determination of proteins and protein-ligand complexes.
• An overview of the general principles of protein structure, function and dynamics, the forces that stabilise proteins and control protein-protein and protein-ligand interactions.
• An overview of the basic requirements for three-dimensional structure prediction and homology-based modelling.

Computer tutorials during the course will include:

Hands-on training in the use of industry-standard structure visualisation and homology modelling programs.

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.

 7 p.m. 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 modeling. Visit to MAX Lab & lunch.

Afternoon: Private discussion of own projects. Modeling of complexes. Evolutionary trace method.

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, computational chemistry and biostatistics. 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.

Each day will include morning (9-12) and afternoon (13.15-17) sessions. Lunch will be at 12, coffee will be served at 10 and 15. Morning sessions will be mostly lectures, while afternoon sessions will be focused on computer tutorials.

Registration deadline: August 16, 2009.  The registration is binding.

Lund University Commissioned Education

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