Bioinformatics III

Graham Kemp > Teaching > Bioinformatics III

Bioinformatics III: Three-dimensional Structure

2004/2005

This course, Bioinformatics III, is part of the International Master's Programme in Bioinformatics.

This course builds on the introductory material on Protein Structure that was given as part of Bioinformatics I. Students should review the contents of those lectures.

News

2005-03-07	Assignment 4 is now available.
2005-02-22	A list of assignments received is available on-line.
2005-01-28	A bug in function tf_ptspts() resulted in the function sometimes returning an incorrect transformation matrix. I've fixed that bug and I've recompiled the transformation library. If the superpositions that you obtained in practical GK-2 were not good as you thought they should have been, please try running your program again.

Aims

To introduce the principles of macromolecular structure determination by NMR and X-ray crystallography.
To present some of the computational challenges in macromolecular structure determination, analysis and modelling.
To introduce some articles from the scientific literature that are related areas covered in this course.

Objectives

At the end of this course, students should:

understand the principles of macromolecular structure determination by NMR and X-ray crystallography;
understand some computational methods used in protein modelling, protein docking, and other areas of structural bioinformatics;
have some experience with software packages that are used in parts of the protein structure determination and modelling processes;
be able to read, interpret and critically assess some articles from the scientific literature in areas covered in this course.

Assessment

This course will be assessed through a series of assignments.

Assignment	Weight	Date set	Date due
Assignment 1 (GK)	15%	1 February 2005	21 February 2005
Assignment 2 (GK)	25%	7 February 2005	7 March 2005
Assignment 3 (GK)	25%	10 February 2005	22 February 2005
Assignment 4 (PGN)	25%	7 March 2005	18 March 2005
Assignment 5 (GK)	10%	3 March 2005	14 March 2005

Marks for the five assignments will be combined to give an overall grade for the course. Grade limits are: 50% for grade 3, 65% for grade 4, 80% for grade 5.

Personnel

Graham Kemp (Examiner)
Per-Georg Nyholm
Vladislav Orekhov
Arjan Snijder (arjan.snijder@molbiotech.chalmers.se)

Lab Accounts

An individual lab account has been created for each student taking this course.

Preliminary Schedule

There are eight weeks in Quarter 3 this year, rather than the usual seven. However, we do not intend having more than 14 lectures.

There will be no lecture on Tuesday 8 February since this is one of the CHARM days. Related to Bioinformatics, you are welcome to attend the Genomics and Bioinformatics Open Day on Tuesday 8 February.

Date	Time	Place	Activity
Tuesday 18 January	13:15-15:00	ES51	Lecture (GK): Protein structure and function; domains
Tuesday 18 January	15:15-17:00	ED6225	Practical (GK): Protein structure and function; domains
Thursday 20 January	10:00-11:45	ES53	Lecture: Cancelled
Thursday 20 January	15:15-17:00	ED6225	Practical (GK): Protein structure and function; domains
Date	Time	Place	Activity
Tuesday 25 January	13:15-15:00	ES51	Lecture (GK): Transformations and superpostion
Tuesday 25 January	15:15-17:00	ED6225	Practical (GK): Transformations and superpostion
Thursday 27 January	10:00-11:45	ES53	Lecture (GK): Comparative modelling
Thursday 27 January	15:15-17:00	ED6225	Practical (GK): Comparative modelling
Date	Time	Place	Activity
Tuesday 1 February	13:15-15:00	ES51	Lecture (GK): Structure comparison; fold recognition
Tuesday 1 February	15:15-17:00	ED6225	Practical
Thursday 3 February	10:00-11:45	ES53	Lecture (PGN): Drug design
Thursday 3 February	15:15-17:00	ED6225	Practical (PGN)
Date	Time	Place	Activity
Thursday 10 February	10:00-11:45	ES53	Lecture (GK): Ab initio protein modelling
Thursday 10 February	15:15-17:00	ED6225	Practical
Date	Time	Place	Activity
Tuesday 15 February	13:15-15:00	ES51	Lecture (GK): Protein surfaces and protein-protein docking
Tuesday 15 February	15:15-17:00	ED6225	Practical (GK): Protein surfaces and protein-protein docking
Thursday 17 February	10:00-11:45	ES53	Lecture (PGN): Ligand conformation - force field methods
Thursday 17 February	15:15-17:00	ED6225	Practical (PGN)
Date	Time	Place	Activity
Tuesday 22 February	13:15-15:00	ES51	Lecture (PGN): Oligosaccaride structure and modelling
Tuesday 22 February	15:15-17:00	Room 2304, Medicinaregatan 7B	Practical (PGN)
Thursday 24 February	10:00-11:45	ES53	Lecture (AS): Macromolecular structure determination by X-ray crystallography
Thursday 24 February	15:15-17:00	ED6225	Practical (AS)
Date	Time	Place	Activity
Tuesday 1 March	13:15-15:00	Swedish NMR Center¹	Lecture (VO): NMR in biology
Tuesday 1 March	15:15-17:00	Swedish NMR Center	Visit to Swedish NMR Center
Thursday 3 March	10:00-11:45	ES53	Lecture (GK): Antibodies; MHC-peptide interactions; protein structure databases
Thursday 3 March	15:15-17:00	ED6225	Practical (GK): Antibodies
Date	Time	Place	Activity
Tuesday 8 March	13:15-15:00	ES51	Lecture (GK): Membrane proteins; Masters projects (1)
Tuesday 8 March	15:15-17:00	ED6225	Practical (GK): Membrane proteins
Thursday 10 March	10:00-11:45	ES53	Lecture (GK): RNA structure analysis and modelling; Masters projects (2)
Thursday 10 March	15:15-17:00	ED6225	Practical

¹ The Swedish NMR Center is at Medicinaregatan 5C (building "2").