| Graham Kemp > Teaching > TDA245 |
Bioinformatics is one of the major growth areas in biotechnology and the biological sciences. It is also an area that presents opportunities for computing science researchers to apply advanced computational techniques to challenging new problems, and often requires new algorithms to be devised.
In this seminar we shall consider the area of structural bioinformatics. This area deals with analysing, modelling and predicting the three-dimensional structures of biological macromolecules like proteins. This is an important area because a molecule's biological function is determined by its three-dimensional structure and, thus, knowledge about these structures can give new insights into biological processes and disease mechanisms.
In the first part of the seminar I shall give a brief introduction to the beauty and complexity of three-dimensional protein structures, and the basic principles of protein conformation. In the second part I shall describe some computational problems in structural bioinformatics to which algorithmic solutions have, or could, be applied.
No previous biochemical knowledge will be assumed!
The algorithm used by DOMAK to identify structural domains is described in:
Siddiqui, A.S. and Barton G.J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Science, 4, 872-884. (Pubmed)
The algorithm used by STRUDL to identify structural domains is described in:
Wernisch, L., Hunting, M. and Wodak, S.J. (1999) Identification of structural domains in proteins by a graph heuristic. Proteins: Structure, Function and Genetics, 35, 338-352. (Pubmed)
The DALI algorithm for pairwise protein structure alignment is described in:
Holm, L. and Sander, C. (1996) Mapping the protein universe. Science, 273, 595-603. (PubMed, on-line)
The SSAP algorithm for pairwise protein structure alignment is described in:
Taylor W.R. and Orengo C.A. (1989) "Protein structure alignment", J. Mol. Biol., 208, 1-22. (PubMed, overview)
A description of a constraint logic programming (CLP) approach to the protein side-chain placement problem is given in:
Swain, M.T. and Kemp, G.J.L. (2001) A CLP approach to the protein side-chain placement problem. In Walsh, T. (ed.) Principles and Practice of Constraint Programming - CP2001, Lecture Notes in Computer Science (vol. 2239), Springer-Verlag, Berlin, pp 479-493.
PDF © Copyright Springer-Verlag, LNCS series
For more information on fold recognition and threading, I recommend the following early articles:
Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure. Science, 253, 164-170.
Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
Sippl, M.J. and Weitckus, S. (1992) Detection of Native-Like Models for Amino Acid Sequences of Unknown Three-Dimensional Structure in a Data Base of Known Protein Conformations. Proteins: Structure, Function and Genetics, 13, 258-271 (Manfred Sippl's publication list)