in collaboration with

Turku Centre for Biotechnology

Institute of Medical Technology

	Keywords: Bioinformatics, WAP, WML, Mutation, Cluster Analysis, Computational Molecular Biology, Protein structure, Microarray data

Our general aim is to analyze, model, and predict the intricate relationships between the different levels of the complex structure of protein molecules, and to develop tools for such tasks. The research domain is related to the protein folding problem - the Holy Grail of computational molecular biology, also termed as "cracking the second half of the genetic code". In the field of bioinformatics, we have set up and maintain several protein structural databases accessible via WWW. Our recent contributions have been in general clustering theory, structural prediction methodology, and development of mutation databases.

Cluster analysis Clustering with unknown number of clusters Inter-clusteral distances in metric and non-metric spaces Representativity of classification	Protein structure prediction Prediction of protein structural families Representative selection Identification of 3D families from the sequence
Mutation databases BTKbase: Mutations for chromosome X-linked agammaglobulinemia KinMutBase: Disease-causing mutations in tyrosine kinase domains A number of other mutation and patient databases Analysis methods on the Web	Mobile bioinformatics BioWAP service
cDNA microarray data analysis

J. Boberg, T. Salakoski, M. Vihinen: 'Representative selection of proteins based on nuclear families', Protein Engineering 5, 501-503, 1995.
J. Boberg, T. Salakoski, M. Vihinen: 'Accurate prediction of protein secondary structural class with fuzzy structural vectors', Protein Engineering 6, 505-512, 1995.
T. Salakoski: 'Prerequisites for accurate prediction of protein folding type: A comparative evaluation of the predictive power of composition and sequence', Mathematics and Molecular Biology IV "From DNA Sequence to Protein Structure and Function", (with J. Boberg and M. Vihinen), Santa Fe, NM, USA, 1995.
T. Salakoski: 'Representative Classification of Protein Structures', Department of Computer Science, University of Turku, and Turku Centre for Computer Science, TUCS Dissertations 6, 1997.
J. Boberg, T. Salakoski: 'Representative noise-free complete-link classification with application to protein structures', Pattern Recognition 3, 467-482, 1997.
T. Salakoski: 'Approaches to representative classification of biological structures and mathematical formalization of homologous classes', Mathematics and Molecular Biology V "Statistics and Inference in Molecular Biology", (with J. Boberg), Santa Fe, NM, USA, 1997.
M. Vihinen, O. Brandau, L.J. Brandau, S. Kwan, I. Lappalainen, T. Lester, J.G. Noordjiz, H.D. Ochs, J.Ollila, S.M. Pienaar, P. Riikonen, B.K. Saha, C.I.E. Smith: 'BTKbase, mutation database for X-linked agammaglobulinemia (XLA)', Nucleic Acids Research 26, 1998, 242-247.
P. Riikonen, T. Salakoski: Bioinformatics in the 21st century: From textual databases to distributed object collections: New mutation and patient registries in the net,Mathematics and Molecular Biology VI "Understanding Structure ", (with M. Vihinen), Santa Fe, NM, USA, 1999.
K. Stenberg, P. Riikonen, M. Vihinen: 'KinMutBase, a database of human disease-causing tyrosine kinase mutations', Nucleic Acids Research 27, 1998, 362-364.
P. Riikonen, M. Vihinen: 'MUTbase:maintenance and analysis of distributed mutation databases',Bioinformatics, Vol. 15 no. 10, 1999, 852-859.
J. Boberg: 'Cluster Analysis. A Mathematical Approach with Applications to Protein Structures', Department of Computer Science, University of Turku, and Turku Centre for Computer Science, TUCS Dissertations 20, 1999.
K. Stenberg, P. Riikonen, M. Vihinen: 'KinMutBase, a database of human disease-causing protein kinase mutations', Nucleic Acids Research,2000, vol 28, No 1, 369-371.