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Diseases are often caused by malfunctioning proteins. Proteins are three-dimensional molecules with different functions, each defined by a gene. Much effort has been invested in sequencing the genomes of various species, including the human genome, however the number of known protein structures lags far behind. Exploring these unknown structures can either be done experimentally, involving a lot of time and costs, or computationally, for which further development is needed. The aim of my project is to use computational methods to built models for protein structures and refine these models to an accuracy level of experimentally determined protein structures.
In the POPULUS approach, we use a genetic algorithm as our conformational space search engine. GAs are well-known to be powerful search and optimisation techniques, and have been used previously in a number of protein modelling efforts ranging from ab initio folding to model-building by homology. In contrast to refinement protocols based on molecular dynamics, Monte Carlo and knowledge-based techniques, which usually start with models created by a single modelling technique, our method uses multiple initial models from a variety of modelling approaches.
In the POPULUS approach, we use a genetic algorithm as our conformational space search engine. GAs are well-known to be powerful search and optimisation techniques, and have been used previously in a number of protein modelling efforts ranging from ab initio folding to model-building by homology. In contrast to refinement protocols based on molecular dynamics, Monte Carlo and knowledge-based techniques, which usually start with models created by a single modelling technique, our method uses multiple initial models from a variety of modelling approaches.
Get the POPULUS software and request a password here.
Use my Hydrophobicity Applet.
My CASP 7 Analysis 1 2 3 4 5 all.
My publications
Offman MN, Fitzjohn PW, Bates PA.
Developing a move-set for protein model refinement.
Bioinformatics. 2006; 22(15):1838-1845; doi:10.1093/bioinformatics/btl192.
Offman MN, Nurtdinov RN, Gelfand MS, Frishman D.
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.
BMC Bioinformatics. 2004 Apr 19;5:41.
Contreras-Moreira B, Fitzjohn PW, Offman M, Smith GR, Bates PA.
Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.
Proteins. 2003;53 Suppl 6:424-9.