Rasmus Fonseca

I am a Ph.d. student from the Department of Computer Science at University of Copenhagen, Denmark (DIKU). I study the problem of predicting the three-dimensional native structure of proteins using computational ab initio methods.

Department of Computer Science University of Copenhagen E-mail: rfonseca@diku.dk Office: 3-0-16 DIKU Supervisor: Pawel Winter (Co-supervisor 2010/2011: Kevin Karplus)

Links

• Curriculum Vitae - My academic CV
• ProGAL - Protein Geometric Algorithm Library. A Java library with algorithms and data structures for analyzing and representing protein structures.
• KredsDesign - Visual hardware simulator. This was my bachelors project.
• Project ideas - Ideas I may never find the time to finish
• Useful implementations - Solutions to small problems that I couldn't find implementations to anywhere else
• Java-implementation that solves the problem of Apollonius (i.e. finding a circle tangent to three other circles)
• Problem of Apollonius in 3D (i.e. finding a sphere tangent to four other spheres. Step-by-step description easily generalized to d-dimensions)
• Principal Components Analysis of hand-shapes visualized with gifs
• Klavs Møller Hansen - myspace - Artist profile for my younger brother

Publications

• Bounding Volumes for Proteins. In progress. 2011
• Ranking Beta Sheet Topologies with Applications to Protein Structure Prediction. R. Fonseca, G. Helles and P. Winter. Journal of Mathematical Modelling and Algorithms, 2011
• Protein Packing Quality using Delaunay Complexes. R. Fonseca. P. Winter and K. Karplus. Proceedings of ISVD 2011. Pages 117-122.
• Adjustable Chain Trees for Proteins. P. Winter and R. Fonseca. Journal of Computational Biology. Online Ahead of Print: 2011
• Ranking Beta Sheet Topologies of Proteins. R. Fonseca, G. Helles and P. Winter. Proceedings of WCECS 2010.
• Protein Structure Prediction using Bee Colony Optimization Metaheuristic. R. Fonseca, M. Paluszewski and P. Winter. Journal of Molecular Modelling and Algorithms, 2010
• Predicting Dihedral Angles of Coil-structure Residues from the Primary Sequence using Neural Networks. R. Fonseca and G. Helles. BMC Bioinformatics 2009, 10:338