Welcome to the home page of Peter Røgen

Contact Information:

Department of Mathematics
Technical University of Denmark
Matematiktorvet, building 303 S
DK-2800 Kgs. Lyngby
Denmark
room 054
Phone direct (+45) 4525-3044
email: Peter.Roegen"snable a"mat.dtu.dk

Research interests:

Knot theory and differential geometry of curves and surfaces in 3-space.
Applications of these to the study of proteins.

Research collaboration

Henrik Bohr, The Quantum Protein Center, QUP, Technical University of Denmark.
Boris Fain, last academic affiliation Computational Structural Biology, Department of Structural Biology Stanford University.
Kresten Lindorff-Larsen, Department of Biochemistry, Institute of Molecular Biology and Physiology August Krogh Building, University of Copenhagen.

Industry connection:

R&D for Aasted-Mikroverk in 2004 and 2005.

Award winning poster

The poster(ps) poster(pdf) titled Automatic classification of protein structure by using Gauss integrals
was elected as one of the 10 best (out of 500) posters at ISMB2002.

Software

Download GI that calculates Gauss Integrals for protein backbones.
Download Sieve that calculates average occurrences of patterns of up to three crossings for protein backbones.
Download GIT that calculates Gauss Integrals for protein backbones and returns a Tuned version such that the resulting protein structure descriptors are as independent as possible and such that each descriptor scales as linearly with RMSD as possible.

Selected publications

Bjørn G. Nielsen, --, Henrik G. Bohr, Gauss-integral based representation of protein structure for predicting the fold class from the sequence, Mathematical and Computer Modeling Volume 43, Issues 3-4 , 2006, 401-412.

--, Evaluating protein structure descriptors and tuning Gauss integral based descriptors J. Phys.: Condens. Matter 17 (2005) S1523-S1538.

K. Lindorff-Larsen, --, E. Paci, M Vendrusscolo & C.M. Dobson, Protein folding and the organization of the protein topology universe, Trends in Biochemical Sciences, 30(1), 13-19. 2005.

R.P. Bywater, T.A. Poulsen, --, P.G. Hjorth, De Novo generation of molecular structures using optimization to select graphs on a given lattice, J. Chem. Inf. Comput. Sci. 44 (3): 856-861 2004.

-- & R. Sinclair, Computing a new family of shape descriptors for proteins, J. Chem. Inf. Comput. Sci. 43, 1740-1747, 2003.

-- & B. Fain, Automatic classification of protein structure by using Gauss integrals, PNAS, 100(1), 119-124, 2003. Reviewed in BioZoom (Danish)

-- & H.G. Bohr, A new family of global protein shape descriptors, Mathematical Biosciences Volume 182, Issue 2, April 2003, Pages 167-181.

R.P. Bywater, A. Sørensen, --, P. G. Hjorth, Construction of the simplest model to explain complex receptor activation kinetics, Journal of Theoretical Biology, 218(2), 139-147, 2002. (Correction printed in J. Theor. Biol. 221 (4): 669-669 APR 21 2003)

-- & H.G. Bohr, On representation of protein backbones with (framed) space curves, Mat-Report No. 2002-14 Dept. of Math. Tech. Univ. of Denmark, ISSN 0904-7611 (Technical Report) 2002. pdf-file ps.gz-file

H.G. Bohr, -- & K.J. Jalkanen, Applications of neural network prediction of conformational states for small peptides from spectra and of fold classes, Computers and Chemistry 26 65-77, 2001.

--, Boundaries of flat compact surfaces in 3-space. Annals of Global Analysis and Geometry, 19(4), 377-407, 2001.

--, Embedding and knotting of flat surfaces in 3-space. Commentarii Mathematici Helvetici, 76(4), 589-606, 2001.

--, Principal normal indicatrices of closed space curves. Geom. Dedicata, 74(1), 49-60, 1999.

--, On density of Vassiliev invariants. J. Knot Theory Ramifications, 8(2), 249-252, 1999.

--, Gauss-Bonnet's Theorem and Closed Frenet Frames. Geom. Dedicata, 73(3), 295-315, 1998.

T. Randrup & --, How to twist a knot, Arch. Math., 68, 252-264, 1997.

T. Randrup & --, Sides of the Mobius strip, Arch. Math., 66, 511-521, 1996.

Short CV

Born 24.03.69

Degrees
1999 Ph.D., Dept. of Mathematics, DTU. The Thesis.
1995 M.Science and Engineering. (cand.polyt.), Dept. of Math., Technical University of Denmark. (DTU) The Thesis.

Positions
2001-2004, Assistant Professor at Dept. of Mathematics, DTU.
2000-2001, Research fellow at Dept. of Mathematics, DTU. (Carlsbergfondet)
1999-2000, Research fellow at Dept. of Mathematics, DTU. (DTU grant)
1999 Feb-July, Research Assistant Professor at Dept. of Mathematics, DTU

Professional activities: Reviewer for Mathematical Reviews.