Simplified Protein Models
Simplified protein models are coarse grained representations of proteins.
They allow for performing large scale studies in silico in order
to analyze features of protein-like systems.
The main attractivity of such models is that they are still computationally
manageable in situations, where the use of more complex models is
completely out of computational reach.
Nevertheless for the aim of structure prediction of real proteins,
well designed protein models with a reasonable balance of
complexity and detail can also provide canditates for further refinement.
Recent studies of protein evolution, thermodynamical, and kinetic
aspects of proteins were still strongly restricted to very simple (often
2-dimensional) protein models.
Our approaches to protein structure prediction in 3-dimensional protein models
have vastly improved the complexity of protein models that can be reasonable
used in large scale computational studies.
In this research area, we are interessted in constraint-based
techniques for the prediction of optimal protein structures in lattice
protein models with strong hydrophobic energy contribution. We solved
the protein structure prediction problem for models on the cubic lattice and
on the much more complex face-centered cubic lattice.
Furthermore, we are interested in all kinds of applications that are enabled
by our key technology of structure prediction. For example, we analyze the
sequence-structure mapping for a better understanding
of protein evolution or construct energy landscapes for finally
investigate protein kinetics.
Protein Structure Prediction
Here, we develop methods to predict the spatial structure of
simplified proteins in HP-type models on the cubic and face-centered
cubic (FCC) lattice. These models are
extensions of Ken Dill's HP-model. Using FCC instead of only the three
dimensional cubic lattice or even two dimensional lattices is
a significant advance, since this
lattice can model real proteins rather accurate and lacks the
so-called parity problem of cubic lattices.
We are still interested in improvements, either in terms of
model complexity or of prediction efficiency.
We have developed and implemented constrained-based methods for
prediction in HP and HPNX models on the cubic and face-centered
In our implementations, we use advanced constraint-techniques, e.g.
general symmetry breaking a la Backofen/Will.
Available Implementations and Services
Online Server for protein structure prediction in HP-model in complex 3D lattices
The standalone offline C++ implementation (source code package)
Global and sequential (vectorial) folding simulations in
arbitrary lattice protein models
High resolution fitting of 3D PDB protein data onto lattices
Contributing group members
- Martin Mann, Cameron Smith, Mohamad
Rabbath, Marlien Edwards, Sebastian Will,
and Rolf Backofen.
CPSP-web-tool : a server for 3D lattice protein studies.
In Bioinformatics, 2009.
- Martin Mann, Daniel Maticzka, Rhodri Saunders, and Rolf Backofen.
Classifying protein-like sequences in arbitrary lattice protein models using LatPack.
In HFSP Journal, 2 no. 6 pp. 396, 2008.
Special issue on protein folding: experimental and theoretical approaches.
Supplementary data can be obtained HERE .
- Martin Mann, Sebastian Will and Rolf Backofen.
CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies.
In BMC Bioinformatics, 9, 230, 2008.
- Sebastian Will and Martin Mann.
Counting protein structures by dfs with dynamic
In Proc. of the Workshop on Constraint Based Methods for
Bioinformatics, page 6, 2006.
- Rolf Backofen and
A constraint-based approach to fast and exact structure
prediction in three-dimensional protein models.
Journal of Constraints, 11 no. 1 pp. 5-30, January 2006.
- Sebastian Will.
Constraint-based hydrophobic core construction for
protein structure prediction in the face-centered-cubic lattice.
In Russ B. Altman, A. Keith Dunker, Lawrence Hunter, and Teri E. Klein,
editors, Proceedings of the Pacific Symposium on Biocomputing 2002 (PSB
2002), pages 661-672, Singapore, 2002. World Scientific Publishing Co.
- Rolf Backofen and Sebastian Will.
Fast, constraint-based threading of HP-sequences to
In Proceedings of 7 th International Conference on Principle and
Practice of Constraint Programming (CP'2001), volume 2239 of Lecture
Notes in Computer Science, pages 494-508, Berlin, 2001.
- Rolf Backofen and Sebastian Will.
Optimally compact finite sphere packings -- hydrophobic
cores in the FCC.
In Proc. of the 12th Annual Symposium on Combinatorial Pattern Matching
(CPM2001), volume 2089 of Lecture Notes in Computer Science,
pages 257-272, Berlin, 2001. Springer-Verlag.
Related Research Topics