Stefan Canzar: Software
Protein Design
A tool that computes provably optimal side-chain placements for protein design.
The code and a short description are available here in section scp.
Marker-Assisted Gene Pyramiding
The problem appears in the plant breeding context. Our software designs a most cost-efficient
schedule of crossing events which leads to an individual uniting in itself all desirable traits
given by an initial set of parental individuals.
Multiple Sequence Alignment
Our tool LASA (Lagrangian Sequence Alignment) aligns multiple sequences optimally.
It uses Lagrangian bounds in a Branch & Bound framework.
If you are interested in the software, please send me an email.
Protein Structure Comparison
A tool for clustering proteins of similar structure.
Hydrogen/Deuterium Exchange (HDX) Rates
The HDX problem appears in the interpretation of experimental data in biochemistry:
Monitoring hyrdrogen-deuterium exchange rates via mass spectrometry is a method used to
obtain information about protein tertiary structure. The output of these experiments provides
aggregate data about the exchange rate of residues in overlapping fragments of the protein
backbone. Our software helps to re-assemble these fragments in order to obtain a global
picture of the protein structure. If you are interested in the software, please send me an email.
Our tool PolyDelayHDX enumerates all optimal solutions plus h-approximate solutions of
type 0 or type 1, for a given h≥0. For the precise definitions of approximation guarantees see
our ALENEX'10 paper
A Polynomial Delay Algorithm for Enumerating Approximate Solutions to the Interval Constrained Coloring Problem.
Compiled with g++ 4.1.2 for Linux-x86 64 bit it can be downloaded from here.
It needs to be linked dynamically to CPLEX 12.2.
Usage: ./polydelayhdx [<h>] <hdx_rates_file>
If h is given, type 0 approximations are computed, otherwise type 1 approximations are ouptput.
The instances used in the experiments described in our paper are available here, including the
underlying true coloring. To evaluate the quality of the generated colorings the true coloring is
assumed to be located in the same directory as the instance itself. If you are interested in the
real-world instances please send me an email.
Minimum String Cover
Our tool for computing a minimum set of substrings that can produce (through concatenation)
a given set of strings is available via Google Code here.