Computational Biology & Biological Physics
Dept. of Astronomy and Theoretical Physics | Faculty of Science | Lund University

Designing sequences in the HP model

Supplementary data for

Mutation-induced fold switching among lattice proteins.
Christian Holzgräfe, Anders Irbäck and Carl Troein,
The Journal of Chemical Physics 135, 195101 (2011)

extending the results of

Enumerating designing sequences in the HP model.
Anders Irbäck and Carl Troein,
Journal of Biological Physics 28, 1-15 (2002)

Click here to download all the designing sequences and their ground states for the HP model for 4 ≤ N ≤ 30 in a plain text format.

Each HPnXX.txt file contains all designable conformations and designing sequence for N = 'XX'. Each line either contains a conformation described by N-1 of the letters 'UDRL', or a sequence that designs the preceeding conformations. Lines with sequences begin with two spaces, followed by a sequence specified by N letters ('H' or 'P'), followed by a single space and finally the number of HH contacts (i.e. minus the ground state energy) as a decimal number. All conformations start with U and the first turn is to the right.

Click here to download the energy histograms for all designing sequences for 4 ≤ N ≤ 22 and N = 27, For other N ≤ 30, the files only include sequences in the neutral net of conformations with designability above the cutoff determined by uniqueness of the prototype sequence.

Reversing a sequence does not alter the energy histogram, so for non-palindrome sequences only one of the directions is listed.

The C++ programs used to generate the files are available upon request. As of 2020, they are still maintained.

Contact Information:
For questions concerning these files and the programs used to generate them: Carl Troein
For questions concerning anything else: Anders Irbäck