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Designing sequences in the HP model

HP protein model examples drawings.

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)
DOI 10.1063/1.3660691

extending the results of

Enumerating designing sequences in the HP model.
Anders Irbäck and Carl Troein,
Journal of Biological Physics 28, 1-15 (2002)
DOI 10.1023/A:1016225010659

All designing sequences and their ground states for the HP model for 4 ≤ N ≤ 30 in a plain text format:
HP_designing.tar.gz

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.

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.
energyhistograms.tar.gz

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

Contact

For corrections and updates, please contact webmaster [at] atp [dot] lu [dot] se

See also: Staff pages