DOI: 10.1002/prot.10239. Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix

Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix

10.1002/prot.10239

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractWe study the designability of all compact 3 × 3 × 3 and 6 × 6 lattice‐protein structures using the Miyazawa–Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e., sequences that have that structure as their unique lowest‐energy state. Previous studies of hydrophobic‐polar (HP) models showed a wide distribution of structure designabilities. Recently, questions were raised concerning the use of a two‐letter (HP) code in such studies. Here, we calculate designabilities using all 20 amino acids, with empirically determined interaction potentials (MJ matrix) and compare with HP model results. We find good qualitative agreement between the two models. In particular, highly designable structures in the HP model are also highly designable in the MJ model—and vice versa—with the associated sequences having enhanced thermodynamic stability. Proteins 2002;49:403–412. © 2002 Wiley‐Liss, Inc.

Bibliography

Li, H., Tang, C., & Wingreen, N. S. (2002). Designability of protein structures: A latticeâmodel study using the MiyazawaâJernigan matrix. Proteins: Structure, Function, and Bioinformatics, 49(3), 403â412. Portico.

Authors 3

Hao Li (first)
Chao Tang (additional)
Ned S. Wingreen (additional)

References 46 Referenced 54

Dates

Type	When
Created	22 years, 10 months ago (Oct. 9, 2002, 1:26 a.m.)
Deposited	1 year, 10 months ago (Sept. 28, 2023, 9:52 p.m.)
Indexed	3 months, 4 weeks ago (April 29, 2025, 9:29 a.m.)
Issued	22 years, 11 months ago (Sept. 23, 2002)
Published	22 years, 11 months ago (Sept. 23, 2002)
Published Online	22 years, 11 months ago (Sept. 23, 2002)
Published Print	22 years, 9 months ago (Nov. 15, 2002)

Funders 0

None

BibTeX

@article{Li_2002, title={Designability of protein structures: A lattice‐model study using the Miyazawa‐Jernigan matrix}, volume={49}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.10239}, DOI={10.1002/prot.10239}, number={3}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Li, Hao and Tang, Chao and Wingreen, Ned S.}, year={2002}, month=sep, pages={403–412} }

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