dorsal/arxiv
View SchemaDesign of amino acid sequences to fold into C_alpha-model proteins
| Authors | A. Amatori, G. Tiana, L. Sutto, J. Ferkinghoff-Borg, A. Trovato, R. A. Broglia |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0505030 |
| URL | https://arxiv.org/abs/q-bio/0505030 |
| DOI | 10.1063/1.1992447 |
Abstract
In order to extend the results obtained with minimal lattice models to more realistic systems, we study a model where proteins are described as a chain of 20 kinds of structureless amino acids moving in a continuum space and interacting through a contact potential controlled by a 20x20 quenched random matrix. The goal of the present work is to design and characterize amino acid sequences folding to the SH3 conformation, a 60-residues recognition domain common to many regulatory proteins. We show that a number of sequences can fold, starting from a random conformation, to within a distance root mean square deviation (dRMSD) of 2.6A from the native state. Good folders are those sequences displaying in the native conformation an energy lower than a sequence--independent threshold energy.
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"abstract": "In order to extend the results obtained with minimal lattice models to more\nrealistic systems, we study a model where proteins are described as a chain of\n20 kinds of structureless amino acids moving in a continuum space and\ninteracting through a contact potential controlled by a 20x20 quenched random\nmatrix. The goal of the present work is to design and characterize amino acid\nsequences folding to the SH3 conformation, a 60-residues recognition domain\ncommon to many regulatory proteins. We show that a number of sequences can\nfold, starting from a random conformation, to within a distance root mean\nsquare deviation (dRMSD) of 2.6A from the native state. Good folders are those\nsequences displaying in the native conformation an energy lower than a\nsequence--independent threshold energy.",
"arxiv_id": "q-bio/0505030",
"authors": [
"A. Amatori",
"G. Tiana",
"L. Sutto",
"J. Ferkinghoff-Borg",
"A. Trovato",
"R. A. Broglia"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1063/1.1992447",
"title": "Design of amino acid sequences to fold into C_alpha-model proteins",
"url": "https://arxiv.org/abs/q-bio/0505030"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "f2f2f7fa-385b-4150-88eb-d1bf50be7f72",
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"type": "Model",
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