dorsal/arxiv
View SchemaReconstruction of protein structures from a vectorial representation
| Authors | Markus Porto, Ugo Bastolla, H. Eduardo Roman, Michele Vendruscolo |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0404015 |
| URL | https://arxiv.org/abs/q-bio/0404015 |
| DOI | 10.1103/PhysRevLett.92.218101 |
| Journal | Phys. Rev. Lett. 92, 218101 (2004) |
Abstract
We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm yields a unique contact map for all 221 globular structures of PDBselect25 of length $N \le 120$. We also show that the reconstructed contact maps allow in turn for the accurate reconstruction of the three-dimensional structure. These results indicate that the reduced vectorial representation provided by the principal eigenvector of the contact map is equivalent to the protein structure itself. This representation is expected to provide a useful tool in bioinformatics algorithms for protein structure comparison and alignment, as well as a promising intermediate step towards protein structure prediction.
{
"annotation_id": "d91ca441-55ea-45e8-86ec-feb1818cf667",
"date_created": "2026-03-02T18:01:31.680000Z",
"date_modified": "2026-03-02T18:01:31.680000Z",
"file_hash": "63d3547c85280edaa40959a34fa5986d3ce2db666682564fe92a5f52eba59c95",
"private": false,
"record": {
"abstract": "We show that the contact map of the native structure of globular proteins can\nbe reconstructed starting from the sole knowledge of the contact map\u0027s\nprincipal eigenvector, and present an exact algorithm for this purpose. Our\nalgorithm yields a unique contact map for all 221 globular structures of\nPDBselect25 of length $N \\le 120$. We also show that the reconstructed contact\nmaps allow in turn for the accurate reconstruction of the three-dimensional\nstructure. These results indicate that the reduced vectorial representation\nprovided by the principal eigenvector of the contact map is equivalent to the\nprotein structure itself. This representation is expected to provide a useful\ntool in bioinformatics algorithms for protein structure comparison and\nalignment, as well as a promising intermediate step towards protein structure\nprediction.",
"arxiv_id": "q-bio/0404015",
"authors": [
"Markus Porto",
"Ugo Bastolla",
"H. Eduardo Roman",
"Michele Vendruscolo"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1103/PhysRevLett.92.218101",
"journal_ref": "Phys. Rev. Lett. 92, 218101 (2004)",
"title": "Reconstruction of protein structures from a vectorial representation",
"url": "https://arxiv.org/abs/q-bio/0404015"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "ead393ae-6663-48f9-8aaf-c4bce0f87754",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}