Atlantis: An integrative database for human proteome structural and functional sites
- 1Scuola Normale Superiore
Abstract
Understanding protein mechanisms in health and disease requires characterizing the functional roles of individual amino acid residues. To explore the role of residues and their mutations, we have developed Atlantis, a database that integrates structural and functional information at the human proteome residue level. A graph database enables complex queries and the retrieval of integrated information for multiple functional analysis of protein systems. A Model Context Protocol (MCP) connector allows the interrogation of the resource through Large Language Models (LLMs) or agentic frameworks for biomedical research. Atlantis annotates over 11M residues across 20k human proteins, identifying hundreds thousands intra- and inter-protein contacts in PDB as well as AlphaFoldDB structures. We also provide the possibility to analyze and integrate predicted 3D complexes inputted by the user, and we showcased these features on hundreds of AlphaFold-multimer complexes of GPCRs and LRRK2 interaction networks. The tool is freely accessible at https://atlantis.bioinfolab.sns.it/.
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BibTeX
@misc{rosa2026atlantis,
title = {{Atlantis: An integrative database for human proteome structural and functional sites}},
author = {N. De Oliveira Rosa and P. Ferronato and M. Varisco and M. Matic and M. Ruscio and P. Miglionico and F. Raimondi},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.29.747983},
url = {https://www.biorxiv.org/content/10.64898/2026.08.29.747983v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Atlantis: An integrative database for human proteome structural and functional sites
AU - N. De Oliveira Rosa
AU - P. Ferronato
AU - M. Varisco
AU - M. Matic
AU - M. Ruscio
AU - P. Miglionico
AU - F. Raimondi
PY - 2026
DA - 2026/08/29
PB - bioRxiv
DO - 10.64898/2026.08.29.747983
UR - https://www.biorxiv.org/content/10.64898/2026.08.29.747983v1
AB - Understanding protein mechanisms in health and disease requires characterizing the functional roles of individual amino acid residues. To explore the role of residues and their mutations, we have developed Atlantis, a database that integrates structural and functional information at the human proteome residue level. A graph database enables complex queries and the retrieval of integrated information for multiple functional analysis of protein systems. A Model Context Protocol (MCP) connector allows the interrogation of the resource through Large Language Models (LLMs) or agentic frameworks for biomedical research. Atlantis annotates over 11M residues across 20k human proteins, identifying hundreds thousands intra- and inter-protein contacts in PDB as well as AlphaFoldDB structures. We also provide the possibility to analyze and integrate predicted 3D complexes inputted by the user, and we showcased these features on hundreds of AlphaFold-multimer complexes of GPCRs and LRRK2 interaction networks. The tool is freely accessible at https://atlantis.bioinfolab.sns.it/.
ER -