AlphaFold Sovereign MCP
Copyright 2024-2026 Santiago Maniches and TOPOLOGICA LLC

This product includes software developed by
TOPOLOGICA LLC (https://topologica.ai).

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Patent Notice
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This product includes implementations of patent-pending innovations
authored by Santiago Maniches (ORCID: 0009-0005-6480-1987):

  - Drift tensor correction framework
  - Topological fingerprinting of protein structures via
    persistent homology over Vietoris-Rips filtrations

These patent rights are licensed to users of this Apache 2.0
distribution under the terms of Apache License, Version 2.0,
Section 3 ("Grant of Patent License"), strictly for the purposes
of using, modifying, and distributing this Work.

Patent rights for use outside this Work — including embedding the
patented methods in derivative or competing products that do not
incorporate this Work — are reserved. See PATENTS.md for details
and inquiries.

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Third-Party Components
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This product makes use of third-party components, each governed by
its own license. A full inventory is published with every release in
the form of CycloneDX and SPDX Software Bills of Materials (SBOMs).

Notable upstream data sources accessed at runtime (no upstream code is
included or redistributed):
  - AlphaFold Protein Structure Database
      (Google DeepMind / EMBL-EBI; CC BY 4.0 for predicted structures;
       includes AlphaMissense annotations, Cheng et al. Science 2023)
  - MONDO Disease Ontology (Monarch Initiative; CC BY 4.0)
  - Human Phenotype Ontology (Jackson Laboratory; HPO license)
  - Open Targets (EMBL-EBI and partners; data CC0 1.0)
  - ClinVar (NCBI; public domain)
  - gnomAD v4 (Broad Institute; CC0 1.0)
  - DisGeNET (MedBioinformatics; free academic tier / commercial license)
  - ChEMBL (EMBL-EBI; CC BY-SA 3.0)
  - Ensembl (EMBL-EBI; data released with no restrictions, code Apache 2.0)

UniProt accessions are used only as protein identifiers; the UniProt
API is not queried as a data source. Gene Ontology, InterPro / Pfam, and
the RCSB Protein Data Bank are not integrated in this release.

This project is independent. It is not affiliated with, endorsed by, or
sponsored by Google DeepMind or EMBL-EBI. "AlphaFold" and the names of
the data sources above are trademarks of their respective owners and are
used solely to describe the public data this software consumes.

Users are responsible for complying with the terms of any upstream
data sources they access through this software.
