---
res:
  bibo_abstract:
  - "The local structure of a protein strongly impacts its function and interactions\r\nwith
    other molecules. Representing local biomolecular environments remains a\r\nkey
    challenge while applying machine learning approaches over protein structures.
    The structural and chemical variability of these environments makes them\r\nchallenging
    to model, and performing representation learning on these objects\r\nremains largely
    under-explored. In this work, we propose representations for\r\nlocal protein
    environments that leverage intermediate features from machine learning force fields
    (MLFFs). We extensively benchmark state-of-the-art MLFFs,\r\ncomparing their performance
    across latent spaces and downstream tasks, and\r\nshow that their embeddings capture
    local structural (e.g., secondary motifs) and\r\nchemical features (e.g., amino
    acid identity and protonation state), organizing\r\nprotein environments into
    a structured manifold. We show that these representations enable zero-shot generalization
    and transfer across diverse downstream\r\ntasks. As a case study, we build a physics-informed,
    uncertainty-aware chemical shift predictor that achieves state-of-the-art accuracy
    in biomolecular NMR\r\nspectroscopy. Our results establish MLFFs as general-purpose,
    reusable representation learners for protein modeling, opening new directions
    in representation learning for structured physical systems. Code and data are
    available at\r\nhttps://github.com/mb012/MLFF_representation.\r\n@eng"
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Meital I
      foaf_name: Bojan, Meital I
      foaf_surname: Bojan
      foaf_workInfoHomepage: http://www.librecat.org/personId=11d88cf5-91ca-11f0-a95f-edf9f08f47b7
  - foaf_Person:
      foaf_givenName: Sanketh
      foaf_name: Vedula, Sanketh
      foaf_surname: Vedula
  - foaf_Person:
      foaf_givenName: Sai A
      foaf_name: Maddipatla, Sai A
      foaf_surname: Maddipatla
      foaf_workInfoHomepage: http://www.librecat.org/personId=e957f5e5-91c9-11f0-a95f-e090f66ecb4d
  - foaf_Person:
      foaf_givenName: Nadav E
      foaf_name: Sellam, Nadav E
      foaf_surname: Sellam
      foaf_workInfoHomepage: http://www.librecat.org/personId=ef280fe0-91c9-11f0-a95f-8dea3f5bc513
  - foaf_Person:
      foaf_givenName: Anar
      foaf_name: Rzayev, Anar
      foaf_surname: Rzayev
      foaf_workInfoHomepage: http://www.librecat.org/personId=2cd60677-9acd-11f1-ae1a-a85ae1c4dd35
  - foaf_Person:
      foaf_givenName: Federico
      foaf_name: Napoli, Federico
      foaf_surname: Napoli
      foaf_workInfoHomepage: http://www.librecat.org/personId=d42e08e7-f4fc-11eb-af0a-d71e26138f1b
    orcid: 0000-0002-9043-136X
  - foaf_Person:
      foaf_givenName: Paul
      foaf_name: Schanda, Paul
      foaf_surname: Schanda
      foaf_workInfoHomepage: http://www.librecat.org/personId=7B541462-FAF6-11E9-A490-E8DFE5697425
    orcid: 0000-0002-9350-7606
  - foaf_Person:
      foaf_givenName: Alexander
      foaf_name: Bronstein, Alexander
      foaf_surname: Bronstein
      foaf_workInfoHomepage: http://www.librecat.org/personId=58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
    orcid: 0000-0001-9699-8730
  bibo_volume: 2026
  dct_date: 2026^xs_gYear
  dct_language: eng
  dct_title: Representing local protein environments with machine learning force fields@
...