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PreprintCited by 16Protein Structure and DynamicsComputational Drug Discovery MethodsMachine Learning in Bioinformatics

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Deep Local Analysis evaluates protein docking conformations with Locally oriented Cubes

Open access
Behbahani, Yasser Mohseni, Crouzet, Simon, Laine, Elodie, Carbone, Alessandra·2022·Bioinformatics
DOI 10.1101/2022.04.05.487134PMC PMC9525006

Preprint — published as 10.1093/bioinformatics/btac551 · Paper page

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Abstract

A bstract: With the recent advances in protein 3D structure prediction, protein interactions are becoming more central than ever before. Here, we address the problem of determining how proteins interact with one another. More specifically, we investigate the possibility of discriminating near-native protein complex conformations from incorrect ones by exploiting local environments around interfacial residues. Deep Local Analysis (DLA)-Ranker is a deep learning framework applying 3D convolutions to a set of locally oriented cubes representing the protein interface. It explicitly considers the local geometry of the interfacial residues along with their neighboring atoms and the regions of the interface with different solvent accessibility. We assessed its performance on three docking benchmarks made of half a million acceptable and incorrect conformations. We show that DLA-Ranker successfully identifies near-native conformations from ensembles generated by molecular docking. It surpasses or competes with other deep learning-based scoring functions. We also showcase its usefulness to discover alternative interfaces. Availability: http://gitlab.lcqb.upmc.fr/dla-ranker/DLA-Ranker.git

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Metadata

Authors
Behbahani, Y. M., Crouzet, S., Laine, E., & Carbone, A.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Carbone, Alessandra
ORCID
Venue
Bioinformatics
Publisher
openRxiv
Published
2022-04-06
Volume
38
Issue
19
Pages
4505-4512
ISSN
1367-4803 (ISSN-L)
DOI
10.1101/2022.04.05.487134
PMC
PMC9525006
OpenAlex
W4291237382
Cited by
16
References
1
Citations by year
2026: 1 · 2025: 4 · 2024: 4 · 2023: 5 · 2022: 2
FWCI
1.22
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Bioinformatics (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by-nc)
  • HAL (submittedVersion)
Funders
  • Agence Nationale de la Recherche (ANR-21-CE17-0046)
  • Centre National de la Recherche Scientifique
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords
protein docking, protein-protein interaction, protein complex conformation, interfacial residues, 3D convolution, solvent accessibility
MeSH terms
Protein Binding, Protein Conformation, Proteins, Molecular Docking Simulation

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