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MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model

2025 · journal full text in PMC · Peer-reviewed

DOI: 10.1093/bib/bbaf524 Original source

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1 task
1 dataset
1 evaluation
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3 evidence claims

Results

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Model or configuration	Metric	Value	Dataset	Evaluation
MegSite + ESM3	AUROC	0.948 unitless	DNA-129_Test	MegSite + ESM3: DNA-binding residue prediction

Claims

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MegSite + ESM3: description: Description Predicts nucleic-acid-binding residues by fusing multimodal ESM3 sequence, structure and function embeddings with ESM-MSA features through cross-attention, alongside an equivariant graph network over the residue contact map. (Reviewed profile (2026-09-16): summary at Bidirectional cross-attention fusion/The architecture of MegSite (paragraph 1); Bidirectional cross-attention fusion/Implementation details (paragraph 2); architecture fact at Results/Performance of different network architectures (paragraph 7); Materials and methods/Multimodal protein language model (paragraph 2); description text also read at Abstract; Results (MegSite architecture overview))
MegSite + ESM3: uses model ESM3: Uses model ESM3 (Methods: MegSite architecture; ESM3 multimodal embeddings integrated with EGNN)
Reported AUC for MegSite + ESM3: Printed value 0.948 (Table 2, DNA-129_Test / ESM3 row, AUC column)

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18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact retrieved at 2026-09-16T10:38:57.558213+00:00 Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_retrieved_at` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact SHA-256 10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12496013/fullTextXML Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1093/bib/bbaf524 Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Missing metadata: licence: reason unextracted Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.missing_metadata.licence.reason` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-09-15T23:33:26Z Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Scope decision included Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.scope_decision` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://pmc.ncbi.nlm.nih.gov/articles/PMC12496013/ Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version journal full text in PMC Source metadata	MegSite: an accurate nucleic acid-binding residue prediction method based on multimodal protein language model Original source ↗ No field-specific location recorded Version: journal full text in PMC Retrieved: 2026-09-16T10:38:57.558213+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

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Stable ID: megsite-2025

areas: proteins-complexes
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12496013/
version: journal full text in PMC
retrieved at: 2026-09-15T23:33:26Z
doi: 10.1093/bib/bbaf524
publication status: peer_reviewed
year: 2025
artifact sha256: 10d13122331813243d83b84fe6f9294eac7e7c03cde082ebed276191ac41089c
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12496013/fullTextXML
artifact retrieved at: 2026-09-16T10:38:57.558213+00:00
scope decision: included
missing metadata: licence: reason: unextracted

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Evidence table

Sources and history