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Enhanced prediction of protein functional identity through the integration of sequence and structural features

PMC11609699.1

DOI: 10.1016/j.csbj.2024.11.028 Original source

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3 configurations
1 task
1 protocol
5 evaluations
40 results
3 evidence claims

Results

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Model or configuration	Metric	Value	Dataset	Evaluation
DeepFRI	Accuracy	80.88 percent	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	AUPRC	0.9067 unitless	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	AUROC	0.8963 unitless	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	F1	0.8143 unitless	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	False positive rate	21.45 percent	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	MCC	0.6790 unitless	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	Precision	79.77 percent	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
DeepFRI	Recall	83.16 percent	FUJISAN test sub-dataset	DeepFRI: Enzyme-pair functional identity: original held-out test
E-value	Accuracy	81.91 percent	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	AUPRC	0.7767 unitless	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	AUROC	0.8890 unitless	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	F1	0.8291 unitless	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	False positive rate	23.92 percent	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	MCC	0.6427 unitless	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	Precision	78.58 percent	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
E-value	Recall	87.75 percent	FUJISAN test sub-dataset	E-value: Enzyme-pair functional identity: original held-out test
ESM2	Accuracy	71.33 percent	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	AUPRC	0.8147 unitless	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	AUROC	0.7991 unitless	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	F1	0.7345 unitless	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	False positive rate	36.67 percent	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	MCC	0.4321 unitless	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	Precision	68.39 percent	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
ESM2	Recall	79.33 percent	FUJISAN test sub-dataset	ESM2: Enzyme functional identity prediction
FUJISAN	Accuracy	87.05 percent	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	AUPRC	0.9413 unitless	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	AUROC	0.9427 unitless	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	F1	0.8728 unitless	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	False positive rate	13.35 percent	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	MCC	0.7421 unitless	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	Precision	87.24 percent	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
FUJISAN	Recall	87.05 percent	FUJISAN test sub-dataset	FUJISAN: Enzyme functional identity prediction
Pfam	Accuracy	61.99 percent	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	AUPRC	– unitless	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	AUROC	– unitless	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	F1	0.7217 unitless	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	False positive rate	74.62 percent	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	MCC	0.3520 unitless	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	Precision	56.92 percent	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test
Pfam	Recall	98.60 percent	FUJISAN test sub-dataset	Pfam: Enzyme-pair functional identity: original held-out test

Claims

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Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction): links:evaluates_task:reported-task-1ebf9b408517f9: Evaluates task Enzyme functional identity prediction (Table 1: ACC (%), Enzyme-pair functional identity: original held-out test)
ESM2 · AUROC · FUJISAN test sub-dataset: attributes.metric_direction: Metric direction higher (Table 1, row ESM2, column AUROC; XML row5 column8)
FUJISAN · AUROC · FUJISAN test sub-dataset: attributes.metric_direction: Metric direction higher (Table 1, row FUJISAN, column AUROC; XML row2 column8)

Models, benchmarks and other records

Configurations (3)

Tasks (1)

Enzyme functional identity prediction

Protocols (1)

Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)

Evaluations (5)

Evidence

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16 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 SHA-256 db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11609699/fullTextXML Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.1016/j.csbj.2024.11.028 Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-17T07:56:15.783679+00:00 Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11609699/fullTextXML Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version PMC11609699.1 Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Stable ID: part2-fujisan-2024

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11609699/fullTextXML
doi: 10.1016/j.csbj.2024.11.028
version: PMC11609699.1
retrieved at: 2026-09-17T07:56:15.783679+00:00
artifact sha256: db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11609699/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

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