Configuration

ESM-IF1

ESM-IF1 designs protein sequences conditioned on backbone coordinates.

Sources

facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

How it worksESM-IF1 workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources

facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

Overview

Model type

Geometric encoder and inverse-folding transformer

Inputs

Protein backbone atom coordinates; the model supports missing backbone spans.

Outputs

Sampled protein sequences or conditional sequence likelihoods.

Access

Official project documentation and implementation: https://github.com/facebookresearch/esm

Sources

facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

10 evaluations · 10 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-PLDDT: De novo backbones based sequence design, length 100 pLDDT Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	88.8 plddt score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-PLDDT: De novo backbones based sequence design, length 100 pLDDT Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 100 pLDDT ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	0.81 sctm score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-SCTM: De novo backbones based sequence design, length 100 scTM Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 100 scTM ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-PLDDT: De novo backbones based sequence design, length 200 pLDDT Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	69.7 plddt score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-PLDDT: De novo backbones based sequence design, length 200 pLDDT Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 200 pLDDT ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-SCTM: De novo backbones based sequence design, length 200 scTM Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	0.635 sctm score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-200-SCTM: De novo backbones based sequence design, length 200 scTM Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 200 scTM ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-PLDDT: De novo backbones based sequence design, length 300 pLDDT Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	74.4 plddt score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-PLDDT: De novo backbones based sequence design, length 300 pLDDT Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 300 pLDDT ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-SCTM: De novo backbones based sequence design, length 300 scTM Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	0.336 sctm score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-300-SCTM: De novo backbones based sequence design, length 300 scTM Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 300 scTM ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-PLDDT: De novo backbones based sequence design, length 400 pLDDT Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	64.6 plddt score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-PLDDT: De novo backbones based sequence design, length 400 pLDDT Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 400 pLDDT ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-SCTM: De novo backbones based sequence design, length 400 scTM Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	0.449 sctm score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-400-SCTM: De novo backbones based sequence design, length 400 scTM Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 400 scTM ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-PLDDT: De novo backbones based sequence design, length 500 pLDDT Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	59 plddt score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-PLDDT: De novo backbones based sequence design, length 500 pLDDT Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 500 pLDDT ↑)
Configuration: ESM-IF1	Task: ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-SCTM: De novo backbones based sequence design, length 500 scTM Dataset subset: CASP, CAMEO and de novo backbones (ProteinBench split)	0.462 sctm score · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-IF1 on ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-500-SCTM: De novo backbones based sequence design, length 500 scTM Inverse folding: recover a sequence for a given backbone. Values are the median over repeated runs. Aggregation: Not reported proteinbench primary benchmark evidence · Table 2, row(ESM-IF1), column(De novo backbones based sequence design, length 500 scTM ↑)

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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How it works, versions and access

Related profile: ESM-IF1. This page retains the exact record and its evaluation context.

This configuration

Protein model evaluated by the ProteinBench authors under their harness.

record: ESM-IF1
configuration: Not reported
entity type: Configuration

How it works

ESM-IF1 designs protein sequences conditioned on backbone coordinates. Geometric-vector-perceptron input processing followed by a sequence-to-sequence transformer. The documented inputs are protein backbone atom coordinates; the model supports missing backbone spans. The output consists of sampled protein sequences or conditional sequence likelihoods.

Sources

facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

Versions and reproducibility

esm_if1_gvp4_t16_142M_UR50. The applicable input limits require configuration-specific checking.

Sources

facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Structure-conditioned design can use partially missing backbones because training included span masking.
Sources
facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

Limitations and conditions

The public checkpoint name contains 142M but the README parameter table reports 124M. This discrepancy is retained rather than silently selecting a total.
Sources
facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-esm-if1

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Geometric encoder and inverse-folding transformer Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Architecture	Geometric-vector-perceptron input processing followed by a sequence-to-sequence transformer. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Inputs	Protein backbone atom coordinates; the model supports missing backbone spans. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Outputs	Sampled protein sequences or conditional sequence likelihoods. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Parameters	The official checkpoint identifier contains 142M but the same repository model table states 124M. Both values are retained as a source discrepancy, without choosing a total. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Known versions	esm_if1_gvp4_t16_142M_UR50. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Training data	CATH 4.3 and predicted UniRef50 structures; README reports 12M structures predicted by AlphaFold2. Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Training cutoff	The official model table identifies CATH 4.3 and predicted UniRef50 structures, but does not state a common latest-structure or sequence date. · Not reported in inspected sources Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Context limits	The reviewed inverse-folding usage and model table do not establish a universal maximum backbone length; the structural graph and selected inference configuration determine resource use. · Not reported in inspected sources Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Weights licence	Separate checkpoint-distribution terms are not stated in the inspected release documentation and licence material. The source-code licence alone is not recorded as an explicit weight grant. · Not reported in inspected sources Sources (2) facebookresearch/esm: README.md; facebookresearch/esm: LICENSE · README.md: Inverse folding and Pre-trained Models; LICENSE: licence text
Access	Official project documentation and implementation: https://github.com/facebookresearch/esm Sources facebookresearch/esm: README.md · README.md: Inverse folding and Pre-trained Models
Code licence	MIT Sources facebookresearch/esm: LICENSE · LICENSE: licence text

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-esm-if1 Individual claims	proteinbench primary benchmark evidence Original source ↗ Tables 2; task methods and corresponding named row Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Paper evaluates this named model under its ProteinBench harness. Association is to the family, not an assertion of checkpoint equivalence or cross-task comparability. Field: `links:family:discovery-model-esm-if1` Claim: model-evaluation-identity-ef56adf7ad06a3da053e Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

1 source records and release history

proteinbench primary benchmark evidence · Original source · 2409.06744v1

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Technical metadata and extraction receipts

Stable ID: proteinbench-method-esm-if1

areas: proteins-complexes
source locator: Table 2, row(ESM-IF1)
missing metadata: checkpoint revision: unreported; parameters: unextracted

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