Omics and molecular biology

Biological model benchmark database

Find models, understand how they are tested, and inspect the evidence behind their results.

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Methods and evaluation records

Biological models and model families. Evaluated versions, configurations and pipelines are linked separately.

Research areaEvidence status

52 matching records

Model · discovered

AlphaGenome

AlphaGenome predicts regulatory activity and variant effects from long DNA sequences, with outputs for expression, splicing, chromatin and contact maps.

DNA and genomes · 4 linked sources

44 evaluations · 52 metric rows

Model · discovered

Boltz-2

Boltz predicts biomolecular complex structures; Boltz-2 also predicts binding affinity.

Molecular interactions · 7 linked sources

1 evaluations · 1 metric rows

Model · discovered

Chai-1

Chai-1 predicts the structures of biomolecular complexes containing proteins, nucleic acids and small molecules.

Proteins and complexes · Molecular interactions · 3 linked sources

5 evaluations · 5 metric rows

Model · discovered

DiffDock-L

DiffDock-L places small-molecule ligands in protein structures using a diffusion docking model.

Molecular interactions · 3 linked sources

1 evaluations · 1 metric rows

Model · discovered

ESM-2

ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.

Proteins and complexes · 4 linked sources

3 evaluations · 11 metric rows

Model · discovered

ESMFold

ESMFold predicts protein structures directly from amino-acid sequence using ESM-2 representations.

Proteins and complexes · 4 linked sources

14 evaluations · 14 metric rows

Model · discovered

Evo 2

Evo 2 models and generates DNA over long contexts at single-nucleotide resolution.

DNA and genomes · Microbes and communities · 5 linked sources

87 evaluations · 92 metric rows

Model · discovered

GEARS

GEARS predicts transcriptional responses to single- and multi-gene perturbations from single-cell perturbation screens.

Cells and tissues · 4 linked sources

1 evaluations · 2 metric rows

Model · discovered

Geneformer

Geneformer represents single-cell transcriptomes as ranked genes and learns contextual gene and cell representations.

Cells and tissues · 3 linked sources

5 evaluations · 5 metric rows

Model · discovered

METAGENE-1

METAGENE-1 is an autoregressive DNA/RNA sequence model trained on wastewater metagenomic data.

Microbes and communities · 5 linked sources

No evaluations linked in this release

Model · discovered

MIMIC

MIMIC represents DNA, RNA, protein and associated molecular measurements in a shared multimodal model.

RNA and transcriptomes · Proteins and complexes · 5 linked sources

No evaluations linked in this release

Model · discovered

mRNA-FM

mRNA-FM encodes coding RNA with codon-level tokens to produce representations for downstream analysis.

RNA and transcriptomes · 3 linked sources

No evaluations linked in this release

Model · discovered

Nucleotide Transformer v2

Nucleotide Transformer v2 represents DNA using an encoder pretrained on multiple species.

DNA and genomes · 8 linked sources

44 evaluations · 44 metric rows

Model · discovered

ProkBERT

ProkBERT is a family of microbial DNA encoders used for sequence representation, promoter prediction and phage identification.

Microbes and communities · 5 linked sources

3 evaluations · 12 metric rows

Model · discovered

ProteinMPNN

ProteinMPNN designs amino-acid sequences for a supplied protein backbone.

Proteins and complexes · 6 linked sources

No evaluations linked in this release

Model · discovered

RhoFold+

RhoFold+ predicts RNA three-dimensional structures from RNA sequence with alignment information.

RNA and transcriptomes · 4 linked sources

6 evaluations · 12 metric rows

Model · discovered

scFoundation

scFoundation produces contextual cell and gene representations from gene-expression measurements.

Cells and tissues · 4 linked sources

No evaluations linked in this release

Model · discovered

scGPT

scGPT learns representations of single-cell molecular measurements and supports task-specific adaptation.

Cells and tissues · 4 linked sources

3 evaluations · 3 metric rows

Model · discovered

scVI

scVI models single-cell RNA counts with a probabilistic latent-variable model that accounts for observed covariates.

Cells and tissues · 3 linked sources

2 evaluations · 24 metric rows

Model · discovered

Agro Nucleotide Transformer

AgroNT learns DNA representations from plant reference genomes for plant molecular prediction tasks.

Genomics · 8 linked sources

12 evaluations · 12 metric rows

Coverage: records and linked evaluations

26,045 records across 16 record types. These counts describe catalogue coverage, not model performance.

Records by kind

result11,291
evaluation8,726
configuration2,389
claim1,112
source930
task495
dataset subset334
protocol334
dataset138
pipeline124
model59
method42
benchmark39
baseline27
evaluator4
service1

Records by research area

RNA and transcriptomes3,773
Proteins and complexes3,308
DNA and genomes2,658
Cells and tissues1,426
Genomics1,415
RNA and transcriptomics1,169
Molecular interactions750
Glycomics498
Molecular omics489
Microbes and communities457

Benchmark evidence coverage

38 of 39 benchmarks have linked evaluations in this release. Zero means no evaluation is linked here, not that the benchmark has never been used.

NABench1,101
Virtual Cell Challenge 20261,048
mRNABench696
ProteinBench556
CAFA438
BEELINE384
Open Problems384
GlycanML323
DART-Eval316
SegmentNT human genome annotation294
GUE280
BEACON221
FLIP155
FLIP2149
PFMBench141
BEND105
CAPRI100
HEST-Benchmark100
CASP90
ProteinGym90
Gene-MTEB80
PerturBench76
scIB69
TDC molecular tasks66
ATOM3D57
RhoFold+ CASP15 natural RNA comparison56
TAPE50
MSAlign molecular retrieval evaluations36
MassSpecGym24
Plant Genomic Benchmark (PGB)24
GENEB22
Genomic Benchmarks18
CAMI16
scFoundation cell-type annotation comparison14
Genie 3 unconditional short monomer comparison13
ESMFold2 Runs N’ Poses comparison11
PLINDER7
MIST CANOPUS molecular retrieval6
PEtab benchmark collection0

About the evidence

Published evaluations and rewire evaluations are records in the same database, with their origin shown beside each result. This release includes 11279 source-checked literature result rows and 12 metric rows from existing rewire runs.

Source checked does not mean independently reproduced. Comparisons require compatible data, protocols and metrics. Missing details stay visible.

Rewire evaluations

Read the protocol, coverage and limitations behind our corrected splice-variant evaluation.

MFASS v2 evaluation →

Correction history

MFASS v1 is superseded. Its original tables and methods remain available as an archived report.

Archived MFASS v1 report →

Collection coverage and remaining gaps

This is a dated collection, not an exhaustive model census. Models, methods, evaluated configurations and pipelines are listed separately. Counts describe records, not unique checkpoints or independent experiments.

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}

Download the database

Release 2026-09-23-2b89723c6dd9 · 2026-09-23

JSONL CSV Evidence table (CSV)Evidence table (JSONL)Evidence and review methods Checksums and release manifest

Original literature downloads

The original 100-paper collection is retained for citation history. These files include six result rows excluded from the current omics scope; use the database release above for the reviewed collection.

Original results CSV Original papers JSON