AlphaFold 3 Server
AlphaFold 3 Server is a candidate method in the molecular-interactions catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
molecular-interactions · 1 linked sources
Omics and molecular biology
Biological model benchmark database
Find models, understand how they are tested, and inspect the evidence behind their results.
Supporting records
Model families and reported methods, linked to their evaluations and sources. Versions are kept distinct where known.
226 matching records · Release 2026-09-16-d74d282221a9
AlphaGenome
AlphaGenome is a candidate method in the dna-genomes catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
dna-genomes · 1 linked sources
Boltz-2
Boltz is a biomolecular interaction model family. Boltz-2 adds affinity prediction to complex-structure prediction.
molecular-interactions · 1 linked sources
Chai-1
Chai-1 is a candidate method in the proteins-complexes, molecular-interactions catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
proteins-complexes · molecular-interactions · 1 linked sources
DiffDock-L
DiffDock-L is a candidate method in the molecular-interactions catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
molecular-interactions · 1 linked sources
DNABERT-2
DNABERT-2 is a DNA encoder pretrained on sequences from multiple species. It supplies representations that can be adapted to genomic tasks.
dna-genomes · 1 linked sources
ESM-2
ESM-2 is a family of protein sequence transformers that produce residue-level and sequence-level representations.
proteins-complexes · 1 linked sources
ESMFold
ESMFold predicts protein structures from individual amino-acid sequences using an ESM-2 representation model and a folding system.
proteins-complexes · 1 linked sources
Evo 2
Evo 2 models and generates DNA at nucleotide resolution using the StripedHyena 2 architecture.
dna-genomes · microbes-communities · 1 linked sources
GEARS
GEARS predicts transcriptional responses to genetic perturbations using single-cell perturbation-screen data.
cells-tissues · 1 linked sources
Geneformer
Geneformer is a candidate method in the cells-tissues catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
cells-tissues · 1 linked sources
Kraken2
Kraken2 is a candidate method in the microbes-communities catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
microbes-communities · 1 linked sources
METAGENE-1
METAGENE-1 is a candidate method in the microbes-communities catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
microbes-communities · 1 linked sources
MetaPhlAn
MetaPhlAn is a candidate method in the microbes-communities catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
microbes-communities · 1 linked sources
MIMIC
MIMIC is a candidate method in the rna-transcriptomes, proteins-complexes catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
rna-transcriptomes · proteins-complexes · 1 linked sources
mRNA-FM
mRNA-FM is the coding-sequence extension of RNA-FM, intended to represent messenger RNA coding regions.
rna-transcriptomes · 1 linked sources
Nucleotide Transformer v2
Nucleotide Transformer v2 is a candidate method in the dna-genomes catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
dna-genomes · 1 linked sources
Pangolin
Pangolin predicts changes in splice-site strength from DNA variants. It accepts variant files or custom sequence inputs.
dna-genomes · 1 linked sources
ProkBERT
ProkBERT is a candidate method in the microbes-communities catalogue. The linked resource identifies the project; a checkpoint-level profile has not yet been extracted.
microbes-communities · 1 linked sources
ProteinMPNN
ProteinMPNN designs amino-acid sequences for a supplied protein backbone, with controls for fixed residues and chains.
proteins-complexes · 1 linked sources
About the evidence
Published evaluations and rewire evaluations are records in the same database, with their origin shown beside each result. This release includes 155 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. Model records include families and paper-specific methods; counts do not represent unique checkpoints.
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"scope": "Specialist omics and molecular models; no clinical assistants or standalone medical imaging.",
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}Download the database
Release 2026-09-16-d74d282221a9 · 2026-09-16
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.