Skip to main content
BIO·ATLASby Bayes Pharma.ai
Search
AccountStart evaluation
Scientific model guide

Protein Design AI Models

Protein design usually spans backbone generation, sequence design, structural filtering and experimental validation. BioAtlas keeps those stages distinct instead of treating generation as proof of function.

Compare selected modelsBenchmark claim ledgerEvaluation methodology
Curated model passports

43 relevant BioAtlas records.

Structure Prediction

AlphaFold 2 / 3

The model that solved the 50-year protein-folding problem.

Evidence4/7 evidence fields documented
AccessLimited open access
ComputeGPU / managed server
BenchmarkCASP14 / complex evaluations
Open evidence passport →
Structure Prediction

RoseTTAFold / All-Atom

The three-track network that followed folding into all-atom space.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkCASP14 / complex modelling
Open evidence passport →
Structure Prediction

OpenFold

A fully open, trainable reproduction of AlphaFold 2.

Evidence3/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Structure Prediction

ESMFold

Structure from a single sequence — no alignment required.

Evidence3/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Structure Prediction

Chai-1 / Chai-2

An AlphaFold3-class complex predictor, made freely usable.

Evidence4/7 evidence fields documented
AccessLimited open access
ComputeGPU / hosted service
BenchmarkComplex and antibody-design evaluations
Open evidence passport →
Protein & Binder Design

RFdiffusion

Diffusion models that hallucinate brand-new proteins.

Evidence5/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkExperimental binder validation
Open evidence passport →
Protein & Binder Design

ESM3

A generative model that reasons over sequence, structure & function at once.

Evidence4/7 evidence fields documented
AccessLimited open access
ComputeGPU / hosted service
BenchmarkGenerative protein evaluations
Open evidence passport →
Protein & Binder Design

Chroma

Programmable protein generation with a diffusion 'grammar'.

Evidence3/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Protein & Binder Design

Latent-X

Push-button, all-atom binder design in the browser.

Evidence2/7 evidence fields documented
AccessProprietary
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Protein & Binder Design

AlphaProteo

High-affinity binder generation from DeepMind.

Evidence2/7 evidence fields documented
AccessProprietary
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Small-Molecule & Chemistry

NVIDIA BioNeMo

The GPU-accelerated toolkit that ships biology's foundation models.

Evidence2/7 evidence fields documented
AccessLimited open access
ComputeNVIDIA GPU / managed service
BenchmarkNot yet curated
Open evidence passport →
Small-Molecule & Chemistry

NeuralPLexer / Enchant

Physics-aware structure + multi-task ADMET foundation models.

Evidence2/7 evidence fields documented
AccessLimited open access
ComputeGPU or managed service
BenchmarkNot yet curated
Open evidence passport →
Small-Molecule & Chemistry

DiffDock

Reframing molecular docking as a diffusion generative problem.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU or managed service
BenchmarkPDBBind
Open evidence passport →
Genomics, DNA & RNA

Evo / Evo 2

A genomic foundation model that reads and writes DNA at scale.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkGenomic sequence evaluations
Open evidence passport →
Genomics, DNA & RNA

AlphaGenome

Reading the genome's 'dark matter' at base-pair resolution.

Evidence2/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Genomics, DNA & RNA

BigRNA

An RNA foundation model for oligonucleotide therapeutics.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
Open evidence passport →
Antibodies & Biologics

Nabla Bio — JAM

Generative design of antibodies against hard membrane targets.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeManaged platform or GPU
BenchmarkNot yet curated
Open evidence passport →
Antibodies & Biologics

IgLM / AntiBERTy

The antibody-specific language models many tools build on.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeManaged platform or GPU
BenchmarkAntibody sequence evaluations
Open evidence passport →
Antibodies & Biologics

LabGenius — EVA

A robotic evolution engine for multi-specific antibodies.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeManaged platform or GPU
BenchmarkNot yet curated
Open evidence passport →
Platforms, Data & Infra

Cradle Bio

Generative protein engineering for any wet lab.

Evidence1/7 evidence fields documented
AccessProprietary
ComputePlatform dependent
BenchmarkNot yet curated
Open evidence passport →
AI-Native Discovery Cos.

Xaira Therapeutics

A $1B+ launch fusing Baker-lab design with drug development.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
Open evidence passport →
AI-Native Discovery Cos.

Generate:Biomedicines

Generative biology turned into a clinical-stage pipeline.

Evidence1/7 evidence fields documented
AccessLimited open access
ComputeVendor managed
BenchmarkNot yet curated
Open evidence passport →
AI-Native Discovery Cos.

Exscientia

The pioneer of AI-designed small molecules in the clinic.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
Open evidence passport →
AI-Native Discovery Cos.

insitro

Machine-learning-driven biology for drug discovery.

Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
Open evidence passport →
Protein & Binder Design

BoltzGen

All-atom generative binder design across proteins, peptides and molecular partners.

Evidence2/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkBinder-design evaluations
Open evidence passport →
Antibodies & Biologics

RFantibody

De novo epitope-specific antibody design from the RFdiffusion lineage.

Evidence4/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkExperimental antibody design
Open evidence passport →
Protein Foundation & Representation

ESM-2

A foundational protein language model for residue- and sequence-level representations.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkProtein representation and structure evaluations
Open evidence passport →
Protein Foundation & Representation

SaProt

Protein language modelling with amino-acid and structural-alphabet tokens.

Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkProtein understanding benchmarks
Open evidence passport →
Protein Foundation & Representation

ProtT5

A widely used protein Transformer for transferable sequence embeddings.

Evidence1/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Protein Foundation & Representation

Ankh

Efficient protein language models for transferable biological representations.

Evidence1/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Protein Foundation & Representation

xTrimoPGLM

A 100B-scale unified protein language model for understanding and generation.

Evidence2/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
RNA Models & Design

RNA-FM

A foundational BERT-style model for non-coding RNA sequence representations.

Evidence2/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Genomics, DNA & RNA

LucaOne

A unified biological foundation model spanning DNA, RNA and protein sequence.

Evidence3/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkDNA/RNA/protein downstream tasks
Open evidence passport →
Structure Prediction

HelixFold3

An open AF3-class biomolecular complex predictor from the PaddleHelix ecosystem.

Evidence2/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
Tissue, Pathology & Imaging

H-Optimus

Large pathology vision foundation models trained across broad tissue and disease diversity.

Evidence1/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Open evidence passport →
How to interpret this topic

Choose by context of use.

Inputs matter

Sequence, structure, ligand, assay and single-cell inputs imply different data-quality and preprocessing assumptions.

Outputs are not interchangeable

A predicted pose, confidence score, affinity estimate, generated sequence and perturbation profile support different decisions.

Benchmarks are protocol-bound

Claims should only be compared when task, dataset, split, metric and evaluation protocol genuinely align.

Validation remains external

BioAtlas records evidence boundaries; prospective scientific and experimental validation is still required for consequential use.