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
AI Molecular Docking and Pose Prediction Models
Docking pose accuracy is not binding-affinity accuracy. BioAtlas separates geometry, ranking, access and benchmark context so model selection stays tied to the actual scientific question.
Curated model passports
21 relevant BioAtlas records.
Open evidence passport →
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
ProteinMPNN / LigandMPNN
Given a shape, design the sequence that folds into it.
Evidence3/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkNot yet curated
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
Chemistry42 / Pharma.AI
Generative chemistry that carried an AI drug into Phase II.
Evidence2/7 evidence fields documented
AccessProprietary
ComputeGPU or managed service
BenchmarkNot yet curated
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
GEMS
Graph neural networks for potency on tough targets.
Evidence1/7 evidence fields documented
AccessProprietary
ComputeGPU or managed service
BenchmarkNot yet curated
Numerion AI Chemistry Platform
The current COSMOS, APEX and EXPO chemistry stack from the company formerly known as Atomwise.
Evidence2/7 evidence fields documented
AccessProprietary
ComputeGPU or managed service
BenchmarkNot yet curated
DiffDock
Reframing molecular docking as a diffusion generative problem.
Evidence4/7 evidence fields documented
AccessOpen source
ComputeGPU or managed service
BenchmarkPDBBind
Schrödinger Platform
Physics-based simulation, now fused with machine learning.
Evidence1/7 evidence fields documented
AccessProprietary
ComputeCPU/GPU / commercial platform
BenchmarkNot yet curated
Cradle Bio
Generative protein engineering for any wet lab.
Evidence1/7 evidence fields documented
AccessProprietary
ComputePlatform dependent
BenchmarkNot yet curated
Isomorphic Labs (IsoDDE)
AlphaFold's spin-off, aiming to 'solve all disease'.
Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
insitro
Machine-learning-driven biology for drug discovery.
Evidence1/7 evidence fields documented
AccessProprietary
ComputeVendor managed
BenchmarkNot yet curated
Uni-Mol / Uni-Mol2
3D molecular foundation models trained on atoms, topology and conformational geometry.
Evidence3/7 evidence fields documented
AccessOpen source
ComputeGPU recommended
BenchmarkMolecular representation/property benchmarks
MolMIM
A latent-variable molecular generator with an informative clustered SMILES space.
Evidence2/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
MegaMolBART
A BART-style chemical language model for molecular embeddings and generation.
Evidence1/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
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
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
UNI / UNI2
General-purpose pathology vision foundation models for tissue representation.
Evidence1/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
Virchow / Virchow2
Large-scale histopathology foundation modelling for transferable tissue representations.
Evidence1/7 evidence fields documented
AccessLimited open access
ComputeGPU recommended
BenchmarkNot yet curated
AIDO Cell 1.0
A multiscale virtual-cell world model for simulating biological interventions and readouts.
Evidence2/7 evidence fields documented
AccessLimited open access
ComputeProvider-managed / accelerator recommended
BenchmarkVirtual Cell Benchmark 1.0
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.