Bio Tools

Cheminformatics

RDKit

Calculate common molecular descriptors and normalize SMILES.

API docs → /api/rdkit/

Structure prediction Protein Design

OpenDDE

Run a protein, DNA/RNA, or ligand co-folding prediction.

API docs → /api/opendde/

Structure prediction Protein Design Property prediction

Boltz-2

Predict a biomolecular complex and optional ligand affinity.

API docs → /api/boltz2/

Structure prediction Protein Design

Chai-1

Predict protein or protein-ligand complex structures with Chai-1.

API docs → /api/chai1/

Structure prediction

Protenix-v2

Predict protein or protein-ligand complex structures with Protenix.

API docs → /api/protenix/

Structure prediction Protein Design

ESMFold 2

Fold a protein from its sequence alone, with no MSA or template search.

API docs → /api/esmfold2/

Structure prediction Antibody design

ImmuneBuilder

Predict an antibody, nanobody, or TCR structure in seconds.

API docs → /api/immunebuilder/

Structure prediction Binder design

HighFold

Predict the structure of a cyclic peptide or a cyclic-peptide complex.

API docs → /api/highfold/

Binder design Protein Design Antibody design

BoltzGen

Design a protein, peptide, nanobody, or antibody binder.

API docs → /api/boltzgen/

Binder design Protein Design

BindCraft

Design de novo protein or peptide binders against a target structure.

API docs → /api/bindcraft/

Molecular simulation

GROMACS

Prepare a solvated molecular-dynamics system from a PDB structure.

API docs → /api/gromacs/

Sequence analysis

IgBLAST

Identify germline V(D)J matches in an antibody sequence.

API docs → /api/igblast/

Antibody design Sequence analysis

BioPhi

Humanize antibody sequences or estimate their humanness.

API docs → /api/biophi/

Antibody design Sequence prediction

AntiFold

Score or sample antibody sequences from an IMGT-numbered structure.

API docs → /api/antifold/

Antibody design Sequence prediction

AbMPNN

Design antibody sequences from a backbone structure.

API docs → /api/abmpnn/

Sequence prediction Protein Design

ProteinMPNN

Design protein sequences for a supplied backbone structure.

API docs → /api/proteinmpnn/

Sequence prediction Protein Design

LigandMPNN

Design protein sequences with ligand-, solubility-, or membrane-aware models.

API docs → /api/ligandmpnn/

Property prediction

ProteinMPNN-ddG

Predict the stability effects of every point mutation in a protein chain.

API docs → /api/proteinmpnn_ddg/

Protein Design Binder design

RFdiffusion

Generate protein backbones unconditionally, around a motif, or against a target.

API docs → /api/rfdiffusion/

Antibody design Protein Design

RFantibody

Design antibody or nanobody backbones against a target structure.

API docs → /api/rfantibody/

Antibody design Protein Design Binder design

Germinal

Design de novo antibodies against a chosen epitope on a target structure.

API docs → /api/germinal/

Antibody design Binder design Protein Design

mBER

Design VHH (nanobody) binders against a target by backprop through AlphaFold-Multimer.

API docs → /api/mber/

Antibody design Sequence prediction Protein Design

IgDesign

Design antibody CDRs against a target antigen by inverse folding.

API docs → /api/igdesign/

Property prediction Protein Design

ThermoMPNN

Predict the stability change of point mutations in a protein structure.

API docs → /api/thermompnn/

Property prediction Cheminformatics

Boltz ADME

Predict lipophilicity, permeability, and solubility for small molecules.

API docs → /api/boltz_adme/

Binder design Protein Design

Genie 3

Generate all-atom protein-binder backbones against a target.

API docs → /api/genie3/

Property prediction Antibody design

DeepSP

Predict 30 spatial developability descriptors for an antibody from sequence alone.

API docs → /api/deepsp/

Property prediction Sequence analysis

DeepImmuno

Score how likely a peptide-MHC class I pair is to provoke a CD8 T-cell response.

API docs → /api/deepimmuno/

Property prediction Sequence analysis

TLimmuno2

Score how likely a peptide-MHC class II pair is to provoke a CD4 T-cell response.

API docs → /api/tlimmuno/

Property prediction Sequence prediction

NetSolP

Predict whether a protein will be soluble and usable when expressed in E. coli.

API docs → /api/netsolp/

Property prediction

DeepSTABp

Predict the melting temperature of a protein from its sequence.

API docs → /api/deepstabp/

Property prediction

AggreScan3D

Map aggregation-prone patches onto a protein structure and score them.

API docs → /api/aggrescan3d/

Property prediction Cheminformatics

DLKcat

Predict an enzyme turnover number from its sequence and a substrate structure.

API docs → /api/dlkcat/

Property prediction Cheminformatics

CatPred

Predict kcat, Km, or Ki for an enzyme and substrate, with an uncertainty estimate.

API docs → /api/catpred/

Sequence analysis Antibody design

Antibody Annotator

Number an antibody or TCR sequence and report its regions and liabilities.

API docs → /api/antibody_annotator/

Structure prediction Cheminformatics

PLACER

Generate an ensemble of protein-ligand poses and side-chain conformations.

API docs → /api/placer/