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Protein design guides

Guides on de novo protein and antibody design, inverse folding, and developability screening.

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Ink illustration of an antibody and a magnified binding domain with an engineered loop.

Antibodies · October 5, 2026

What is antibody engineering?

Antibody engineering changes an antibody's sequence or structure to improve binding, reduce immunogenicity, tune effector function or create new formats. Learn the core techniques and computational workflows.

Two protein chains with low-PAE residue pairs highlighted at their interface and faint flexible tails

Structures · October 2, 2026

ipSAE explained

ipSAE is an interface confidence score for AlphaFold2, AlphaFold3 and Boltz that ignores disordered tails. Learn how it is calculated, why it beats ipTM and what 0.6 to 0.8 mean.

Ink illustration of a designed antibody domain approaching a target protein.

Antibodies · September 24, 2026

What is Chai-2? De novo antibody design explained

Understand what Chai-2 designs, what its experimental hit rates mean, how access works, and which open tools address related antibody and protein binder tasks.

Ink illustration of an antibody and enlarged variable domains with framework sites highlighted.

Antibodies · August 26, 2026

How to use BioPhi online

Learn how to run BioPhi online, choose between Sapiens and OASis modes, prepare VH and VL inputs, interpret humanness scores and mutations, troubleshoot warnings, and validate humanized antibodies.

Ink illustration of several designed protein binder candidates beside a target protein.

Design · August 26, 2026

How to use BoltzGen online

Learn how to run BoltzGen online, choose a binder protocol and target site, configure a design campaign, interpret ranked structures and metrics, and plan experimental validation.

Antibody backbone connected to candidate peptide sequences for inverse folding.

Antibodies · August 25, 2026

How to use AntiFold online

Learn how to use AntiFold online, prepare an IMGT-numbered antibody structure, choose chains and design regions, sample sequences, interpret likelihood scores, and validate candidates.

Paired antibody domains and alternative loop motifs representing variant assessment.

Antibodies · August 25, 2026

How to use CoSiNE online

Learn how to run CoSiNE online to predict variant effects for paired antibodies. Prepare a DMS CSV, choose heavy, light or combined scoring, and interpret the results.

Paired antibody variable domains beside a droplet containing antibody symbols.

Antibodies · August 25, 2026

How to use DeepViscosity online

Learn how to run DeepViscosity online from paired antibody Fv sequences, prepare the required CSV, interpret Prob_Mean, Prob_Std, classes, and DeepSP descriptors, and plan experimental validation.

Ink illustration of alternative antibody binding loops beside an antigen surface.

Antibodies · August 23, 2026

How to use DiffAb online

Learn how to run DiffAb online, prepare an antibody or antibody–antigen PDB, choose among five CDR design modes, interpret native output files, and validate unranked candidates.

Ink illustration of antibody variable domains with charge and hydrophobic surface patches.

Antibodies · August 23, 2026

How to use TAP2 online

Learn how to run TAP2 online with antibody VH and VL sequences, and how to interpret PSH, PPC, PNC, SFvCSP and CDR-length flags. See how ProteinIQ reconstructed and validated the method.

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