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The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

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Related Experiment Video

Updated: Jan 11, 2026

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

Evaluating BindCraft for Generative Design of High-Affinity Peptides.

Mike Filius^1,2, Thanasis Patsos^1,2, Hugo Minnee^1,2

¹Leiden Academic Center for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands.

ACS Chemical Biology

|November 18, 2025

Summary

This summary is machine-generated.

BindCraft, a generative AI platform, successfully designs high-affinity peptides for drug discovery by analyzing protein structures. This approach shows promise for developing new peptide therapeutics against targets like MDM2 and WDR5.

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Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

Area of Science:

Computational biology
Drug discovery
Protein engineering

Background:

Developing high-affinity ligands from protein structures is crucial but challenging.
Short peptides offer therapeutic potential but de novo generation of functional peptides is difficult due to their lack of stable structures.

Purpose of the Study:

To evaluate BindCraft, a structure-guided generative modeling platform, for de novo peptide design and high-affinity ligand discovery.
To assess BindCraft's ability to generate functional peptides based solely on target protein structures.

Main Methods:

Utilized BindCraft, a structure-guided generative AI platform, for de novo peptide design.
Synthesized and experimentally validated generated peptides against oncology targets MDM2 and WDR5.
Employed competition assays and affinity measurements (K_D) to confirm binding specificity and potency.

Main Results:

BindCraft generated 70 unique peptides for MDM2; 7 of 15 synthesized peptides showed nanomolar affinity and site-specific binding.
Six of nine designed peptides for WDR5 bound with submicromolar affinity to the MYC binding site.
Peptide optimization using BindCraft's predictions improved WDR5 binder potency sixfold to a K_D of 39 nM.

Conclusions:

BindCraft demonstrates significant success in generating high-affinity peptides for specific protein targets, rivaling traditional display technologies.
The platform shows potential for accelerating the development of peptide-based therapeutics.
Further evaluation is needed, as BindCraft did not yield binders for PD-1 and PD-L1 targets in this study.