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PDBbind+: A Platform for Collection of Experimental Binding Affinity Data

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PDBbind+:A Platform for Collection of Experimental Binding Affinity Data

Provided by TargetMol

PDBbind is dedicated to systematically collecting three-dimensional structural information of various complexes from the Protein Data Bank, along with their corresponding experimental affinity data. It plays an irreplaceable role in developing computational methods and related studies that describe target—ligand interactions.

PDBbind 2021 marked a major update, featuring a significantly enhanced web platform, a substantially expanded collection of experimental affinity data, and greatly improved complex structure files. The PDBbind 2024 edition has now been released. We encourage

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Highlights of PDBbind Version 2025

Measurable Data Growth

The PDBbind+ database continues to expand. The total number of binding data entries in version 2025 has reached 35,924. This represents an approximate 7% increase compared to version 2024 and an increase of over 50% compared to the last free-accessible release (version 2020).

The new release includes carefully curated binding data for four categories of complexes:

o Protein-ligand complexes: 29001 entries
o Protein-protein complexes: 5077 entries
o Protein-nucleic acid complexes: 1584 entries
o Nucleic acid-ligand complexes: 262 entries

Refined Structural Processing & Quality Control

Each complex included in PDBbind comes with a set of processed structural files. To compile version 2025, we have further upgraded our processing workflow. This upgraded workflow has been applied not only to newly added entries but also to entries from the previous version.

Integration of New On-Line Computing Tool

In addition to COMET(target-fishing for bioactive molecules) and PLANET(ultra-fast structure-based virtual screening), the PDBbind+ platform has incorporated a new tool termed STELLAR. This deep-learning model is developed for the prediction of ligand dissociation rate constants (koff), a critical feature in protein-ligand binding.

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