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Updated: Feb 5, 2026
Protein Purification-free Method of Binding Affinity Determination by Microscale Thermophoresis
Published on: August 15, 2013
Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity
Maciej Wójcikowski1, Michał Kukiełka2, Marta M Stepniewska-Dziubinska1
1Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, Warsaw, Poland.
Motivation:
Fingerprints (FPs) are the most common small molecule representation in cheminformatics. There are a wide variety of FPs, and the Extended Connectivity Fingerprint (ECFP) is one of the best-suited for general applications. Despite the overall FP abundance, only a few FPs represent the 3D structure of the molecule, and hardly any encode protein-ligand interactions.
Results:
Here, we present a Protein-Ligand Extended Connectivity (PLEC) FP that implicitly encodes protein-ligand interactions by pairing the ECFP environments from the ligand and the protein. PLEC FPs were used to construct different machine learning models tailored for predicting protein-ligand affinities (pKi∕d). Even the simplest linear model built on the PLEC FP achieved Rp = 0.817 on the Protein Databank (PDB) bind v2016 'core set', demonstrating its descriptive power.
Availability And Implementation:
The PLEC FP has been implemented in the Open Drug Discovery Toolkit (https://github.com/oddt/oddt).
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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