Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions.

ABSTRACT:

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 Dat

SUBMITTER: Wojcikowski M 

PROVIDER: S-EPMC6477977 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature