Automatic recognition of ligands in electron density by machine learning.

ABSTRACT:

Motivation

The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting.

Results

Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identi

SUBMITTER: Kowiel M 

PROVIDER: S-EPMC6361236 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature