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Updated: May 1, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
CABS-flex predictions of protein flexibility compared with NMR ensembles
Michal Jamroz1, Andrzej Kolinski1, Sebastian Kmiecik1
1Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw 02-093, Poland.
Motivation:
Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.
Results:
Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes.
Availability And Implementation:
The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex.
Contact:
sekmi@chem.uw.edu.pl
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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