Related Experiment Video
Updated: Dec 10, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Multifidelity Statistical Machine Learning for Molecular Crystal Structure Prediction
Olga Egorova1, Roohollah Hafizi2, David C Woods1
1Statistical Sciences Research Institute, University of Southampton, Southampton, SO17 1BJ, U.K.
Abstract:
The prediction of crystal structures from first-principles requires highly accurate energies for large numbers of putative crystal structures. High accuracy of solid state density functional theory (DFT) calculations is often required, but hundreds or more structures can be present in the low energy region of interest, so that the associated computational costs are prohibitive. Here, we apply statistical machine learning to predict expensive hybrid functional DFT (PBE0) calculations using a multifidelity approach to re-evaluate the energies of crystal structures predicted with an inexpensive force field. The method uses an autoregressive Gaussian process, making use of less expensive GGA DFT (PBE) calculations to bridge the gap between the force field and PBE0 energies. The method is benchmarked on the crystal structure landscapes of three small, hydrogen-bonded organic molecules and shown to produce accurate predictions of energies and crystal structure ranking using small numbers of the most expensive calculations; the PBE0 energies can be predicted with errors of less than 1 kJ mol-1 with between 4.2 and 6.8% of the cost of the full calculations. As the model that we have developed is probabilistic, we discuss how the uncertainties in predicted energies impact the assessment of the energetic ranking of crystal structures.
More Related Videos
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
10:45Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
Published on: March 20, 2021