An open-source framework for fast-yet-accurate calculation of quantum mechanical features.
Phys Chem Chem Phys
; 24(17): 10599-10610, 2022 May 04.
Article
in English
| MEDLINE | ID: covidwho-1805671
ABSTRACT
We present the open-source framework kallisto that enables the efficient and robust calculation of quantum mechanical features for atoms and molecules. For a benchmark set of 49 experimental molecular polarizabilities, the predictive power of the presented method competes against second-order perturbation theory in a converged atomic-orbital basis set at a fraction of its computational costs. The calculation of isotropic molecular polarizabilities is robust for a data set of more than 80 000 molecules. We present furthermore a generally applicable van der Waals radius model that is rooted on atomic static polarizabilites. Efficiency tests show that such radii can even be calculated for small- to medium-size proteins where the largest system (SARS-CoV-2 spike protein) has 42 539 atoms. Following the work of Domingo-Alemenara et al. [Domingo-Alemenara et al., Nat. Commun., 2019, 10, 5811], we present computational predictions for retention times for different chromatographic methods and describe how physicochemical features improve the predictive power of machine-learning models that otherwise only rely on two-dimensional features like molecular fingerprints. Additionally, we developed an internal benchmark set of experimental super-critical fluid chromatography retention times. For those methods, improvements of up to 10.6% are obtained when combining molecular fingerprints with physicochemical descriptors. Shapley additive explanation values show furthermore that the physical nature of the applied features can be retained within the final machine-learning models. We generally recommend the kallisto framework as a robust, low-cost, and physically motivated featurizer for upcoming state-of-the-art machine-learning studies.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
COVID-19
Type of study:
Prognostic study
Limits:
Humans
Language:
English
Journal:
Phys Chem Chem Phys
Journal subject:
Biophysics
/
Chemistry
Year:
2022
Document Type:
Article
Affiliation country:
D2cp01165d
Similar
MEDLINE
...
LILACS
LIS