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Functional dynamics of substrate recognition in tem beta-lactamase
Title
Functional dynamics of substrate recognition in tem beta-lactamase
Author
Jacobs, Donald J., Avery, Chris, Baker, Lonnie
Date Created
2022
Subjects--Topical
Machine learning, Molecular dynamics
Description
The beta-lactamase enzyme provides effective resistance to beta-lactam antibiotics due to substrate recognition controlled by point mutations. Recently, extended-spectrum and inhibitor-resistant mutants have become a global health problem. Here, t...
JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Title
JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
Author
Jacobs, Donald J., Avery, Chris
Date Created
2021
Subjects--Topical
Biology, Proteins
Description
Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized soft...
Molecular function recognition by supervised projection pursuit machine learning
Title
Molecular function recognition by supervised projection pursuit machine learning
Author
Jacobs, Donald J., Grear, Tyler, Avery, Chris, Patterson, John
Date Created
2021
Subjects--Topical
Molecular biology, Pharmaceutical chemistry
Description
Identifying mechanisms that control molecular function is a significant challenge in pharmaceutical science and molecular engineering. Here, we present a novel projection pursuit recurrent neural network to identify functional mechanisms in the co...