Search results | J. Murrey Atkins Library

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...

Title: MATLAB tool for probability density assessment and nonparametric estimation
Author: Jacobs, Donald J., Farmer, Jenny
Date Created: 2022
Subjects--Topical: Statistics, Entropy
Description: A MATLAB function is presented for nonparametric probability density estimation, based on an iterative method that employs the principle of maximum entropy and characteristic properties of single order statistics. Featuring a robust and adaptive d...

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...

Title: Victory tax: a holistic income tax system
Author: Jacobs, Donald J.
Date Created: 2021
Subjects--Topical: Income tax, Tax deductions
Description: How can an income tax system be designed to exploit human nature and a free market to create a poverty free society, while balancing budgets without disproportional tax burdens? Such a tax system, with universal character, is deduced from the foll...

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...

Title: Universal sample size invariant measures for uncertainty quantification in density estimation
Author: Jacobs, Donald J., Farmer, Jenny, Merino, Zach, Merino, Zach
Date Created: 2019
Subjects--Topical: Statistics, Entropy
Description: Previously, we developed a high throughput non-parametric maximum entropy method (PLOS ONE, 13(5): e0196937, 2018) that employs a log-likelihood scoring function to characterize uncertainty in trial probability density estimates through a scaled q...

Title: High throughput nonparametric probability density estimation
Author: Jacobs, Donald J., Farmer, Jenny
Date Created: 2018
Subjects--Topical: Statistics, Probabilities
Description: In high throughput applications, such as those found in bioinformatics and finance, it is important to determine accurate probability distribution functions despite only minimal information about data characteristics, and without using human subje...

Title: Statistical measures to quantify similarity between molecular dynamics simulation trajectories
Author: Jacobs, Donald J., Farmer, Jenny, Kanwal, Fareeha, Nikulsin, Nikita
Date Created: 2017
Subjects--Topical: Molecular dynamics, Statistics
Description: Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD) trajectories, functional differences are often inferred from differences in ...

Title: JED: a Java essential dynamics program for comparative analysis of protein trajectories
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
Date Created: 2017
Subjects--Topical: Biology, Proteins
Description: Background: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to dete...

Title: Rigidity emerges during antibody evolution in three distinct antibody systems: evidence from QSFR analysis of fab fragments
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Immunoglobulins, Biology
Description: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assess...

Title: A virtual pebble game to ensemble average graph rigidity
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2015
Subjects--Topical: Probabilities, Proteins
Description: Background: The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies...

Title: Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle
Author: Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
Date Created: 2014
Subjects--Topical: Immunoglobulins, Biology
Description: Le Chatelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Chatelier's principle states t...

Title: Variations within class-a beta-lactamase physiochemical properties reflect evolutionary and environmental patterns, but not antibiotic specificity
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2013
Subjects--Topical: Biology, Bacteria
Description: The bacterial enzyme beta-lactamase hydrolyzes the beta-lactam ring of penicillin and chemically related antibiotics, rendering them ineffective. Due to rampant antibiotic overuse, the enzyme is evolving new resistance activities at an alarming ra...

Title: Calculating ensemble averaged descriptions of protein rigidity without sampling
Author: Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Biology, Proteins
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Bioinformatics, Statistics
Description: We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility ...

Title: Best probability density function for random sampled data
Author: Jacobs, Donald J.
Date Created: 2009
Subjects--Topical: Statistics, Probabilities
Description: The maximum entropy method is a theoretically sound approach to construct an analytical form for the probability density function (pdf) given a sample of random events. In practice, numerical methods employed to determine the appropriate Lagrange ...

Title: Conformational entropy of an ideal cross-linking polymer chain
Author: Jacobs, Donald J., Vorov, Oleg, Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Proteins, Entropy
Description: We present a novel analytical method to calculate conformational entropy of ideal cross-linking polymers from the configuration integral by employing a Mayer series expansion. Mayer-functions describing chemical bonds within the chain and for cros...

Title: Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
Author: Jacobs, Donald J., Livesay, Dennis R.
Date Created: 2008
Subjects--Topical: Bacteria, Proteins
Description: Background: Gram-negative bacteria use periplasmic-binding proteins (bPBP) to transport nutrients through the periplasm. Despite immense diversity within the recognized substrates, all members of the family share a common fold that includes two do...

Title: Decomposing dynamical couplings in mutated scFv antibody fragments into stabilizing and destabilizing effects
Author: Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, Uddin, Shahid, Casas-Finet, Jose
Subjects--Topical: Amino acid sequence, Immunoglobulins
Description: Conformational fluctuations within scFv antibodies are characterized by a novel perturbation-response decomposition of molecular dynamics trajectories. Both perturbation and response profiles are stratified into stabilizing and destabilizing condi...