Search results | J. Murrey Atkins Library

Title: A new obligate CXCL4-CXCL12 heterodimer for studying chemokine heterodimer activities and mechanisms
Author: Nesmelova, Irina, Ngyuen, Khanh T.P., Dreau, Didier, Volkman, Brian
Date Created: 2022
Subjects--Topical: Chemokines, Proteins
Description: Chemokines form a family of proteins with critical roles in many biological processes in health and disease conditions, including cardiovascular, autoimmune diseases, infections, and cancer. Many chemokines engage in heterophilic interactions to f...

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: 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: Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications
Author: Truman, Andrew, Zheng, Bo, Omkar, Siddhi, Takakuwa, Jade E.
Date Created: 2022
Subjects--Topical: Proteins, Molecular biology
Description: Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and the inability of current technologies to distinguish direct ver...

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: Fluocinolone acetonide enhances anterograde mitochondria trafficking and promotes neuroprotection against the paclitaxel induced peripheral neuropathy
Author: Tiwari, Arjun Prasad, Albin, Bayne, Yang, In Hong, Tristan, Lee Ji
Date Created: 2023
Subjects--Topical: Proteins, Biomolecules
Description: Paclitaxel (PTX)-induced peripheral neuropathy (PIPN) is a debilitating health condition which is a result of degeneration of peripheral nerves found in extremities. Currently, there are no established treatment methods that can prevent or protect...

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: 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: 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...