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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: 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...