Search results
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Title
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Calculating ensemble averaged descriptions of protein rigidity without sampling
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Author
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Jacobs, Donald J., Gonzalez, Luis C., Wang, Hui, Livesay, Dennis R.
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Date Created
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2012
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Subjects--Topical
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Biology, Proteins
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Description
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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...
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Title
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JED: a Java essential dynamics program for comparative analysis of protein trajectories
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Author
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Jacobs, Donald J., Ramaprasad, Azhagiya Singam Ettayapuram, David, Charles C.
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Date Created
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2017
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Subjects--Topical
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Biology, Proteins
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Description
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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...
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Title
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JEDi: Java essential dynamics inspector - a molecular trajectory analysis toolkit
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Author
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Jacobs, Donald J., Avery, Chris
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Date Created
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2021
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Subjects--Topical
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Biology, Proteins
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Description
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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...
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Title
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Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Chatelier's principle
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Author
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Jacobs, Donald J., Li, Tong, Livesay, Dennis R.
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Date Created
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2014
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Subjects--Topical
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Immunoglobulins, Biology
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Description
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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...
