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Tag Archives: transition-paths
PSA: A Method for Quantifying Macromolecular Pathways

PSA: A Method for Quantifying Macromolecular Pathways

Transition pathways in high dimensional spaces, such as the ones produced by advanced algorithms to sample large conformational changes in macromolecules, are difficult to analyze quantitatively. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA is implemented in the MDAnalysis library.

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DBIO-APS Student Travel Award for Sean Seyler

DBIO-APS Student Travel Award for Sean Seyler

Sean Seyler was awarded a Shirley Chan Student Travel Award from the Division of Biological Physics (DBIO) of the American Physical Society to present his research on Quantifying macromolecular conformational transition pathways at the 2015 March Meeting in San Antonio, TX.

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Sean Seyler

Sean Seyler

Sean is a Ph.D. candidate in physics working on computational methods for sampling and quantifying macromolecular conformational transitions. He began work in the lab in August 2012.

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Simulations of membrane proteins

Simulations of membrane proteins

Many proteins in the living cell can be understood as molecular machines that use a source of energy to produce mechanical or chemical work. My lab’s primary interest is in those proteins located in the cell membrane that move nutrients, signalling molecules, or waste products into and out of the cell. We study their molecular mechanisms of action by detailed molecular dynamics simulations, which provide a “movie” of full atomic detail of a working protein.