Hernán F. Stamati

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The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear(More)
The purpose of this work is to derive a mathematical framework for manipulating protein structures in a particular coordinate set that includes the angles between the protein’s bonds. The ability to predict the spatial location of every atom in the protein upon changes on its bond angles is a crucial part of any algorithmic procedure that selectively(More)
The automatic classification of the wealth of molecular configurations gathered in simulation in the form of a few coordinates that help to explain the main states and transitions of the system is a recurring problem in computational molecular biophysics. We use the recently proposed ScIMAP algorithm to automatically extract motion parameters from(More)
The analysis of molecular motion starting from extensive sampling of molecular configurations remains an important and challenging task in computational biology. Existing methods require a significant amount of time to extract the most relevant motion information from such data sets. In this work, we provide a practical tool for molecular motion analysis.(More)
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