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Molecular docking is a popular way to screen for novel drug compounds. The method involves aligning small molecules to a protein structure and estimating their binding affinity. To do this rapidly for tens of thousands of molecules requires an effective representation of the binding region of the target protein. This paper presents an algorithm for(More)
BACKGROUND Molecular docking seeks to predict the geometry and affinity of the binding of a small molecule to a given protein of known structure. Rigid docking has long been used to screen databases of small molecules, because docking techniques that account for ligand flexibility have either been too slow or have required significant human intervention.(More)
IcePick is a system for computationally selecting diverse sets of molecules. It computes the dissimilarity of the surface-accessible features of two molecules, taking into account conformational flexibility. Then, the intrinsic diversity of an entire set of molecules is calculated from a spanning tree over the pairwise dissimilarities. IcePick's(More)
Date Dedication For Mom and Dad. iii Acknowledgments I would like to extend the greatest thanks to Dr. Andreas Savakis, for the immense amount of encouragement and advice he has provided in the course of this research. The members of my committee, Dr. Cockburn and Dr. Luo, have also given valuable assistance in the form of feedback and revisions. I would(More)
This design-research thesis proposes the redesign of Tide Lock Park in Alexandria, Virginia as an exploration of light. By researching the cultural history of artificial lighting as well as the sculptural use of light as art, this thesis seeks to distinguish lighting design that goes beyond functional and safety concerns to include design that honors the(More)
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