Stefan Doerr

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PURPOSE To evaluate the effectiveness of fractionated stereotactic radiotherapy (SFRT) in the treatment of optic nerve sheath meningioma (ONSM). METHODS AND MATERIALS Between 1993 and 2005, 109 patients (113 eyes) with primary (n = 37) or secondary (n = 76) ONSM were treated according to a prospective protocol with SFRT to a median dose of 54 Gy. All(More)
High-throughput molecular dynamics (MD) simulations are a computational method consisting of using multiple short trajectories, instead of few long ones, to cover slow biological time scales. Compared to long trajectories this method offers the possibility to start the simulations in successive batches, building a knowledgeable model of the available data(More)
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve(More)
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein(More)
Motivation An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Results Here we(More)
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known force fields, and applying standardized protocols for running the(More)
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