Viewing profile — momeara

Campus IT department has declared a major incident with campus internet connectivity unavailable. This is causing problems for the first day of classes, see for example https://www…

Hey Chris--We're right now using a mix of commercial and open source software like Omega, Corina, AMSOL, and Mol2DB. Probably the slowest step is generating the partial charges for…

Co-author here (AMA)--A large-scale docking screen of 116M molecules takes ~1100 cpu days on our cluster, working out to about 1 mol/sec, which is very fast for virtual screening. …

Here is patent [1]. The key idea is to add a glucosyltransferase from Lactobacillus, which consumes simple sugars and produces complex sugars. It is not clear to me that this will …

Hi Chris, You bring up very good issues and perhaps I'm being too optimistic. I definitely agree that there isn't going to be one single mapping of sequence --> energy landscape an…

autoencoders are unsupervised learning where CNNs are supervised. Learning the input space can be thought of as a form of regularization when training data is scarce. http://www.de…

Molecular dynamics simulations can be used to answer a range of structural biology questions, but abstractly many of them can be phrased as evaluating the difference in free energy…

Several people have asked for background material for the workshop-- (Wallach, 2015, http://arxiv.org/pdf/1510.02855.pdf ) AtomNet: A Deep Convolutional Neural Network for Bioactiv…