Sometimes you just want to quickly move a copy of a script, image or binary from, for example, your local (linux) machine to another (linux) machine. The usual tool would be SCP, but this can get complicated when there are several layers of ssh and sometimes it doesn’t work at all (as is the case for transfers between the Department of Statistics computers and the outside world).
Continue readingMonthly Archives: July 2020
ProCare: cavity similarity searching and its applications to fragment-based drug design
ProCare [1] is a package developed at the University of Strasbourg which is able to align and score the similarity of protein cavities. The aim is to find ligand binding sites between different proteins that are similar enough to bind the same ligand. The method used in ProCare is designed to look particularly at fragment (~⅓ size of a druglike ligand) binding sites. The aim is to predict potential fragment hits by comparing the cavities of the targets.
Continue readingJournal Club: the Dynamics of Affinity Maturation
Last week at our group meeting I presented on a paper titled “T-cell Receptor Variable beta Domains Rigidify During Affinity Maturation” by Monica L. Fernández-Quintero, Clarissa A. Seidler and Klaus R. Liedl. The authors use metadynamics simulations of the same T-cell Receptor (TCR) at different stages of affinity maturation to study the conformational landscape of the complementarity-determining regions (CDRs), and how this might relate to an increase in affinity. Not only do they conclude that affinity maturation leads to rigidification of CDRs in solution, but they also present some evidence for the conformational selection model of biomolecular binding events in TCR-antigen interactions.
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