Thijs Beuming

TL;DR: The optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.

TL;DR: An approach to designing tight-binding ligands with a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches is reported, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.

TL;DR: The models suggest that the binding site for cocaine and cocaine analogs is deeply buried between transmembrane segments 1, 3, 6 and 8, and overlaps with the binding sites for the substrates dopamine and amphetamine, as well as for benztropine-like DAT inhibitors.

TL;DR: A comprehensive sequence alignment of all known prokaryotic and eukaryotic NSS proteins, based on the crystal structure of the leucine transporter from Aquifex aeolicus (LeuT), finds important similarities and differences among the sequences of N SS proteins in regions likely to determine selectivity in substrate binding and mechanisms of transport regulation.

TL;DR: PDZBase is a database that aims to contain all known PDZ-domain-mediated protein-protein interactions and can be queried through both sequence motif and keyword-based searches.