AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

Inhibition of protein-protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection method...

Topographical mapping of calmodulin-target enzyme interaction domains.

Calmodulin derivatives, specifically biotinylated in domains I and III, were synthesized to address the structures of calmodulin necessary for binding to its target enzymes in active conformations. By binding avidin to these biotinylated calmodulins, the role of specific sequences of the calmodulin molecule in target enzyme interactions could then be evaluated. The role of domain I in these int...

Task-Centric User Interfaces

Simultaneous Nanoscale Surface Charge and Topographical Mapping.

Nanopipettes are playing an increasingly prominent role in nanoscience, for sizing, sequencing, delivery, detection, and mapping interfacial properties. Herein, the question of how to best resolve topography and surface charge effects when using a nanopipette as a probe for mapping in scanning ion conductance microscopy (SICM) is addressed. It is shown that, when a bias modulated (BM) SICM sche...

Expert-Guided Generative Topographical Modeling with Visual to Parametric Interaction

Introduced by Bishop et al. in 1996, Generative Topographic Mapping (GTM) is a powerful nonlinear latent variable modeling approach for visualizing high-dimensional data. It has shown useful when typical linear methods fail. However, GTM still suffers from drawbacks. Its complex parameterization of data make GTM hard to fit and sensitive to slight changes in the model. For this reason, we exten...