with Tomer Sidi, Shiri Bahiri-Elitzur, and Tamir Tuller
Accepted to PNAS (2024) pdf, Supplementary_info, code, web-server

CyToStruct - External Application Hooking for Cytoscape

with Sergey Nepomnyachiy and Nir Ben-Tal install, Bitbucket (including source code and demos) and slides from a workshop Sergey did

CyToStruct is a Cytoscape app that allows the user to configure scripts for running external programs. These scripts are templates, and CyToStruct will inject node/edge dependent data into these and then pass the script on to external programs. The application we had in mind was running molecular viewers that show the details of nodes and edges. Because CyToStruct is so general, we can support any molecular viewer (our demos include four).

VISTAL - A two-dimensional visualization tool for structural alignments

with Barry Honig download linux executable, example

VISTAL describes structures as a series of secondary structure elements, and places matched residues one on top of each other colored according to the three-dimensional distance of their Ca atoms.