Rapid prediction of crucial hotspot interactions for icosahedral viral capsid self-assembly by energy landscape atlasing validated by mutagenesis

1 code implementation • 2 Jan 2020 • Ruijin Wu, Rahul Prabhu, Aysegul Ozkan, Meera Sitharam

We combine ab-initio predictions at two scales: at the interface-scale, we predict the importance (cruciality) of an interaction for successful subassembly across each interface between VP monomers; and at the capsid-scale, we predict the cruciality of an interface for successful capsid assembly.

Efficient Atlasing and Search of Configuration Spaces of Point-Sets Constrained by Distance Intervals

1 code implementation • 18 May 2018 • Aysegul Ozkan, Rahul Prabhu, Troy Baker, James Pence, Jorg Peters, Meera Sitharam

For configurations of point-sets that are pairwise constrained by distance intervals, the EASAL software implements a suite of algorithms that characterize the structure and geometric properties of the configuration space.

Computational Geometry

Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity

1 code implementation • 16 Mar 2012 • Rahul Prabhu, Meera Sitharam, Aysegul Ozkan, Ruijin Wu

We describe a novel geometric methodology for analyzing free-energy and kinetics of assembly driven by short-range pair-potentials in an implicit solvent, and provides illustrations of its unique capabilities.

Computational Geometry