GeomBD

by Christopher C. Roberts

GeomBD2 is a rigid body Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine non-specific ligand-receptor association residence times, and to visualize common sites of non-specific association of substrates on receptor surfaces.

[1] Roberts, C. C. and Chang, C-E. A.*, Modeling of Enhanced Catalysis in Multi-enzyme Nanostructures: Effect of Molecular Scaffolds, Spatial Organization, and Concentration. J. of Chemical Theory and Computation, 2015 [link]

[2] Roberts, C. C. and Chang, C-E. A.*, Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multi-enzyme Nanostructures with All-Atom Brownian Dynamics Simulations. J. of Physical Chemistry B. 2016 [link]


T-Analyst

by Rizi Ai

T-Analyst is a user-friendly computer program for analyzing protein dynamics and conformational changes from MD simulations in internal bond-angle-torsion coordinates. The program is provided with tutorial and full source code in Perl.

[1] Ai, R., Fatmi, Q. and Chang, C-E. A., T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles. J. of Computer-Aided Molecular Design. 2010 [link]