GeomBD

Rigid Body Brownian Dynamics

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]


eBGDD: Energy Barrier Guided Drug Design (under development)

by Hari Datt Pandey

eBGDD is a computational approach for investigating drug unbinding kinetics using molecular dynamics simulations and milestoning theory. The underlying strategy is described in Tang, Z.; Chen, S.-H.; Chang, C. A. J. Chem. Theory Comput. 2020, 16, 1882–1895 (bioRxiv 169607). Simulation input files from that paper are available here.

We are in the process of automating key parts of the eBGDD workflow (including dimensionality reduction, pathway identification, and milestoning calculations) in a Python package and accompanying series of Jupyter notebooks, which will be made freely available on GitHub. Check back here for updates!


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]

MD_traj for Ab42 coil conformation

by Kingsley Wu


PLpro 1us MD trajectories

(100K frames, no water)

by Yuliana Bosken and Timothy Cholko

SARS-CoV-2 6W9C APO

SARS-CoV-2 6WRH APO

SARS-CoV-2 6W9C-3k A pose

SARS-CoV 4OW0 APO

SARS-CoV 4OW0-3k

MD Input Files

Water trajectories are also available upon request.