DOT2: Macromolecular docking with improved biophysical models

Victoria A. Roberts, Elaine E. Thompson, Michael E. Pique, Martin S. Perez, L. F. Ten Eyck
2013 Journal of Computational Chemistry  
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size
more » ... nd spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
doi:10.1002/jcc.23304 pmid:23695987 pmcid:PMC4370774 fatcat:umuos6b5xbb4xacmtjnc7yajg4