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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 sizedoi:10.1002/jcc.23304 pmid:23695987 pmcid:PMC4370774 fatcat:umuos6b5xbb4xacmtjnc7yajg4