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DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. ... The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. ... Acknowledgments We thank Susan Lindsey for creation of the DOT2 web site and assistance with software development and infrastructure. ...doi:10.1002/jcc.23304 pmid:23695987 pmcid:PMC4370774 fatcat:umuos6b5xbb4xacmtjnc7yajg4