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Methods For Automated Structure Determination for Ligands Within a Protein-Ligand Complex


We present Afitt (OpenEye Scientific Software, Inc), a software package for automated ligand conformation generation and placement within algorithmically identified unfilled electron density. Following real space refinement, the ligand solution is sent for subsequent refinement by Refmac or CNX, via coordinate and dictionary files. We have validated Afitt on forty publicly available data sets, chosen because it contains examples of highly strained ligand conformations (J. Med. Chem. 2004, 47, 2499-2510). We show that Afitt can automatically generate low-strain ligand conformation and placement solutions for every example. Furthermore, in each case refinement of the new solution gives a fit equivalent to the original model.