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Figure 4
Use of PRODRG-generated topologies. (a) GlcNAc5 in ChiB (van Aalten et al., 2001BB3). Left, stereo diagram of the ligand molecule before (cyan) and after (green) refinement with a PRODRG-generated topology. The surrounding protein is shown as a semitransparent cartoon. Right, text drawing used to generate the topology. (b) As (a) for Triton X-100 in SCP-2L (Haapalainen et al., 2001BB22). (c) Ligand from a high-resolution structure (cyan molecule) of human neutrophil collagenase (Gavuzzo et al., 2000BB20) re-refined at lower resolution with topologies generated either with PRODRG (green molecule) or with LIBCHECK (orange molecule). Again, the protein is shown as a semitransparent cartoon. To the right, the chemical structure of the ligand [2-(biphenyl-4-sulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid] is given. (d) As (c) for (3-amino-2,5-dioxo-1-pyrrolidinyl)-acetic acid in Cryphonectria parasitica endothiapepsin (Erskine et al., 2003BB15). (e, f) Effect of poor input geometries on the quality of generated topologies as indicated by the r.m.s.d. between small-molecule coordinates from the `ideal' starting structure and the same structure after refinement at lower resolution. The refinement of HGPRT as described in Table 3[link] is repeated with topologies generated from coordinates perturbed by a given random shift (filled squares). In addition, the corresponding refinement results using topologies produced in a coordinate-independent manner are given (empty diamonds). For PRODRG this means topologies were generated from TXT-mode drawings; for XPLO2D the topologies available from HIC-Up were used and for LIBCHECK the ligands were drawn in SKETCHER. Weights are kept at the values given in Table 3[link]. (e) shows the results for refinement with CNS and (f) for REFMAC5.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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