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. 2007 May 22;8(Suppl 4):S10. doi: 10.1186/1471-2105-8-S4-S10

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Copyright © 2007 Yoon et al; licensee BioMed Central Ltd.

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Structural examples of environments from validation clusters. Examples of pairs of environments from three of the validation clusters discussed in the text are shown. The structures were oriented by superimposing the PROSITE patterns, and the arrows indicate the atoms around which the microenvironments were centered. All residues containing atoms within the 7.5-Angstrom environment are depicted. The three comparisons show varying degrees of similarities among environments in the same cluster, ranging from nearly identical (a) to somewhat diverse (c). (a) The environments in the cluster containing residues from the PROTEIN_KINASE_TYR PROSITE motif are quite similar (top: PDB identifier 1fvr; bottom: 1luf). (b, c) The UBIQUITIN_CONJUGAT_1 (top: 1ayz; bottom: 1wzv) and STAPH_STREP_TOXIN_2 (top: 1aw7; bottom: 1ck1) clusters show greater degrees of structural variability. These images were produced using PyMol [28].