title: Objective identification of residue ranges for the superposition of protein structures.
abstract: BACKGROUND
  The automation of objectively selecting amino acid residue ranges for structure superpositions is important for meaningful and consistent protein structure analyses. So far there is no widely-used standard for choosing these residue ranges for experimentally determined protein structures, where the manual selection of residue ranges or the use of suboptimal criteria remain commonplace.
  
  
  RESULTS
  We present an automated and objective method for finding amino acid residue ranges for the superposition and analysis of protein structures, in particular for structure bundles resulting from NMR structure calculations. The method is implemented in an algorithm, CYRANGE, that yields, without protein-specific parameter adjustment, appropriate residue ranges in most commonly occurring situations, including low-precision structure bundles, multi-domain proteins, symmetric multimers, and protein complexes. Residue ranges are chosen to comprise as many residues of a protein domain that increasing their number would lead to a steep rise in the RMSD value. Residue ranges are determined by first clustering residues into domains based on the distance variance matrix, and then refining for each domain the initial choice of residues by excluding residues one by one until the relative decrease of the RMSD value becomes insignificant. A penalty for the opening of gaps favours contiguous residue ranges in order to obtain a result that is as simple as possible, but not simpler. Results are given for a set of 37 proteins and compared with those of commonly used protein structure validation packages. We also provide residue ranges for 6351 NMR structures in the Protein Data Bank.
  
  
  CONCLUSIONS
  The CYRANGE method is capable of automatically determining residue ranges for the superposition of protein structure bundles for a large variety of protein structures. The method correctly identifies ordered regions. Global structure superpositions based on the CYRANGE residue ranges allow a clear presentation of the structure, and unnecessary small gaps within the selected ranges are absent. In the majority of cases, the residue ranges from CYRANGE contain fewer gaps and cover considerably larger parts of the sequence than those from other methods without significantly increasing the RMSD values. CYRANGE thus provides an objective and automatic method for standardizing the choice of residue ranges for the superposition of protein structures.
authors: Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str, 9, 60438 Frankfurt am Main, Germany.
authors: Donata K
authors: DK
authors: Kirchner
authors: Peter
authors: P
authors: Güntert
references: Nature. 1996 May 23;381(6580):272
references: 8692262
references: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2269-75
references: 15572780
references: Nat Struct Biol. 1996 Aug;3(8):662-5
references: 8756320
references: Proc Natl Acad Sci U S A. 2010 May 25;107(21):9644-9
references: 20445084
references: J Biomol NMR. 2004 Jun;29(2):207-8
references: 15014235
references: J Biomol NMR. 2005 Apr;31(4):357-61
references: 15929003
references: Protein Sci. 2005 Jan;14(1):224-30
references: 15576557
references: J Biomol NMR. 1996 Dec;8(4):477-86
references: 9008363
references: Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14374-9
references: 11724947
references: Acta Crystallogr D Biol Crystallogr. 2000 Jun;56(Pt 6):714-21
references: 10818348
references: FEBS Lett. 2007 Feb 6;581(3):462-8
references: 17239860
references: Proteins. 2006 Aug 15;64(3):665-72
references: 16736493
references: Protein Eng. 1997 Jun;10(6):737-41
references: 9278289
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W375-83
references: 17452350
references: J Mol Biol. 1979 Feb 15;128(1):49-79
references: 430571
references: J Mol Biol. 1997 Oct 17;273(1):283-98
references: 9367762
references: Nat Struct Mol Biol. 2006 Mar;13(3):184-5; discussion 185
references: 16518382
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: Acta Crystallogr D Biol Crystallogr. 1995 Mar 1;51(Pt 2):127-35
references: 15299312
references: Nature. 2006 Mar 2;440(7080):52-7
references: 16511487
references: Nucleic Acids Res. 2003 Jul 1;31(13):3370-4
references: 12824330
references: J Am Chem Soc. 2006 Oct 11;128(40):13112-22
references: 17017791
references: J Mol Graph. 1996 Feb;14(1):51-5, 29-32
references: 8744573
references: BMC Bioinformatics. 2010 Jul 01;11:363
references: 20594332
references: Acta Crystallogr D Biol Crystallogr. 2002 Feb;58(Pt 2):195-208
references: 11807243
references: Protein Eng. 1996 Nov;9(11):1063-5
references: 8961360
references: Protein Sci. 1992 Jun;1(6):736-51
references: 1304915
references: J Biol Chem. 1999 Aug 6;274(32):22597-603
references: 10428839
references: Proteins. 2005 Jun 1;59(4):673-86
references: 15822099
references: Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):651-5
references: 15647366
references: J Biomol NMR. 2004 Dec;30(4):463-4
references: 15630569
references: J Biomol NMR. 2004 Jun;29(2):205-6
references: 15014234
references: Proteins. 2007 Mar 1;66(4):778-95
references: 17186527
references: J Mol Biol. 2002 May 24;319(1):209-27
references: 12051947