Effective techniques for protein structure mining.

Retrieval and characterization of protein structure relationships are instrumental in a wide range of tasks in structural biology. The classification of protein structures (COPS) is a web service that provides efficient access to structure and sequence similarities for all currently available protein structures. Here, we focus on the application of COPS to the problem of template selection in homology modeling.

[1]  David S Wishart,et al.  RefDB: A database of uniformly referenced protein chemical shifts , 2003, Journal of biomolecular NMR.

[2]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[3]  Manfred J. Sippl,et al.  QSCOP - SCOP quantified by structural relationships , 2007, Bioinform..

[4]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[5]  Johannes Fischer,et al.  SimShift: Identifying structural similarities from NMR chemical shifts , 2006, Bioinform..

[6]  Alan R Davidson,et al.  A folding space odyssey , 2008, Proceedings of the National Academy of Sciences.

[7]  Eric Oldfield,et al.  Chemical shifts and three-dimensional protein structures , 1995, Journal of biomolecular NMR.

[8]  M. Jaskólski,et al.  Protein crystallography for non‐crystallographers, or how to get the best (but not more) from published macromolecular structures , 2008, The FEBS journal.

[9]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[10]  Cyrus Chothia,et al.  Genomic and structural aspects of protein evolution. , 2009, The Biochemical journal.

[11]  David S. Wishart,et al.  PREDITOR: a web server for predicting protein torsion angle restraints , 2006, Nucleic Acids Res..

[12]  Manfred J. Sippl,et al.  Detection of unrealistic molecular environments in protein structures based on expected electron densities , 2010, Journal of biomolecular NMR.

[13]  E. Koonin.  Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .

[14]  A. Murzin,et al.  Evolution of protein fold in the presence of functional constraints. , 2006, Current opinion in structural biology.

[15]  Joonhee Kim,et al.  Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases , 2010, Nature Structural &Molecular Biology.

[16]  John Orban,et al.  NMR structures of two designed proteins with high sequence identity but different fold and function , 2008, Proceedings of the National Academy of Sciences.

[17]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[18]  Markus Gruber,et al.  COPS—a novel workbench for explorations in fold space , 2009, Nucleic Acids Res..

[19]  SödingJohannes.  Protein homology detection by HMM--HMM comparison , 2005 .

[20]  Matthew H J Cordes,et al.  Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds , 2008, Proceedings of the National Academy of Sciences.

[21]  John Orban,et al.  Proteins that switch folds. , 2010, Current opinion in structural biology.

[22]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[23]  Francisco Melo,et al.  The Protein-DNA Interface database , 2010, BMC Bioinformatics.

[24]  C. Sander,et al.  Errors in protein structures , 1996, Nature.

[25]  Huilin Li,et al.  Structure of the CED-4–CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans , 2005, Nature.

[26]  Suganthi Balasubramanian,et al.  Protein alchemy: Changing β-sheet into α-helix , 1997, Nature Structural Biology.

[27]  Brian F. Volkman,et al.  Interconversion between two unrelated protein folds in the lymphotactin native state , 2008, Proceedings of the National Academy of Sciences.

[28]  C. Pál,et al.  An integrated view of protein evolution , 2006, Nature Reviews Genetics.

[29]  Catherine L. Worth,et al.  Structural and functional constraints in the evolution of protein families , 2009, Nature Reviews Molecular Cell Biology.

[30]  H. Dyson,et al.  Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.

[31]  S. Yokoyama,et al.  Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 Å resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD , 2006, Protein science : a publication of the Protein Society.

[32]  T. Schwede,et al.  Protein structure homology modeling using SWISS-MODEL workspace , 2008, Nature Protocols.

[33]  Manfred J Sippl,et al.  Fold space unlimited. , 2009, Current opinion in structural biology.

[34]  Markus Gruber,et al.  QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure , 2007, Nucleic Acids Res..

[35]  R. Kolodny,et al.  Sequence-similar, structure-dissimilar protein pairs in the PDB , 2007, Proteins.

[36]  Oleg Jardetzky,et al.  Probability‐based protein secondary structure identification using combined NMR chemical‐shift data , 2002, Protein science : a publication of the Protein Society.

[37]  M. Sippl.  Recognition of errors in three‐dimensional structures of proteins , 1993, Proteins.

[38]  Manfred J. Sippl,et al.  A note on difficult structure alignment problems , 2008, Bioinform..

[39]  Karl Frank,et al.  COPS Benchmark: interactive analysis of database search methods , 2010, Bioinform..

[40]  Simon W. Ginzinger,et al.  SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database , 2009, Journal of biomolecular NMR.

[41]  F. Richards,et al.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. , 1992, Biochemistry.

[42]  Jason J. Lavinder,et al.  Direct single-molecule observation of a protein living in two opposed native structures , 2009, Proceedings of the National Academy of Sciences.

[43]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[45]  Alexey G. Murzin,et al.  Metamorphic Proteins , 2008, Science.

[46]  Manfred J. Sippl,et al.  Thirty years of environmental health research--and growing. , 1996, Nucleic Acids Res..

[47]  K. Ginalski.  Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.

[48]  Charles D Schwieters,et al.  The Xplor-NIH NMR molecular structure determination package. , 2003, Journal of magnetic resonance.

[49]  S. Balasubramanian,et al.  Protein alchemy: changing beta-sheet into alpha-helix. , 1997, Nature structural biology.

[50]  Burkhard Rost,et al.  Evaluation of template‐based models in CASP8 with standard measures , 2009, Proteins.

[51]  Yigong Shi,et al.  Structure of the apoptotic protease-activating factor 1 bound to ADP , 2005, Nature.

[52]  Manfred J. Sippl,et al.  Visualization of unfavorable interactions in protein folds , 2008, Bioinform..

[53]  Markus Gruber,et al.  A discrete view on fold space , 2008, Bioinform..