A K Dunker

Summary

Affiliation: Washington State University
Country: USA

Publications

  1. ncbi Intrinsic disorder and protein function
    A Keith Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Biochemistry 41:6573-82. 2002
  2. ncbi Intrinsic protein disorder in complete genomes
    A K Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164 4660, USA
    Genome Inform Ser Workshop Genome Inform 11:161-71. 2000
  3. ncbi Comparing predictors of disordered protein
    X Li
    School of Electrical Engineering and Computer Sciences, Washington State University, Pullman, WA 99164 2752, USA
    Genome Inform Ser Workshop Genome Inform 11:172-84. 2000
  4. ncbi Sequence complexity of disordered protein
    P Romero
    School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington 99164 4660, USA
    Proteins 42:38-48. 2001
  5. ncbi Intrinsically disordered protein
    A K Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164 4660, USA
    J Mol Graph Model 19:26-59. 2001
  6. ncbi Evolutionary rate heterogeneity in proteins with long disordered regions
    Celeste J Brown
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    J Mol Evol 55:104-10. 2002
  7. ncbi Clusterin, a binding protein with a molten globule-like region
    R W Bailey
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 4660, USA
    Biochemistry 40:11828-40. 2001
  8. ncbi The importance of intrinsic disorder for protein phosphorylation
    Lilia M Iakoucheva
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Nucleic Acids Res 32:1037-49. 2004
  9. ncbi Identification and functions of usefully disordered proteins
    A Keith Dunker
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
    Adv Protein Chem 62:25-49. 2002
  10. ncbi Intrinsic disorder in cell-signaling and cancer-associated proteins
    Lilia M Iakoucheva
    Department of Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
    J Mol Biol 323:573-84. 2002

Collaborators

Detail Information

Publications61

  1. ncbi Intrinsic disorder and protein function
    A Keith Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Biochemistry 41:6573-82. 2002
  2. ncbi Intrinsic protein disorder in complete genomes
    A K Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164 4660, USA
    Genome Inform Ser Workshop Genome Inform 11:161-71. 2000
    ..Overall, intrinsic disorder appears to be a common, with eucaryotes perhaps having a higher percentage of native disorder than archaea or bacteria...
  3. ncbi Comparing predictors of disordered protein
    X Li
    School of Electrical Engineering and Computer Sciences, Washington State University, Pullman, WA 99164 2752, USA
    Genome Inform Ser Workshop Genome Inform 11:172-84. 2000
    ..Five predictors were developed, compared with each other, and with previous work. The best of these shows substantially improved generalization compared to our previously published predictor...
  4. ncbi Sequence complexity of disordered protein
    P Romero
    School of Electrical Engineering and Computer Science, Washington State University, Pullman, Washington 99164 4660, USA
    Proteins 42:38-48. 2001
    ....
  5. ncbi Intrinsically disordered protein
    A K Dunker
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164 4660, USA
    J Mol Graph Model 19:26-59. 2001
    ....
  6. ncbi Evolutionary rate heterogeneity in proteins with long disordered regions
    Celeste J Brown
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    J Mol Evol 55:104-10. 2002
    ..More work is needed to understand the underlying causes of the variability in the evolutionary rates of intrinsically ordered and disordered protein...
  7. ncbi Clusterin, a binding protein with a molten globule-like region
    R W Bailey
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 4660, USA
    Biochemistry 40:11828-40. 2001
    ..We propose that natively disordered regions with amphipathic helices form a dynamic, molten globule-like binding site and provide clusterin the ability to bind to a variety of molecules...
  8. ncbi The importance of intrinsic disorder for protein phosphorylation
    Lilia M Iakoucheva
    School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
    Nucleic Acids Res 32:1037-49. 2004
    ....
  9. ncbi Identification and functions of usefully disordered proteins
    A Keith Dunker
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
    Adv Protein Chem 62:25-49. 2002
  10. ncbi Intrinsic disorder in cell-signaling and cancer-associated proteins
    Lilia M Iakoucheva
    Department of Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
    J Mol Biol 323:573-84. 2002
    ..Our data suggest that intrinsically unstructured proteins play key roles in cell-signaling, regulation and cancer, where coupled folding and binding is a common mechanism...
  11. ncbi Beta-lactoglobulin molten globule induced by high pressure
    J Yang
    Department of Food Science and Human Nutrition, Washington State University, Pullman, Washington 99164-6376, USA
    J Agric Food Chem 49:3236-43. 2001
    ..Overall, these results suggest that HHP treatments induce beta-LG into hydrophobic molten globule structures that remain stable for at least 3 months...
  12. ncbi Crystallization and structure-function of calsequestrin
    Chulhee Kang
    Department of Biochemistry and Biophysics, Washington State University, Pullman, Washington, USA
    Methods Mol Biol 172:281-94. 2002
  13. ncbi Polymerization of calsequestrin. Implications for Ca2+ regulation
    HaJeung Park
    School of Molecular Biosciences, Department of Chemistry, Washington State University, Pullman, WA 99164, USA
    J Biol Chem 278:16176-82. 2003
    ....
  14. ncbi Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions
    Hongbo Xie
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    J Proteome Res 6:1882-98. 2007
    ..The first paper of the series describes our statistical approach, outlines the major findings, and provides illustrative examples of biological processes and functions positively and negatively correlated with intrinsic disorder...
  15. ncbi Intrinsic disorder in the Protein Data Bank
    Tanguy Le Gall
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Biomol Struct Dyn 24:325-42. 2007
    ....
  16. ncbi Intrinsic disorder and functional proteomics
    Predrag Radivojac
    School of Informatics, Indiana University, Bloomington, Indiana, USA
    Biophys J 92:1439-56. 2007
    ..The future of the prediction of protein disorder and the future uses of such predictions in functional proteomics comprise the last section of this article...
  17. ncbi DisProt: the Database of Disordered Proteins
    Megan Sickmeier
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Nucleic Acids Res 35:D786-93. 2007
    ..In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at http://www.disprot.org...
  18. ncbi Abundance of intrinsic disorder in protein associated with cardiovascular disease
    Yugong Cheng
    Molecular Kinetics, Inc, Indianapolis, Indiana 46268, USA
    Biochemistry 45:10448-60. 2006
    ..Thus, our data suggest that intrinsically disordered proteins might play key roles in cardiovascular disease...
  19. ncbi Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorder
    Jessica Walton Chen
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:888-98. 2006
    ..Although many think of such conserved domains as being ordered, in fact a significant number of them contain regions of disorder that are likely to be crucial to their functions...
  20. ncbi Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions
    Slobodan Vucetic
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    J Proteome Res 6:1899-916. 2007
    ....
  21. ncbi Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins
    Hongbo Xie
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    J Proteome Res 6:1917-32. 2007
    ....
  22. ncbi Characterization of molecular recognition features, MoRFs, and their binding partners
    Vladimir Vacic
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Proteome Res 6:2351-66. 2007
    ..Implications of these findings for the development of MoRF-partner interaction predictors are discussed. In addition, structural changes upon MoRF-to-partner complex formation were examined for several illustrative examples...
  23. ncbi Mining alpha-helix-forming molecular recognition features with cross species sequence alignments
    Yugong Cheng
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Biochemistry 46:13468-77. 2007
    ..87 +/- 0.10, 0.87 +/- 0.11, and 0.87 +/- 0.08 over 10 cross validations, respectively. We present the results of these analyses and validation examples to discuss the potential improvement of the alpha-MoRF-PredII prediction accuracy...
  24. ncbi Prediction of intrinsic disorder and its use in functional proteomics
    Vladimir N Uversky
    School of Medicine, Indiana University, Indianapolis, USA
    Methods Mol Biol 408:69-92. 2007
    ..A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes...
  25. ncbi Protein intrinsic disorder toolbox for comparative analysis of viral proteins
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 9:S4. 2008
    ..This exercise provides an example showing how the combined use of intrinsic disorder predictions and relational databases provides an improved understanding of the functional and structural behaviour of viral proteins...
  26. ncbi The unfoldomics decade: an update on intrinsically disordered proteins
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
    BMC Genomics 9:S1. 2008
    ..The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins...
  27. ncbi Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions
    Siyuan Ren
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 9:S26. 2008
    ..Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs)...
  28. ncbi Analysis of molecular recognition features (MoRFs)
    Amrita Mohan
    School of Informatics, Indiana University, Bloomington, IN 47408, USA
    J Mol Biol 362:1043-59. 2006
    ..The results of this study will advance the understanding of protein-protein interactions and help towards the future development of useful protein-protein binding site predictors...
  29. ncbi Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling
    Vladimir N Uversky
    Molecular Kinetics, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
    J Mol Recognit 18:343-84. 2005
    ....
  30. ncbi Protein flexibility and intrinsic disorder
    Predrag Radivojac
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    Protein Sci 13:71-80. 2004
    ....
  31. ncbi Optimizing long intrinsic disorder predictors with protein evolutionary information
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    J Bioinform Comput Biol 3:35-60. 2005
    ..6 +/- 1.3%) and VL2 (80.9 +/- 1.4%). The new disorder predictors with the corresponding datasets are freely accessible through the web server at http://www.ist.temple.edu/disprot...
  32. ncbi Comparing and combining predictors of mostly disordered proteins
    Christopher J Oldfield
    Molecular Kinetics, Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
    Biochemistry 44:1989-2000. 2005
    ....
  33. ncbi Natively disordered proteins: functions and predictions
    Pedro Romero
    Center for Computational Biology and Bioinformatics, Indiana University Purdue University Indianapolis, 714 North Senate Avenue, Indianapolis, IN 46202, USA
    Appl Bioinformatics 3:105-13. 2004
    ..Application of disorder predictions to cell-signalling, cancer-associated and control protein databases supports the widespread occurrence of protein disorder in these processes...
  34. ncbi Order, disorder, and flexibility: prediction from protein sequence
    Lilia M Iakoucheva
    The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Structure 11:1316-7. 2003
    ....
  35. ncbi Flavors of protein disorder
    Slobodan Vucetic
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    Proteins 52:573-84. 2003
    ..Overall, the results herein support the flavor-function approach as a useful complement to structural genomics as a means for automatically assigning possible functions to sequences...
  36. ncbi Coupled folding and binding with alpha-helix-forming molecular recognition elements
    Christopher J Oldfield
    Molecular Kinetics Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
    Biochemistry 44:12454-70. 2005
    ..Application of this algorithm to databases of genomics and functionally annotated proteins indicates that alpha-MoREs are likely to play important roles protein-protein interactions involved in signaling events...
  37. ncbi Exploiting heterogeneous sequence properties improves prediction of protein disorder
    Zoran Obradovic
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    Proteins 61:176-82. 2005
    ..As the results of the CASP6 experiment showed, this new predictor has achieved the highest accuracy yet and significantly improved performance on short disordered regions, while maintaining high performance on long disordered regions...
  38. ncbi DisProt: a database of protein disorder
    Slobodan Vucetic
    Center for Information Science and Technology, Temple University Philadelphia, PA 19122, USA
    Bioinformatics 21:137-40. 2005
    ..AVAILABILITY: www.disprot.org..
  39. ncbi Another window into disordered protein function
    A Keith Dunker
    Structure 15:1026-8. 2007
    ..In this issue of Structure, Zhang et al. (2007) show that these "dual personality fragments" are distinct from both structured and disordered protein and are functionally important...
  40. ncbi Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks
    Wei Zhang
    Indiana University School of Informatics, Indiana University Purdue University, Indianapolis, Indiana 46202, USA
    Proteins 71:61-7. 2008
    ..These results support the usefulness of the sequence-alignment benchmarks as a means to evaluate secondary structure assignment. The SKSP server and the benchmarks can be accessed at http://sparks.informatics.iupui.edu..
  41. ncbi Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatment
    Marc S Cortese
    Department of Biochemistry and Molecular Biology and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    J Proteome Res 4:1610-8. 2005
    ..In this way, large numbers of totally unstructured proteins could be identified with minimal effort...
  42. ncbi Predicting intrinsic disorder from amino acid sequence
    Zoran Obradovic
    Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    Proteins 53:566-72. 2003
    ..This experiment supports the predictability of intrinsic disorder from amino acid sequence...
  43. ncbi Exploring alternative knowledge representations for protein secondary-structure prediction
    Uros Midic
    Center for Information Science and Technology, Temple University, 1805 N Broad St, 303 Wachman Hall, Philadelphia, PA 19129, USA
    Int J Data Min Bioinform 1:286-313. 2007
    ..We also investigated the possibility of exploiting the prediction of connected pairs of beta-sheet residues and the prediction of residue contact maps for the improvement of accuracy of secondary-structure prediction...
  44. ncbi Protein disorder is positively correlated with gene expression in Escherichia coli
    Oleg Paliy
    Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio 45435, USA
    J Proteome Res 7:2234-45. 2008
    ..coli cultures and was not caused by a small subset of genes showing exceptionally high concordance in their disorder and expression levels. Global analysis was complemented by detailed consideration of several groups of proteins...
  45. ncbi Potato virus A genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core
    Kimmo I Rantalainen
    Department of Applied Chemistry and Microbiology, PO Box 27, FIN 00014, University of Helsinki, Finland
    Virology 377:280-8. 2008
    ..Further experimentation is required to understand the functional regulation achieved via this property...
  46. ncbi Intrinsically disordered proteins in human diseases: introducing the D2 concept
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Annu Rev Biophys 37:215-46. 2008
    ..From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept...
  47. ncbi Improved amino acid flexibility parameters
    David K Smith
    Biochemistry Department, The University of Hong Kong, Pok Fu Lam, Hong Kong Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
    Protein Sci 12:1060-72. 2003
    ..These new parameters have a higher correlation with experimentally determined B-factors than parameters from earlier methods...
  48. ncbi Structural basis for regulation of protein phosphatase 1 by inhibitor-2
    Thomas D Hurley
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Biol Chem 282:28874-83. 2007
    ....
  49. ncbi Composition Profiler: a tool for discovery and visualization of amino acid composition differences
    Vladimir Vacic
    Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
    BMC Bioinformatics 8:211. 2007
    ..Composition Profiler is a web-based tool for semi-automatic discovery of enrichment or depletion of amino acids, either individually or grouped by their physico-chemical or structural properties...
  50. ncbi Flexible nets. The roles of intrinsic disorder in protein interaction networks
    A Keith Dunker
    Department of Biochemistry and Molecular Biology, and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    FEBS J 272:5129-48. 2005
    ..An important research direction will be to determine what fraction of protein-protein interaction in regulatory networks relies on intrinsic disorder...
  51. ncbi Length-dependent prediction of protein intrinsic disorder
    Kang Peng
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Bioinformatics 7:208. 2006
    ..However, these predictors are less successful on short disordered regions (< or =30 residues). A probable cause is a length-dependent amino acid compositions and sequence properties of disordered regions...
  52. ncbi Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms
    Pedro R Romero
    School of Informatics, Indiana University-Purdue University Indianapolis, 535 West Michigan Street, IT475, Indianapolis, IN 46202, USA
    Proc Natl Acad Sci U S A 103:8390-5. 2006
    ..Associating alternative splicing with protein disorder enables the time- and tissue-specific modulation of protein function needed for cell differentiation and the evolution of multicellular organisms...
  53. ncbi Intrinsic disorder in transcription factors
    Jiangang Liu
    School of Informatics, Indiana University-Purdue University Indianapolis, 535 West Michigan Street, Indianapolis, Indiana 46202, USA
    Biochemistry 45:6873-88. 2006
    ..Overall, our data reflected the fact that eukaryotes with well-developed gene transcription machinery require transcription factor flexibility to be more efficient...
  54. ncbi Rational drug design via intrinsically disordered protein
    Yugong Cheng
    Molecular Kinetics Inc, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
    Trends Biotechnol 24:435-42. 2006
    ..This novel strategy, based on intrinsically disordered protein, has the potential to increase significantly the discovery rate for new molecule entities...
  55. ncbi Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs
    Vladimir N Uversky
    Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:1829-42. 2006
    ..The results of this analysis are consistent with the conclusion that high-risk HPVs are characterized by the increased amount of intrinsic disorder in transforming proteins E6 and E7...
  56. ncbi Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions
    Jessica Walton Chen
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, 46202, USA
    J Proteome Res 5:879-87. 2006
    ..Most regions of conserved predicted disorder detected were short, with less than 10% of those found exceeding 30 residues in length...
  57. ncbi Disorder and sequence repeats in hub proteins and their implications for network evolution
    Zsuzsanna Dosztanyi
    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, Hungary
    J Proteome Res 5:2985-95. 2006
    ....
  58. ncbi Addressing the intrinsic disorder bottleneck in structural proteomics
    Christopher J Oldfield
    Center for Eukaryotic Structural Genomics, Biochemistry Department, University of Wisconsin, Madison, Wisconsin 53706, USA
    Proteins 59:444-53. 2005
    ..Our study indicates that the efficiency of structural proteomics of eukaryotes can be improved significantly by removing targets predicted to be disordered by an algorithm chosen to provide optimal performance...
  59. ncbi Classification and knowledge discovery in protein databases
    Predrag Radivojac
    Center for Information Science and Technology, Temple University, USA
    J Biomed Inform 37:224-39. 2004
    ..In our experiments, training classifiers specialized to the class distributions of each cluster resulted in a further decrease in classification error...
  60. ncbi Combining prediction, computation and experiment for the characterization of protein disorder
    Clay Bracken
    Department of Biochemistry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
    Curr Opin Struct Biol 14:570-6. 2004
    ..Combining prediction, computation and experimentation is proposed to accelerate and enhance the characterization of intrinsically disordered protein...
  61. ncbi Investigation of transmembrane proteins using a computational approach
    Jack Y Yang
    Department of Radiology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    BMC Genomics 9:S7. 2008
    ....