A Dunker

Summary

Affiliation: Indiana University
Country: USA

Publications

  1. 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
  2. pmc 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
  3. pmc The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, University of South Florida Tampa, FL 33612, USA Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
    F1000 Biol Rep 5:1. 2013
  4. pmc Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing
    Poornima Bhat-Nakshatri
    Department of Surgery, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN 46202, USA
    BMC Med Genomics 6:21. 2013
  5. pmc Changes in predicted protein disorder tendency may contribute to disease risk
    Yang Hu
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
    BMC Genomics 12:S2. 2011
  6. pmc Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Virol J 6:69. 2009
  7. pmc A comparative analysis of viral matrix proteins using disorder predictors
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Virol J 5:126. 2008
  8. pmc Archaic chaos: intrinsically disordered proteins in Archaea
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Syst Biol 4:S1. 2010
  9. pmc Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
    Christopher J Oldfield
    Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W, 10th Street, Indianapolis, IN 46202, USA
    BMC Genomics 9:S1. 2008
  10. pmc Unfoldomics of human diseases: linking protein intrinsic disorder with diseases
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 10:S7. 2009

Collaborators

Detail Information

Publications84

  1. 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...
  2. pmc 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...
  3. pmc The case for intrinsically disordered proteins playing contributory roles in molecular recognition without a stable 3D structure
    Vladimir N Uversky
    Department of Molecular Medicine, USF Health Byrd Alzheimer s Research Institute, University of South Florida Tampa, FL 33612, USA Institute for Biological Instrumentation, Russian Academy of Sciences 142290 Pushchino, Moscow Region, Russia
    F1000 Biol Rep 5:1. 2013
    ..Finally, we discuss whether 'intrinsically disordered protein' (IDP) represents a useful new concept...
  4. pmc Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing
    Poornima Bhat-Nakshatri
    Department of Surgery, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN 46202, USA
    BMC Med Genomics 6:21. 2013
    ..The endogenous targets of ERα:estradiol (E2)-mediated alternative splicing and the influence of extracellular kinases that phosphorylate ERα on E2-induced splicing are unknown...
  5. pmc Changes in predicted protein disorder tendency may contribute to disease risk
    Yang Hu
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
    BMC Genomics 12:S2. 2011
    ..Recent advances in next generation sequencing technologies enable genome-wide identification of novel nucleotide variations in a specific population or cohort...
  6. pmc Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Virol J 6:69. 2009
    ..The 1918 H1N1 virus was a highly virulent strain that killed 20-50 million people. The cause of its virulence remains poorly understood...
  7. pmc A comparative analysis of viral matrix proteins using disorder predictors
    Gerard Kian Meng Goh
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Virol J 5:126. 2008
    ..9 (Suppl. 2), S4) revealed that HIV matrix protein p17 possesses especially high levels of predicted intrinsic disorder (PID). In this study, we analyzed the PID patterns in matrix proteins of viruses related and unrelated to HIV-1...
  8. pmc Archaic chaos: intrinsically disordered proteins in Archaea
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Syst Biol 4:S1. 2010
    ....
  9. pmc Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
    Christopher J Oldfield
    Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W, 10th Street, Indianapolis, IN 46202, USA
    BMC Genomics 9:S1. 2008
    ..febs j 2005, 272:5129-5148)...
  10. pmc Unfoldomics of human diseases: linking protein intrinsic disorder with diseases
    Vladimir N Uversky
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    BMC Genomics 10:S7. 2009
    ..This raises questions regarding the involvement of IDPs and IDRs in various diseases...
  11. pmc 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
    ....
  12. pmc Protein disorder in the human diseasome: unfoldomics of human genetic diseases
    Uros Midic
    Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
    BMC Genomics 10:S12. 2009
    ..2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases...
  13. pmc 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...
  14. pmc 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)...
  15. pmc 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research
    Jack Y Yang
    Department of Radiation Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts 02114, USA
    BMC Genomics 11:I1. 2010
    ..Joydeep Ghosh (UT Austin), Dr. Aidong Zhang (Buffalo) and Dr. Zhi-Hua Zhou (Nanjing) for their significant contributions to the field of intelligent biological medicine...
  16. pmc In-silico prediction of disorder content using hybrid sequence representation
    Marcin J Mizianty
    Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
    BMC Bioinformatics 12:245. 2011
    ..We show that these predictions may over-or under-predict the overall amount of disorder, which motivates development of novel tools for direct and accurate sequence-based prediction of the disorder content...
  17. pmc 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...
  18. pmc 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...
  19. pmc 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...
  20. doi Drugs for 'protein clouds': targeting intrinsically disordered transcription factors
    A Keith Dunker
    Institute for Intrinsically Disordered Protein Research, The Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Curr Opin Pharmacol 10:782-8. 2010
    ..However, challenges remain in the field of drug development for 'protein clouds'; such development is still in its earliest stage...
  21. 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...
  22. pmc Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations
    Shide Liang
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    Biochemistry 48:399-414. 2009
    ..Finally, disorder predictions revealed that secondary structures at the interface of unstable complexes exhibited greater disorder than the stable complexes...
  23. 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
    ....
  24. 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...
  25. 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...
  26. ncbi Function and structure of inherently disordered proteins
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, USA
    Curr Opin Struct Biol 18:756-64. 2008
    ....
  27. pmc Intrinsic disorder in scaffold proteins: getting more from less
    Marc S Cortese
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Prog Biophys Mol Biol 98:85-106. 2008
    ..In other words, scaffold proteins utilize several ID-facilitated mechanisms to enhance function, and by doing so, get more functionality from less structure...
  28. pmc TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorder
    Andrew Campen
    Department of Computer and Information Science, Indiana University Purdue University Indianapolis, IN 46202, USA
    Protein Pept Lett 15:956-63. 2008
    ..A web-based server has been created to apply the TOP-IDP scale to predict intrinsically disordered proteins (http://www.disprot.org/dev/disindex.php)...
  29. pmc 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...
  30. pmc Retro-MoRFs: identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA E Mails B X A K D
    Int J Mol Sci 11:3725-47. 2010
    ..This hypothesis provides new grounds for exploring the mysteries of protein-protein interaction networks at the genome level...
  31. pmc SPA: Short peptide analyzer of intrinsic disorder status of short peptides
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Genes Cells 15:635-46. 2010
    ..As evident from the data analysis, this method provides more reliable prediction of the intrinsic disorder status of short peptides...
  32. pmc Understanding protein non-folding
    Vladimir N Uversky
    Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Biochim Biophys Acta 1804:1231-64. 2010
    ..about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases?..
  33. 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...
  34. 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
    ....
  35. ncbi Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasome
    Uros Midic
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W 10th Street, Indianapolis, IN 46202, USA
    Protein Pept Lett 16:1533-47. 2009
    ..Based on these observations the human-genetic-disease-associated unfoldome was created. This minireview describes several illustrative examples of ordered and intrinsically disordered members of the human diseasome...
  36. 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...
  37. pmc Analysis of structured and intrinsically disordered regions of transmembrane proteins
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Mol Biosyst 5:1688-1702. 2009
    ....
  38. 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
    ....
  39. 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...
  40. 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...
  41. pmc 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...
  42. pmc 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...
  43. 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...
  44. ncbi A computational investigation of allostery in the catabolite activator protein
    Liwei Li
    Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
    J Am Chem Soc 129:15668-76. 2007
    ..This finding prompted us to propose a new mechanism by which CAP triggers the transcription activation that is based on an order to disorder transition mediated by cAMP binding as well as DNA...
  45. 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
    ....
  46. pmc PONDR-FIT: a meta-predictor of intrinsically disordered amino acids
    Bin Xue
    Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
    Biochim Biophys Acta 1804:996-1010. 2010
    ..Increased understanding of the underlying mechanism by which such meta-predictors give improved predictions will likely promote the further development of protein disorder predictors. Access to PONDR-FIT is available at www.disprot.org...
  47. pmc 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...
  48. pmc CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions
    Bin Xue
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W 10th Street, HS 5009, Indianapolis, IN 46202, USA
    FEBS Lett 583:1469-74. 2009
    ..A consensus binary predictor, based on the artificial neural networks, NN-CDF, was developed by using output of the individual CDFs. The consensus method outperforms the individual predictors by 4-5% in the averaged accuracy...
  49. pmc 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...
  50. pmc 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...
  51. 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..
  52. pmc 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...
  53. pmc Engineering productive enzyme confinement
    A Keith Dunker
    Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W 10th Street, Suite 5000, Indianapolis, IN 46202, USA
    Trends Biotechnol 25:189-90. 2007
    ..These findings provide an approach for dissecting the effect of various contributors to enzyme activity and thereby provide a means for fine-tuning the entrapping matrices to optimize enzyme performance in a rational way...
  54. 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...
  55. pmc 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
    ....
  56. 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
  57. 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...
  58. 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...
  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 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
    ..If applicable, most entries also list the biological function(s) of each disordered region, how each region of disorder is used for function, as well as provide links to PubMed abstracts and major protein databases...
  61. pmc 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
    ....
  62. 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
    ....
  63. 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...
  64. 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...
  65. 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...
  66. 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
  67. 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...
  68. 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...
  69. pmc 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
    ....
  70. pmc 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
    ....
  71. pmc 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...
  72. pmc 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...
  73. 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...
  74. doi Signal transduction via unstructured protein conduits
    A Keith Dunker
    Nat Chem Biol 4:229-30. 2008
  75. 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...
  76. 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
  77. 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
    ....
  78. ncbi Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition
    Predrag Radivojac
    School of Informatics, Indiana University, Bloomington, Indiana, USA
    Proteins 63:398-410. 2006
    ..These findings add to the growing list of examples in which intrinsically disordered protein regions are indicated to provide the basis for cell signaling and regulation...
  79. pmc 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...
  80. pmc A protein domain-based interactome network for C. elegans early embryogenesis
    Mike Boxem
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Cell 134:534-45. 2008
    ..This interactome modeling strategy revealed insights into C. elegans centrosome function and is applicable to other biological processes in this and other organisms...
  81. ncbi Comparing skeletal and cardiac calsequestrin structures and their calcium binding: a proposed mechanism for coupled calcium binding and protein polymerization
    HaJeung Park
    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164 4660, USA
    J Biol Chem 279:18026-33. 2004
    ....
  82. 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...
  83. 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
    ....
  84. doi Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes
    Amrita Mohan
    School of Informatics, Indiana University, Bloomington, IN 47401, USA
    Mol Biosyst 4:328-40. 2008
    ..It also provides new insights into the evolution of intrinsic disorder in the context of adapting to a parasitic lifestyle and lays the foundation for further work on the subject...

Research Grants15

  1. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2006
    ..abstract_text> ..
  2. Mining the Structural Genomics Initiative for Disorder
    A Dunker; Fiscal Year: 2009
    ..Alsoof importance is that this workwill significantly increase the sequence-function informationobtained from the structural genomics initiative with very little incremental increase over the current investment. ..
  3. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2005
    ..The proposed research has important implications for cancer research for, as will be shown, many cancer-associated proteins have large regions of putative intrinsic disorder. ..
  4. Cancer drug discovery using disordered protein targets
    A Dunker; Fiscal Year: 2003
    ..The ultimate final product will be a new methodology and expert analysis to accelerate drug lead identification via interaction with disordered regions of cancer-associated proteins. ..
  5. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2003
    ..abstract_text> ..
  6. Tools to accelerate protein structure determination
    A Dunker; Fiscal Year: 2003
    ..abstract_text> ..
  7. BIOINFORMATICS, DISORDERED PROTEINS, AND FUNCTION
    A Dunker; Fiscal Year: 2002
    ..Thus, understanding the interplay of sequence, flexibility, order / disorder, complexity, structure and function clearly relates to human health. ..
  8. BIOINFORMATICS, DISORDERED PROTEINS, AND FUNCTION
    A Dunker; Fiscal Year: 2001
    ..Thus, understanding the interplay of sequence, flexibility, order / disorder, complexity, structure and function clearly relates to human health. ..
  9. Mining the Structural Genomics Initiative for Disorder
    A Dunker; Fiscal Year: 2006
    ..Also of importance is that this work will significantly increase the sequence-function information obtained from the structural genomics initiative with very little incremental increase over the current investment. ..
  10. Mining the Structural Genomics Initiative for Disorder
    A Dunker; Fiscal Year: 2007
    ..Also of importance is that this work will significantly increase the sequence-function information obtained from the structural genomics initiative with very little incremental increase over the current investment. ..
  11. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2005
    ..abstract_text> ..
  12. Bioinformatics linkage of protein disorder and function
    A Dunker; Fiscal Year: 2004
    ..abstract_text> ..
  13. Bioinformatic tool for cancer protein analysis
    A Dunker; Fiscal Year: 2002
    ..The database, augmented with methods for studying counter example proteins, will provide the basis for design of novel approaches to the development of cancer treatments and/or drug discovery. ..
  14. BIOINFORMATICS, DISORDERED PROTEINS, AND FUNCTION
    A Dunker; Fiscal Year: 2000
    ..Thus, understanding the interplay of sequence, flexibility, order / disorder, complexity, structure and function clearly relates to human health. ..