Research Topics
| A DunkerSummaryAffiliation: Indiana University Country: USA Publications
Research Grants
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Detail Information
Publications
Rational drug design via intrinsically disordered proteinYugong 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...
Changes in predicted protein disorder tendency may contribute to disease riskYang 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...- Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 virusesGerard 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... - A comparative analysis of viral matrix proteins using disorder predictorsGerard 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... - Archaic chaos: intrinsically disordered proteins in ArchaeaBin Xue
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
BMC Syst Biol 4:S1. 2010.... - Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partnersChristopher 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)... - Unfoldomics of human diseases: linking protein intrinsic disorder with diseasesVladimir 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... - Investigation of transmembrane proteins using a computational approachJack Y Yang
Department of Radiology, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
BMC Genomics 9:S7. 2008.... - Protein disorder in the human diseasome: unfoldomics of human genetic diseasesUros 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... - Protein intrinsic disorder toolbox for comparative analysis of viral proteinsGerard 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... - Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regionsSiyuan 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)... - 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine researchJack 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... - In-silico prediction of disorder content using hybrid sequence representationMarcin 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... - Composition Profiler: a tool for discovery and visualization of amino acid composition differencesVladimir 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... - Length-dependent prediction of protein intrinsic disorderKang 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... - The unfoldomics decade: an update on intrinsically disordered proteinsA 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... - Flexible nets. The roles of intrinsic disorder in protein interaction networksA 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... 
Drugs for 'protein clouds': targeting intrinsically disordered transcription factorsA 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...- Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculationsShide 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... - Comparing and combining predictors of mostly disordered proteinsChristopher J Oldfield
Molecular Kinetics, Inc, 6201 La Pas Trail, Suite 160, Indianapolis, Indiana 46268, USA
Biochemistry 44:1989-2000. 2005.... - Coupled folding and binding with alpha-helix-forming molecular recognition elementsChristopher 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... - Function and structure of inherently disordered proteinsA 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.... - Abundance of intrinsic disorder in protein associated with cardiovascular diseaseYugong 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... - Intrinsic disorder in scaffold proteins: getting more from lessMarc 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... - TOP-IDP-scale: a new amino acid scale measuring propensity for intrinsic disorderAndrew 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)... - Prediction of intrinsic disorder and its use in functional proteomicsVladimir 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... - Mining alpha-helix-forming molecular recognition features with cross species sequence alignmentsYugong 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... - Structural basis for regulation of protein phosphatase 1 by inhibitor-2Thomas D Hurley
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
J Biol Chem 282:28874-83. 2007.... - Intrinsically disordered proteins in human diseases: introducing the D2 conceptVladimir 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... - Intrinsic disorder in the Protein Data BankTanguy 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.... - SPA: Short peptide analyzer of intrinsic disorder status of short peptidesBin 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... - Understanding protein non-foldingVladimir 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?.. - Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasomeUros 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... - Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder PredictionBin 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... - Analysis of structured and intrinsically disordered regions of transmembrane proteinsBin Xue
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
Mol Biosyst 5:1688-1702. 2009.... - Natively disordered proteins: functions and predictionsPedro 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... - Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVsVladimir 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... - Conservation of intrinsic disorder in protein domains and families: II. functions of conserved disorderJessica 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... - Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatmentMarc 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... - A computational investigation of allostery in the catabolite activator proteinLiwei 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... - Characterization of molecular recognition features, MoRFs, and their binding partnersVladimir 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... - DisProt: the Database of Disordered ProteinsMegan 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... - Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regionsJessica 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... - Intrinsic disorder in transcription factorsJiangang 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... - Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signalingVladimir N Uversky
Molecular Kinetics, 6201 La Pas Trail, Suite 160, Indianapolis, IN 46268, USA
J Mol Recognit 18:343-84. 2005.... - PONDR-FIT: a meta-predictor of intrinsically disordered amino acidsBin 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... - CDF it all: consensus prediction of intrinsically disordered proteins based on various cumulative distribution functionsBin 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... - Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organismsPedro 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... - Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarksWei 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.. - Protein disorder is positively correlated with gene expression in Escherichia coliOleg 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... - Engineering productive enzyme confinementA 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... - Protein flexibility and intrinsic disorderPredrag Radivojac
Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
Protein Sci 13:71-80. 2004.... - Exploring alternative knowledge representations for protein secondary-structure predictionUros 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... - Intrinsic disorder and protein functionA Keith Dunker
School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
Biochemistry 41:6573-82. 2002 - Addressing the intrinsic disorder bottleneck in structural proteomicsChristopher 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... - Optimizing long intrinsic disorder predictors with protein evolutionary informationKang 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... - Classification and knowledge discovery in protein databasesPredrag 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... - DisProt: a database of protein disorderSlobodan Vucetic
Center for Information Science and Technology, Temple University Philadelphia, PA 19122, USA
Bioinformatics 21:137-40. 2005..AVAILABILITY: www.disprot.org.. - The importance of intrinsic disorder for protein phosphorylationLilia M Iakoucheva
School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
Nucleic Acids Res 32:1037-49. 2004.... - Order, disorder, and flexibility: prediction from protein sequenceLilia M Iakoucheva
The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
Structure 11:1316-7. 2003.... - Predicting intrinsic disorder from amino acid sequenceZoran 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... - Flavors of protein disorderSlobodan 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... - Intrinsic disorder in cell-signaling and cancer-associated proteinsLilia 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... - Crystallization and structure-function of calsequestrinChulhee Kang
Department of Biochemistry and Biophysics, Washington State University, Pullman, Washington, USA
Methods Mol Biol 172:281-94. 2002 - Exploiting heterogeneous sequence properties improves prediction of protein disorderZoran 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... - Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regionsSlobodan Vucetic
Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
J Proteome Res 6:1899-916. 2007.... - Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteinsHongbo Xie
Center for Information Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
J Proteome Res 6:1917-32. 2007.... - Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regionsHongbo 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... - Another window into disordered protein functionA 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... - Intrinsic disorder and functional proteomicsPredrag 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... - 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... - Signal transduction via unstructured protein conduitsA Keith Dunker
Nat Chem Biol 4:229-30. 2008 - Evolutionary rate heterogeneity in proteins with long disordered regionsCeleste 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... - Polymerization of calsequestrin. Implications for Ca2+ regulationHaJeung Park
School of Molecular Biosciences, Department of Chemistry, Washington State University, Pullman, WA 99164, USA
J Biol Chem 278:16176-82. 2003.... - Improved amino acid flexibility parametersDavid 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... - Identification and functions of usefully disordered proteinsA Keith Dunker
School of Molecular Biosciences, Washington State University, Pullman, Washington 99164, USA
Adv Protein Chem 62:25-49. 2002 - Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognitionPredrag 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... - Comparing skeletal and cardiac calsequestrin structures and their calcium binding: a proposed mechanism for coupled calcium binding and protein polymerizationHaJeung Park
School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
J Biol Chem 279:18026-33. 2004.... - A protein domain-based interactome network for C. elegans early embryogenesisMike 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... - Combining prediction, computation and experiment for the characterization of protein disorderClay 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... - Disorder and sequence repeats in hub proteins and their implications for network evolutionZsuzsanna Dosztanyi
Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, 1518 Budapest, Hungary
J Proteome Res 5:2985-95. 2006.... - Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotesAmrita 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 Grants
- Bioinformatics linkage of protein disorder and functionA Dunker; Fiscal Year: 2006..abstract_text> ..
- Mining the Structural Genomics Initiative for DisorderA 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. ..
- Bioinformatics linkage of protein disorder and functionA 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. ..
- Cancer drug discovery using disordered protein targetsA 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. ..
- Tools to accelerate protein structure determinationA Dunker; Fiscal Year: 2003..abstract_text> ..
- Bioinformatic tool for cancer protein analysisA 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. ..
- BIOINFORMATICS, DISORDERED PROTEINS, AND FUNCTIONA Dunker; Fiscal Year: 2002..Thus, understanding the interplay of sequence, flexibility, order / disorder, complexity, structure and function clearly relates to human health. ..
- Mining the Structural Genomics Initiative for DisorderA 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. ..