A. Dunker

  • 29187 Citations
  • 82 h-Index
1969 …2019
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Publications 1969 2019

2007

Pacific symposium on biocomputing 2007

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2007, In : Unknown Journal.

Research output: Contribution to journalArticle

29 Citations (Scopus)

Prediction of intrinsic disorder and its use in functional proteomics.

Uversky, V. N., Radivojac, P., Iakoucheva, L. M., Obradovic, Z. & Dunker, A., 2007, In : Methods in molecular biology (Clifton, N.J.). 408, p. 69-92 24 p.

Research output: Contribution to journalArticle

Proteomics
Intrinsically Disordered Proteins
Proteins
Proteome
Computational Biology
121 Citations (Scopus)

Structural basis for regulation of protein phosphatase 1 by inhibitor-2

Hurley, T., Yang, J., Zhang, L., Goodwin, K. D., Zou, Q., Cortese, M., Dunker, A. & De Paoli-Roach, A., Sep 28 2007, In : Journal of Biological Chemistry. 282, 39, p. 28874-28883 10 p.

Research output: Contribution to journalArticle

Protein Phosphatase 1
Phosphoprotein Phosphatases
Metal ions
Crystal structure
Amino Acids
2006
119 Citations (Scopus)

Abundance of intrinsic disorder in protein associated with cardiovascular disease

Cheng, Y., LeGall, T., Oldfield, C. J., Dunker, A. & Uversky, V. N., Sep 5 2006, In : Biochemistry. 45, 35, p. 10448-10460 13 p.

Research output: Contribution to journalArticle

Cardiovascular Diseases
Proteins
Intrinsically Disordered Proteins
Protein Databases
Distribution functions
268 Citations (Scopus)

Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

Romero, P. R., Zaidi, S., Fang, Y. Y., Uversky, V. N., Radivojac, P., Oldfield, C. J., Cortese, M. S., Sickmeier, M., LeGall, T., Obradovic, Z. & Dunker, A., May 30 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 22, p. 8390-8395 6 p.

Research output: Contribution to journalArticle

Alternative Splicing
Proteins
Protein Isoforms
Protein Databases
Recombinant DNA
434 Citations (Scopus)

Analysis of Molecular Recognition Features (MoRFs)

Mohan, A., Oldfield, C. J., Radivojac, P., Vacic, V., Cortese, M. S., Dunker, A. & Uversky, V. N., Oct 6 2006, In : Journal of Molecular Biology. 362, 5, p. 1043-1059 17 p.

Research output: Contribution to journalArticle

Proteins
Computational Biology
Chemical Databases
Explosions
Protein Binding
83 Citations (Scopus)

Calmodulin signaling: Analysis and prediction of a disorder-dependent molecular recognition

Radivojac, P., Vucetic, S., O'Connor, T. R., Uversky, V. N., Obradovic, Z. & Dunker, A., May 1 2006, In : Proteins: Structure, Function and Genetics. 63, 2, p. 398-410 13 p.

Research output: Contribution to journalArticle

Molecular recognition
Calmodulin
Intrinsically Disordered Proteins
Cell signaling
Calmodulin-Binding Proteins
86 Citations (Scopus)

Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions

Chen, J. W., Romero, P., Uversky, V. N. & Dunker, A., Apr 2006, In : Journal of Proteome Research. 5, 4, p. 879-887 9 p.

Research output: Contribution to journalArticle

Conservation
Sequence Alignment
Databases
Proteins
Proteome
84 Citations (Scopus)

Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder

Chen, J. W., Romero, P., Uversky, V. N. & Dunker, A., Apr 2006, In : Journal of Proteome Research. 5, 4, p. 888-898 11 p.

Research output: Contribution to journalArticle

Conservation
Proteins
Archaeal Proteins
RNA-Binding Proteins
Bacterial Proteins
228 Citations (Scopus)

Disorder and sequence repeats in hub proteins and their implications for network evolution

Dosztányi, Z., Chen, J., Dunker, A., Simon, I. & Tompa, P., Nov 2006, In : Journal of Proteome Research. 5, 11, p. 2985-2995 11 p.

Research output: Contribution to journalArticle

Proteins
Protein Interaction Maps
Gene Duplication
Caenorhabditis elegans
Drosophila melanogaster
360 Citations (Scopus)

Intrinsic disorder in transcription factors

Liu, J., Perumal, N. B., Oldfield, C. J., Su, E. W., Uversky, V. N. & Dunker, A., Jun 6 2006, In : Biochemistry. 45, 22, p. 6873-6888 16 p.

Research output: Contribution to journalArticle

Transcription Factors
Eukaryota
AT-Hook Motifs
Intrinsically Disordered Proteins
Molecular recognition
466 Citations (Scopus)

Length-dependent prediction of protein in intrinsic disorder

Peng, K., Radivojac, P., Vucetic, S., Dunker, A. & Obradovic, Z., Apr 17 2006, In : BMC Bioinformatics. 7, 208.

Research output: Contribution to journalArticle

Disorder
Predictors
Proteins
Protein
Dependent

Pacific symposium on biocomputing 2006

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2006, In : Unknown Journal.

Research output: Contribution to journalArticle

99 Citations (Scopus)

Protein intrinsic disorder and human papillomaviruses: Increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs

Uversky, V. N., Roman, A., Oldfield, C. J. & Dunker, A., Aug 2006, In : Journal of Proteome Research. 5, 8, p. 1829-1842 14 p.

Research output: Contribution to journalArticle

Oncogene Proteins
Intrinsically Disordered Proteins
Proteome
Bioinformatics
Proteins
170 Citations (Scopus)

Rational drug design via intrinsically disordered protein

Cheng, Y., LeGall, T., Oldfield, C. J., Mueller, J. P., Van, Y. Y. J., Romero, P., Cortese, M. S., Uversky, V. N. & Dunker, A., Oct 2006, In : Trends in Biotechnology. 24, 10, p. 435-442 8 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Drug Design
Proteins
Pharmaceutical Preparations
Drug Discovery
2005
68 Citations (Scopus)

Addressing the intrinsic disorder bottleneck in structural proteomics

Oldfield, C. J., Ulrich, E. L., Cheng, Y., Dunker, A. & Markley, J. L., May 15 2005, In : Proteins: Structure, Function and Genetics. 59, 3, p. 444-453 10 p.

Research output: Contribution to journalArticle

Proteomics
Genomics
Proteins
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance spectroscopy
428 Citations (Scopus)

Coupled folding and binding with α-helix-forming molecular recognition elements

Oldfield, C. J., Cheng, Y., Cortese, M. S., Romero, P., Uversky, V. N. & Dunker, A., Sep 20 2005, In : Biochemistry. 44, 37, p. 12454-12470 17 p.

Research output: Contribution to journalArticle

Molecular recognition
Proteins
Genomics
Nucleic Acids
Conformations
166 Citations (Scopus)

DisProt: A database of protein disorder

Vucetic, S., Obradovic, Z., Vacic, V., Radivojac, P., Peng, K., Iakoucheva, L. M., Cortese, M. S., Lawson, J. D., Brown, C. J., Sikes, J. G., Newton, C. D. & Dunker, A., Jan 1 2005, In : Bioinformatics. 21, 1, p. 137-140 4 p.

Research output: Contribution to journalArticle

Protein Databases
Disorder
Proteins
Protein
PubMed
345 Citations (Scopus)

Exploiting heterogeneous sequence properties improves prediction of protein disorder

Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P. & Dunker, A., 2005, In : Proteins: Structure, Function and Genetics. 61, SUPPL. 7, p. 176-182 7 p.

Research output: Contribution to journalArticle

Weights and Measures
Proteins
Experiments
749 Citations (Scopus)

Flexible nets: The roles of intrinsic disorder in protein interaction networks

Dunker, A., Cortese, M. S., Romero, P., Iakoucheva, L. M. & Uversky, V. N., Oct 2005, In : FEBS Journal. 272, 20, p. 5129-5148 20 p.

Research output: Contribution to journalArticle

Protein Interaction Maps
Proteins
Intrinsically Disordered Proteins
Cell Physiological Phenomena
Physiology
4 Citations (Scopus)

Improving protein secondary-structure prediction by predicting ends of secondary-structure segments

Midic, U., Dunker, A. & Obradovic, Z., 2005, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05. Vol. 2005. 1594959

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Proteins
Amino acids
Neural networks
36 Citations (Scopus)

Interaction between cardiac calsequestrin and drugs with known cardiotoxicity

Park, I. Y., Kim, E. J., Park, H., Fields, K., Dunker, A. & Kang, C., Jan 2005, In : Molecular Pharmacology. 67, 1, p. 97-104 8 p.

Research output: Contribution to journalArticle

Calsequestrin
Pharmaceutical Preparations
Tricyclic Antidepressive Agents
Anthracyclines
Cardiotoxicity
35 Citations (Scopus)

Intrinsic disorder and prote in modifications: Building an SVM predictor for methylation

Daily, K. M., Radivojac, P. & Dunker, A., 2005, Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '05. Vol. 2005. 1594957

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Methylation
Arginine
Proteins
Support vector machines
Screening
257 Citations (Scopus)

Optimizing long intrinsic disorder predictors with protein evolutionary information

Peng, K., Vucetic, S., Radivojac, P., Brown, C. J., Dunker, A. & Obradovic, Z., Feb 2005, In : Journal of Bioinformatics and Computational Biology. 3, 1, p. 35-60 26 p.

Research output: Contribution to journalArticle

Proteins
Amino acids
Servers
Neural networks
Amino Acids

Pacific symposium on biocomputing 2005

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2005, In : Unknown Journal.

Research output: Contribution to journalArticle

567 Citations (Scopus)

Showing your ID: Intrinsic disorder as an ID for recognition, regulation and cell signaling

Uversky, V. N., Oldfield, C. J. & Dunker, A., Sep 2005, In : Journal of Molecular Recognition. 18, 5, p. 343-384 42 p.

Research output: Contribution to journalArticle

Cell signaling
Proteins
Molecular recognition
DNA-Directed RNA Polymerases
HMGA Proteins
47 Citations (Scopus)

Uncovering the unfoldome: Enriching cell extracts for unstructured proteins by acid treatment

Cortese, M. S., Baird, J. P., Uversky, V. N. & Dunker, A., Sep 2005, In : Journal of Proteome Research. 4, 5, p. 1610-1618 9 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Cell Extracts
Acids
Proteins
Gels
2004
59 Citations (Scopus)

Classification and knowledge discovery in protein databases

Radivojac, P., Chawla, N. V., Dunker, A. & Obradovic, Z., Aug 2004, In : Journal of Biomedical Informatics. 37, 4, p. 224-239 16 p.

Research output: Contribution to journalArticle

Protein Databases
Data mining
Noise
Logistic Models
Proteins
105 Citations (Scopus)

Combining prediction, computation and experiment for the characterization of protein disorder

Bracken, C., Iakoucheva, L. M., Romero, P. R. & Dunker, A., Oct 2004, In : Current Opinion in Structural Biology. 14, 5, p. 570-576 7 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Mass Spectrometry
Magnetic Resonance Spectroscopy
Genome
Proteins
102 Citations (Scopus)

Comparing skeletal and cardiac calsequestrin structures and their calcium binding: A proposed mechanism for coupled calcium binding and protein polymerization

Park, H., Park, Y. I., Kim, E., Youn, B., Fields, K., Dunker, A. & Kang, C., Apr 23 2004, In : Journal of Biological Chemistry. 279, 17, p. 18026-18033 8 p.

Research output: Contribution to journalArticle

Calsequestrin
Calcium-Binding Proteins
Polymerization
Calcium
Ions
26 Citations (Scopus)

Feature selection filters based on the permutation test

Radivojac, P., Obradovic, Z., Dunker, A. & Vucetic, S., 2004, Lecture Notes in Artificial Intelligence (Subseries of Lecture Notes in Computer Science). Boulicaut, J-F., Esposito, F., Pedreschi, D. & Giannotti, F. (eds.). Vol. 3201. p. 334-346 13 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Permutation Test
p-Value
Feature Selection
Feature extraction
Filtering
112 Citations (Scopus)

Natively disordered proteins: Functions and predictions

Romero, P., Obradovic, Z. & Dunker, A., 2004, In : Applied Bioinformatics. 3, 2-3, p. 105-113 9 p.

Research output: Contribution to journalArticle

Proteins
prediction
proteins
Eukaryota
eukaryotic cells
213 Citations (Scopus)

Protein flexibility and intrinsic disorder

Radivojac, P., Obradovic, Z., Smith, D. K., Zhu, G., Vucetic, S., Brown, C. J., Lawson, J. D. & Dunker, A., Jan 2004, In : Protein Science. 13, 1, p. 71-80 10 p.

Research output: Contribution to journalArticle

Proteins
Amino Acids
3'-(1-butylphosphoryl)adenosine
Hydrophilicity
Hydrophobic and Hydrophilic Interactions
132 Citations (Scopus)

The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partner

Bourhis, J. M., Johansson, K., Receveur-Bréchot, V., Oldfield, C. J., Dunker, A., Canard, B. & Longhi, S., Feb 2004, In : Virus Research. 99, 2, p. 157-167 11 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteolysis
Trifluoroethanol
Phosphoproteins
Hydrodynamics
930 Citations (Scopus)

The importance of intrinsic disorder for protein phosphorylation

Iakoucheva, L. M., Radivojac, P., Brown, C. J., O'Connor, T. R., Sikes, J. G., Obradovic, Z. & Dunker, A., 2004, In : Nucleic Acids Research. 32, 3, p. 1037-1049 13 p.

Research output: Contribution to journalArticle

Phosphorylation
Proteins
Intrinsically Disordered Proteins
Amino Acids
Eukaryotic Cells
2003

Erratum: Isolation of chloroform-resistant mutants of filamentous phage: Localization in models of phage structure (Journal of Molecular Biology (1999) 287 (449-457))

Oh, J. S., Davies, D. R., Lawson, J. D., Arnold, G. E. & Dunker, A., Nov 14 2003, In : Journal of Molecular Biology. 334, 1, p. 173-174 2 p.

Research output: Contribution to journalArticle

Chloroform
Bacteriophages
Molecular Biology

Erratum: Polymerization of calsequestrin. Implications for Ca2+ regulation (The Journal of Biological Chemistry (2003) 278 (16176-16182))

Park, H., Wu, S., Dunker, A. & Kang, C., Oct 24 2003, In : Journal of Biological Chemistry. 278, 43, p. 42728 1 p.

Research output: Contribution to journalArticle

Calsequestrin
Polymerization
290 Citations (Scopus)

Flavors of protein disorder

Vucetic, S., Brown, C. J., Dunker, A. & Obradovic, Z., Sep 1 2003, In : Proteins: Structure, Function and Genetics. 52, 4, p. 573-584 12 p.

Research output: Contribution to journalArticle

Flavors
Proteins
Intrinsically Disordered Proteins
Amino Acids
Protein Databases
110 Citations (Scopus)

Improved amino acid flexibility parameters

Smith, D. K., Radivojac, P., Obradovic, Z., Dunker, A. & Zhu, G., May 1 2003, In : Protein Science. 12, 5, p. 1060-1072 13 p.

Research output: Contribution to journalArticle

Amino Acids
Proteins
Factor X
X ray crystallography
X Ray Crystallography
25 Citations (Scopus)

Ligand and flavor binding functional properties of β-lactoglobulin in the molten globule state induced by high pressure

Yang, J., Powers, J. R., Clark, S., Dunker, A. & Swanson, B. G., Mar 2003, In : Journal of Food Science. 68, 2, p. 444-452 9 p.

Research output: Contribution to journalArticle

lactoglobulins
norisoprenoids
Lactoglobulins
Hydrostatic Pressure
high pressure treatment
38 Citations (Scopus)

Order, disorder, and flexibility: Prediction from protein sequence

Iakoucheva, L. M. & Dunker, A., Nov 2003, In : Structure. 11, 11, p. 1316-1317 2 p.

Research output: Contribution to journalArticle

Proteins
85 Citations (Scopus)

Polymerization of calsequestrin: Implications for Ca2+ regulation

Park, H., Wu, S., Dunker, A. & Kang, C., May 2 2003, In : Journal of Biological Chemistry. 278, 18, p. 16176-16182 7 p.

Research output: Contribution to journalArticle

Calsequestrin
Polymerization
Dimerization
Oligomerization
Canidae
295 Citations (Scopus)

Predicting Intrinsic Disorder From Amino Acid Sequence

Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., Brown, C. J. & Dunker, A., 2003, In : Proteins: Structure, Function and Genetics. 53, SUPPL. 6, p. 566-572 7 p.

Research output: Contribution to journalArticle

Amino Acid Sequence
Amino Acids
Proteins
Experiments
Sampling
51 Citations (Scopus)

Prediction of boundaries between intrinsically ordered and disordered protein regions.

Radivojac, P., Obradović, Z., Brown, C. J. & Dunker, A., 2003, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 216-227 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intrinsically Disordered Proteins
Logistic Models
Databases
Amino Acids
Proteins

Protein function, folding, and dynamics in the proteinomic era

Biorn, A. C., Daggett, V., DeGrado, W. F., Dunker, A., Radford, S. E., Raleigh, D. P., Rosenblatt, M., Urbauer, J. & Wand, A. J., Feb 1 2003, In : Protein Science. 12, 2, p. 389-397 9 p.

Research output: Contribution to journalArticle

2002
4 Citations (Scopus)

Crystallization and structure-function of calsequestrin.

Kang, C., Trumble, W. R. & Dunker, A., 2002, In : Methods in molecular biology (Clifton, N.J.). 172, p. 281-294 14 p.

Research output: Contribution to journalArticle

Calsequestrin
Biological Models
Molecular Models
X Ray Crystallography
Protein Folding
287 Citations (Scopus)

Evolutionary rate heterogeneity in proteins with long disordered regions

Brown, C. J., Takayama, S., Campen, A. M., Vise, P., Marshall, T. W., Oldfield, C. J., Williams, C. J. & Dunker, A., 2002, In : Journal of Molecular Evolution. 55, 1, p. 104-110 7 p.

Research output: Contribution to journalArticle

protein
Proteins
proteins
genetic distance
Binding Sites
27 Citations (Scopus)

Hydrophobic probe binding of β-lactoglobulin in the native and molten globule state induced by high pressure as affected by pH, KIO3 and N-ethylmaleimide

Yang, J., Powers, J. R., Clark, S., Dunker, A. & Swanson, B. G., Aug 28 2002, In : Journal of Agricultural and Food Chemistry. 50, 18, p. 5207-5214 8 p.

Research output: Contribution to journalArticle

lactoglobulins
Lactoglobulins
Hydrostatic Pressure
Ethylmaleimide
Hydrostatic pressure
294 Citations (Scopus)

Identification and functions of usefully disordered proteins

Dunker, A., Brown, C. J. & Obradovic, Z., 2002, In : Advances in Protein Chemistry. 62, p. 25-49 25 p.

Research output: Contribution to journalArticle

Proteins
23 Citations (Scopus)

Improving sequence alignments for intrinsically disordered proteins.

Radivojac, P., Obradovic, Z., Brown, C. J. & Dunker, A., 2002, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. p. 589-600 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intrinsically Disordered Proteins
Sequence Alignment
Aptitude
Proteins