A. Dunker

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

2010
25 Citations (Scopus)

Retro-MoRFS: Identifying protein binding sites by normal and reverse alignment and intrinsic disorder prediction

Xue, B., Dunker, A. & Uversky, V. N., Oct 2010, In : International Journal of Molecular Sciences. 11, 10, p. 3725-3747 23 p.

Research output: Contribution to journalArticle

Molecular recognition
Binding sites
Protein Binding
Binding Sites
alignment
7 Citations (Scopus)

SPA: Short peptide analyzer of intrinsic disorder status of short peptides

Xue, B., Hsu, W. L., Lee, J. H., Lu, H., Dunker, A. & Uversky, V. N., Jun 2010, In : Genes to Cells. 15, 6, p. 635-646 12 p.

Research output: Contribution to journalArticle

Peptides
Datasets
697 Citations (Scopus)

Understanding protein non-folding

Uversky, V. N. & Dunker, A., Jun 2010, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1804, 6, p. 1231-1264 34 p.

Research output: Contribution to journalArticle

Protein Folding
Intrinsically Disordered Proteins
Proteins
Biophysics
Biochemistry
66 Citations (Scopus)

Viral disorder or disordered viruses: Do viral proteins possess unique features?

Xue, B., Williams, R. W., Oldfield, C. J., Goh, G. K. M., Dunker, A. & Uversky, V. N., 2010, In : Protein and Peptide Letters. 17, 8, p. 932-951 20 p.

Research output: Contribution to journalArticle

Viral Proteins
Viruses
Proteins
Overlapping Genes
Viral Structural Proteins
2009
44 Citations (Scopus)

Analysis of structured and intrinsically disordered regions of transmembrane proteins

Xue, B., Li, L., Meroueh, S., Uversky, V. N. & Dunker, A., 2009, In : Molecular BioSystems. 5, 12, p. 1688-1702 15 p.

Research output: Contribution to journalArticle

Membrane Proteins
Proteins
Water
Amino Acids
Protein Transport
16 Citations (Scopus)

A new machine learning approach for protein phosphorylation site prediction in plants

Gao, J., Agrawal, G. K., Thelen, J. J., Obradovic, Z., Dunker, A. & Xu, D., 2009, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5462 LNBI. p. 18-29 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5462 LNBI).

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

Protein Phosphorylation
Phosphorylation
Learning systems
Machine Learning
Proteins
88 Citations (Scopus)

CDF it all: Consensus prediction of intrinsically disordered proteins based on various cumulative distribution functions

Xue, B., Oldfield, C. J., Dunker, A. & Uversky, V. N., May 6 2009, In : FEBS Letters. 583, 9, p. 1469-1474 6 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Distribution functions
Proteins
Error analysis
Neural networks
171 Citations (Scopus)

Close encounters of the third kind: Disordered domains and the interactions of proteins

Tompa, P., Fuxreiter, M., Oldfield, C. J., Simon, I., Dunker, A. & Uversky, V. N., 2009, In : BioEssays. 31, 3, p. 328-335 8 p.

Research output: Contribution to journalArticle

Protein Interaction Domains and Motifs
Proteins
Wiskott-Aldrich Syndrome Protein
Microfilament Proteins
Protein Folding
41 Citations (Scopus)

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations

Liang, S., Li, L., Hsu, W. L., Pilcher, M. N., Uversky, V., Zhou, Y., Dunker, A. & Meroueh, S., Jan 20 2009, In : Biochemistry. 48, 2, p. 399-414 16 p.

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Free energy
Molecular dynamics
Computer simulation
Entropy
1 Citation (Scopus)

Intrinsically disordered proteins and their recognition functions

Uversky, V. N., Fuxreiter, M., Oldfield, C. J., Dunker, A. & Tompa, P., Jan 1 2009, Computational Protein-Protein Interactions. CRC Press, p. 223-252 30 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Intrinsically Disordered Proteins
proteins
Molecular recognition
primary contact
Bioinformatics
106 Citations (Scopus)

Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation

Rancurel, C., Khosravi, M., Dunker, A., Romero, P. R. & Karlin, D., Oct 2009, In : Journal of Virology. 83, 20, p. 10719-10736 18 p.

Research output: Contribution to journalArticle

Overlapping Genes
Proteins
genes
proteins
Reading Frames

Pacific symposium on biocomputing 2009

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2009, In : Unknown Journal.

Research output: Contribution to journalArticle

266 Citations (Scopus)

Predicting intrinsic disorder in proteins: An overview

He, B., Wang, K., Liu, Y., Xue, B., Uversky, V. N. & Dunker, A., Aug 2009, In : Cell Research. 19, 8, p. 929-949 21 p.

Research output: Contribution to journalArticle

Inosine Diphosphate
Intrinsically Disordered Proteins
Proteins
Protein Folding
Research Personnel
43 Citations (Scopus)

Protein intrinsic disorder and influenza virulence: The 1918 H1N1 and H5N1 viruses

Goh, G. K. M., Dunker, A. & Uversky, V. N., 2009, In : Virology Journal. 6, 69.

Research output: Contribution to journalArticle

H5N1 Subtype Influenza A Virus
H1N1 Subtype Influenza A Virus
Human Influenza
Virulence
Proteins
4 Citations (Scopus)

Protein sequence alignment and structural disorder: A substitution matrix for an extended alphabet

Midic, U., Dunker, A. & Obradovic, Z., 2009, Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09. p. 27-31 5 p.

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

Sequence Alignment
Substitution reactions
Proteins
Amino acids
Amino Acids
41 Citations (Scopus)

Unfoldomics of human genetic diseases: Illustrative examples of ordered and intrinsically disordered members of the human diseasome

Midic, U., Oldfield, C. J., Dunker, A., Obradovic, Z. & Uversky, V. N., Dec 2009, In : Protein and Peptide Letters. 16, 12, p. 1533-1547 15 p.

Research output: Contribution to journalArticle

Inborn Genetic Diseases
Medical Genetics
Intrinsically Disordered Proteins
Proteins
Genes
2008
35 Citations (Scopus)

A comparative analysis of viral matrix proteins using disorder predictors

Goh, G. K. M., Dunker, A. & Uversky, V. N., 2008, In : Virology Journal. 5, 126.

Research output: Contribution to journalArticle

Viral Matrix Proteins
HIV-1
Proteins
Equine infectious anemia virus
Human Immunodeficiency Virus Proteins
136 Citations (Scopus)

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

Boxem, M., Maliga, Z., Klitgord, N., Li, N., Lemmens, I., Mana, M., de Lichtervelde, L., Mul, J. D., van de Peut, D., Devos, M., Simonis, N., Yildirim, M. A., Cokol, M., Kao, H. L., de Smet, A. S., Wang, H., Schlaitz, A. L., Hao, T., Milstein, S., Fan, C. & 17 others, Tipsword, M., Drew, K., Galli, M., Rhrissorrakrai, K., Drechsel, D., Koller, D., Roth, F. P., Iakoucheva, L. M., Dunker, A., Bonneau, R., Gunsalus, K. C., Hill, D. E., Piano, F., Tavernier, J., van den Heuvel, S., Hyman, A. A. & Vidal, M., Aug 8 2008, In : Cell. 134, 3, p. 534-545 12 p.

Research output: Contribution to journalArticle

Embryonic Development
Proteins
Biological Phenomena
Centrosome
Proteome
19 Citations (Scopus)

Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks

Zhang, W., Dunker, A. & Zhou, Y., Apr 2008, In : Proteins: Structure, Function and Genetics. 71, 1, p. 61-67 7 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Benchmarking
Sequence Alignment
Proteins
Electric sparks
50 Citations (Scopus)

Biochemistry: Controlled chaos

Uversky, V. N. & Dunker, A., Nov 28 2008, In : Science. 322, 5906, p. 1340-1341 2 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Biochemistry
348 Citations (Scopus)

Flexible nets: Disorder and induced fit in the associations of p53 and 14-3-3 with their partners

Oldfield, C. J., Meng, J., Yang, J. Y., Qu, M. Q., Uversky, V. N. & Dunker, A., Mar 20 2008, In : BMC Genomics. 9, SUPPL. 1, S1.

Research output: Contribution to journalArticle

Proteins
Sexual Partners
Intrinsically Disordered Proteins
Physiological Phenomena
Protein Interaction Maps
632 Citations (Scopus)

Function and structure of inherently disordered proteins

Dunker, A., Silman, I., Uversky, V. N. & Sussman, J. L., Dec 2008, In : Current Opinion in Structural Biology. 18, 6, p. 756-764 9 p.

Research output: Contribution to journalArticle

Proteins
Sexual Partners
Alternative Splicing
Post Translational Protein Processing
Computational Biology
737 Citations (Scopus)

Intrinsically disordered proteins in human diseases: Introducing the D 2 concept

Uversky, V. N., Oldfield, C. J. & Dunker, A., 2008, In : Annual Review of Biophysics. 37, p. 215-246 32 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteins
Synucleins
Neurodegenerative diseases
Cell signaling
85 Citations (Scopus)

Intrinsic disorder in pathogenic and non-pathogenic microbes: Discovering and analyzing the unfoldomes of early-branching eukaryotes

Mohan, A., Sullivan, W., Radivojac, P., Dunker, A. & Uversky, V. N., 2008, In : Molecular BioSystems. 4, 4, p. 328-340 13 p.

Research output: Contribution to journalArticle

Eukaryota
Proteome
Proteins
Genes
Intrinsically Disordered Proteins
173 Citations (Scopus)

Intrinsic disorder in scaffold proteins: Getting more from less

Cortese, M. S., Uversky, V. N. & Dunker, A., Sep 2008, In : Progress in Biophysics and Molecular Biology. 98, 1, p. 85-106 22 p.

Research output: Contribution to journalArticle

Proteins
Connectin
Glycogen Synthase Kinase 3
Crowding
Aptitude
19 Citations (Scopus)

Investigation of transmembrane proteins using a computational approach

Yang, J. Y., Yang, M. Q., Dunker, A., Deng, Y. & Huang, X., Mar 20 2008, In : BMC Genomics. 9, SUPPL. 1, S7.

Research output: Contribution to journalArticle

Proteins
Decision Trees
Computational Biology
Tertiary Protein Structure
Amino Acid Sequence
72 Citations (Scopus)

Malleable machines in transcription regulation: The Mediator complex

Tóth-Petróczy, Á., Oldfield, C. J., Simon, I., Takagi, Y., Dunker, A., Uversky, V. N. & Fuxreiter, M., Dec 2008, In : PLoS Computational Biology. 4, 12, e1000243.

Research output: Contribution to journalArticle

Mediator Complex
Mediator
Transcription
Yeast
Saccharomyces cerevisiae
35 Citations (Scopus)

Natively Disordered Proteins

Daughdrill, G. W., Pielak, G. J., Uversky, V. N., Cortese, M. S. & Dunker, A., Jan 31 2008, Protein Folding Handbook. Wiley-VCH Verlag GmbH, Vol. 1. p. 275-357 83 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins

Pacific symposium on biocomputing 2008

Altman, R. B., Dunker, A., Hunter, L. & Klein, T. E., 2008, In : Unknown Journal.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Potato virus A genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core

Rantalainen, K. I., Uversky, V. N., Permi, P., Kalkkinen, N., Dunker, A. & Mäkinen, K., Aug 1 2008, In : Virology. 377, 2, p. 280-288 9 p.

Research output: Contribution to journalArticle

Potyvirus
Solanum tuberosum
Genome
Viruses
Trypsin
23 Citations (Scopus)

Protein disorder is positively correlated with gene expression in escherichia coli

Paliy, O., Gargac, S. M., Cheng, Y., Uversky, V. N. & Dunker, A., Jun 2008, In : Journal of Proteome Research. 7, 6, p. 2234-2245 12 p.

Research output: Contribution to journalArticle

Gene expression
Escherichia coli
Gene Expression
RNA
Proteins
22 Citations (Scopus)

Protein intrinsic disorder toolbox for comparative analysis of viral proteins

Goh, G. K. M., Dunker, A. & Uversky, V. N., Sep 16 2008, In : BMC Genomics. 9, SUPPL. 2, S4.

Research output: Contribution to journalArticle

Viral Proteins
Human Immunodeficiency Virus Proteins
Proteins
Virion
Human Influenza
41 Citations (Scopus)

Short Linear Motifs recognized by SH2, SH3 and Ser/Thr Kinase domains are conserved in disordered protein regions

Ren, S., Uversky, V. N., Chen, Z., Dunker, A. & Obradovic, Z., Sep 16 2008, In : BMC Genomics. 9, SUPPL. 2, S26.

Research output: Contribution to journalArticle

Phosphotransferases
Proteins
Signal Transduction
Amino Acids
114 Citations (Scopus)

Signal transduction via unstructured protein conduits

Dunker, A. & Uversky, V. N., Apr 2008, In : Nature Chemical Biology. 4, 4, p. 229-230 2 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Signal Transduction
Cell Cycle
Proteins
Phosphorylation
363 Citations (Scopus)

The unfoldomics decade: An update on intrinsically disordered proteins

Dunker, A., Oldfield, C. J., Meng, J., Romero, P., Yang, J. Y., Chen, J. W., Vacic, V., Obradovic, Z. & Uversky, V. N., Sep 16 2008, In : BMC Genomics. 9, SUPPL. 2, S1.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteins
Alternative Splicing
Drug Discovery
Proteome
204 Citations (Scopus)

TOP-IDP-scale: A new amino acid scale measuring propensity for intrinsic disorder

Campen, A., Williams, R. M., Brown, C. J., Meng, J., Uversky, V. N. & Dunker, A., Sep 2008, In : Protein and Peptide Letters. 15, 9, p. 956-963 8 p.

Research output: Contribution to journalArticle

Inosine Diphosphate
Intrinsically Disordered Proteins
Amino Acids
Simulated annealing
Servers
2007
60 Citations (Scopus)

A computational investigation of allostery in the catabolite activator protein

Li, W., Uversky, V. N., Dunker, A. & Meroueh, S., Dec 19 2007, In : Journal of the American Chemical Society. 129, 50, p. 15668-15676 9 p.

Research output: Contribution to journalArticle

Cyclic AMP Receptor Protein
DNA
Proteins
Free energy
Calorimetry
14 Citations (Scopus)

Another Window into Disordered Protein Function

Dunker, A., Sep 11 2007, In : Structure. 15, 9, p. 1026-1028 3 p.

Research output: Contribution to journalArticle

Multiple Personality Disorder
Proteins
300 Citations (Scopus)

Characterization of molecular recognition features, MoRFs, and their binding partners

Vacic, V., Oldfield, C. J., Mohan, A., Radivojac, P., Cortese, M. S., Uversky, V. N. & Dunker, A., Jun 2007, In : Journal of Proteome Research. 6, 6, p. 2351-2366 16 p.

Research output: Contribution to journalArticle

Molecular recognition
Proteins
Proteome
Antigen-Antibody Complex
Hydrogen
194 Citations (Scopus)

Composition Profiler: A tool for discovery and visualization of amino acid composition differences

Vacic, V., Uversky, V. N., Dunker, A. & Lonardi, S., Jun 19 2007, In : BMC Bioinformatics. 8, 211.

Research output: Contribution to journalArticle

Amino Acids
Amino acids
Visualization
Proteins
Protein
578 Citations (Scopus)

DisProt: The database of disordered proteins

Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z. & Dunker, A., Jan 2007, In : Nucleic Acids Research. 35, SUPPL. 1

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Protein Databases
Carrier Proteins
Sexual Partners
Computational Biology
19 Citations (Scopus)

Engineering productive enzyme confinement

Dunker, A. & Fernández, A., May 2007, In : Trends in Biotechnology. 25, 5, p. 189-190 2 p.

Research output: Contribution to journalArticle

Enzymes
Enzyme activity
Silicon Dioxide
Catalyst activity
Tuning
3 Citations (Scopus)

Exploring alternative knowledge representations for protein secondary-structure prediction

Midic, U., Dunker, A. & Obradovic, Z., 2007, In : International Journal of Data Mining and Bioinformatics. 1, 3, p. 286-313 28 p.

Research output: Contribution to journalArticle

Secondary Protein Structure
Knowledge representation
Proteins
contact
360 Citations (Scopus)

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions

Xie, H., Vucetic, S., Iakoucheva, L. M., Oldfield, C. J., Dunker, A., Uversky, V. N. & Obradovic, Z., May 2007, In : Journal of Proteome Research. 6, 5, p. 1882-1898 17 p.

Research output: Contribution to journalArticle

Biological Phenomena
Proteins
Intrinsically Disordered Proteins
Databases
Bioinformatics
186 Citations (Scopus)

Functional anthology of intrinsic disorder. 2. cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions

Vucetic, S., Xie, H., Iakoucheva, L. M., Oldfield, C. J., Dunker, A., Obradovic, Z. & Uversky, V. N., May 2007, In : Journal of Proteome Research. 6, 5, p. 1899-1916 18 p.

Research output: Contribution to journalArticle

Proteins
Intrinsically Disordered Proteins
Biological Phenomena
Proteome
Bioinformatics
263 Citations (Scopus)

Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins

Xie, H., Vucetic, S., Iakoucheva, L. M., Oldfield, C. J., Dunker, A., Obradovic, Z. & Uversky, V. N., May 2007, In : Journal of Proteome Research. 6, 5, p. 1917-1932 16 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Post Translational Protein Processing
Ligands
Proteins
Biological Phenomena
1 Citation (Scopus)

Intrinsically disordered proteins: An update

Dunker, A., Oldfield, C. J., Meng, J., Romero, P., Yang, J. Y., Obradovic, Z. & Uversky, V. N., 2007, Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE. p. 49-58 10 p. 4375544

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

Intrinsically Disordered Proteins
Proteins
Textbooks
Biochemistry
Neural networks
486 Citations (Scopus)

Intrinsic disorder and functional proteomics

Radivojac, P., Iakoucheva, L. M., Oldfield, C. J., Obradovic, Z., Uversky, V. N. & Dunker, A., Mar 2007, In : Biophysical Journal. 92, 5, p. 1439-1456 18 p.

Research output: Contribution to journalArticle

Intrinsically Disordered Proteins
Proteomics
Proteins
Computational Biology
Molecular Biology
97 Citations (Scopus)

Intrinsic disorder in the protein data bank

Le Gall, T., Romero, P. R., Cortese, M. S., Uversky, V. N. & Dunker, A., Feb 2007, In : Journal of Biomolecular Structure and Dynamics. 24, 4, p. 325-341 17 p.

Research output: Contribution to journalArticle

Databases
Proteins
Amino Acids
X Ray Crystallography
Intrinsically Disordered Proteins
199 Citations (Scopus)

Mining α-helix-forming molecular recognition features with cross species sequence alignments

Cheng, Y., Oldfield, C. J., Meng, J., Romero, P., Uversky, V. N. & Dunker, A., Nov 27 2007, In : Biochemistry. 46, 47, p. 13468-13477 10 p.

Research output: Contribution to journalArticle

Molecular recognition
Sequence Alignment
Proteins
Amino Acids
Databases