A. Dunker

  • 31134 Citations
  • 84 h-Index
1969 …2020

Research output per year

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Publications

2010

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites

Gao, J., Thelen, J. J., Dunker, A. K. & Xu, D., Dec 1 2010, In : Molecular and Cellular Proteomics. 9, 12, p. 2586-2600 15 p.

Research output: Contribution to journalArticle

163 Scopus citations

N-terminal domains of DELLA proteins are intrinsically unstructured in the absence of interaction with GID1/gibberellic acid receptors

Sun, X., Jones, W. T., Harvey, D., Edwards, P. J. B., Pascal, S. M., Kirk, C., Considine, T., Sheerin, D. J., Rakonjac, J., Oldfield, C. J., Xue, B., Dunker, A. K. & Uversky, V. N., Apr 9 2010, In : Journal of Biological Chemistry. 285, 15, p. 11557-11571 15 p.

Research output: Contribution to journalArticle

48 Scopus citations

Pacific symposium on biocomputing 2010

Altman, R. B., Dunker, A. K., Hunter, L. & Klein, T. E., Dec 1 2010, In : Pacific Symposium on Biocomputing 2010, PSB 2010. p. v-vii

Research output: Contribution to journalEditorial

PONDR-FIT: A meta-predictor of intrinsically disordered amino acids

Xue, B., Dunbrack, R. L., Williams, R. W., Dunker, A. K. & Uversky, V. N., Apr 1 2010, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1804, 4, p. 996-1010 15 p.

Research output: Contribution to journalArticle

584 Scopus citations

Preface

Longhi, S., Dunker, A. & Uversky, V. N., Sep 9 2010, In : Unknown Journal.

Research output: Contribution to journalArticle

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

Xue, B., Dunker, A. K. & Uversky, V. N., Oct 1 2010, In : International journal of molecular sciences. 11, 10, p. 3725-3747 23 p.

Research output: Contribution to journalArticle

29 Scopus citations

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

Xue, B., Hsu, W. L., Lee, J. H., Lu, H., Dunker, A. K. & Uversky, V. N., Jun 1 2010, In : Genes to Cells. 15, 6, p. 635-646 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

Understanding protein non-folding

Uversky, V. N. & Dunker, A. K., Jun 1 2010, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1804, 6, p. 1231-1264 34 p.

Research output: Contribution to journalReview article

762 Scopus citations

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. K. & Uversky, V. N., Oct 26 2010, In : Protein and Peptide Letters. 17, 8, p. 932-951 20 p.

Research output: Contribution to journalReview article

72 Scopus citations
2009

Analysis of structured and intrinsically disordered regions of transmembrane proteins

Xue, B., Li, L., Meroueh, S. O., Uversky, V. N. & Dunker, A. K., Dec 1 2009, In : Molecular BioSystems. 5, 12, p. 1688-1702 15 p.

Research output: Contribution to journalArticle

46 Scopus citations

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

Gao, J., Agrawal, G. K., Thelen, J. J., Obradovic, Z., Dunker, A. K. & Xu, D., Aug 11 2009, Bioinformatics and Computational Biology - First International Conference, BICoB 2009, Proceedings. 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

17 Scopus citations

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

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

Research output: Contribution to journalArticle

94 Scopus citations

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

Tompa, P., Fuxreiter, M., Oldfield, C. J., Simon, I., Dunker, A. K. & Uversky, V. N., Apr 27 2009, In : BioEssays. 31, 3, p. 328-335 8 p.

Research output: Contribution to journalArticle

178 Scopus citations

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. K. & Meroueh, S. O., Jan 20 2009, In : Biochemistry. 48, 2, p. 399-414 16 p.

Research output: Contribution to journalArticle

43 Scopus citations

Intrinsically disordered proteins and their recognition functions

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

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

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

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

Research output: Contribution to journalArticle

115 Scopus citations

Pacific symposium on biocomputing 2009

Altman, R. B., Dunker, A. K., Hunter, L. & Klein, T. E., Dec 1 2009, In : Pacific Symposium on Biocomputing 2009, PSB 2009. p. v-vi

Research output: Contribution to journalEditorial

Predicting intrinsic disorder in proteins: An overview

He, B., Wang, K., Liu, Y., Xue, B., Uversky, V. N. & Dunker, A. K., Aug 1 2009, In : Cell Research. 19, 8, p. 929-949 21 p.

Research output: Contribution to journalReview article

285 Scopus citations

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

Goh, G. K. M., Dunker, A. K. & Uversky, V. N., Aug 10 2009, In : Virology Journal. 6, 69.

Research output: Contribution to journalArticle

49 Scopus citations

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

Midic, U., Dunker, A. K. & Obradovic, Z., Nov 9 2009, Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09. p. 27-31 5 p. (Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics, StReBio '09).

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

5 Scopus citations

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

Midic, U., Oldfield, C. J., Dunker, A. K., Obradovic, Z. & Uversky, V. N., Dec 1 2009, In : Protein and Peptide Letters. 16, 12, p. 1533-1547 15 p.

Research output: Contribution to journalArticle

46 Scopus citations
2008

A comparative analysis of viral matrix proteins using disorder predictors

Goh, G. K. M., Dunker, A. K. & Uversky, V. N., Nov 10 2008, In : Virology Journal. 5, 126.

Research output: Contribution to journalArticle

41 Scopus citations

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. K., 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

143 Scopus citations

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

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

Research output: Contribution to journalArticle

21 Scopus citations

Biochemistry: Controlled chaos

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

Research output: Contribution to journalShort survey

54 Scopus citations

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. K., Mar 20 2008, In : BMC genomics. 9, SUPPL. 1, S1.

Research output: Contribution to journalArticle

375 Scopus citations

Function and structure of inherently disordered proteins

Dunker, A. K., Silman, I., Uversky, V. N. & Sussman, J. L., Dec 1 2008, In : Current Opinion in Structural Biology. 18, 6, p. 756-764 9 p.

Research output: Contribution to journalReview article

669 Scopus citations

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

823 Scopus citations

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

Mohan, A., Sullivan, W. J., Radivojac, P., Dunker, A. K. & Uversky, V. N., Mar 28 2008, In : Molecular BioSystems. 4, 4, p. 328-340 13 p.

Research output: Contribution to journalArticle

91 Scopus citations

Intrinsic disorder in scaffold proteins: Getting more from less

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

Research output: Contribution to journalReview article

183 Scopus citations

Investigation of transmembrane proteins using a computational approach

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

Research output: Contribution to journalArticle

20 Scopus citations

Malleable machines in transcription regulation: The Mediator complex

Tóth-Petróczy, Á., Oldfield, C. J., Simon, I., Takagi, Y., Dunker, A. K., Uversky, V. N. & Fuxreiter, M., Dec 1 2008, In : PLoS Computational Biology. 4, 12, e1000243.

Research output: Contribution to journalArticle

76 Scopus citations

Natively Disordered Proteins

Daughdrill, G. W., Pielak, G. J., Uversky, V. N., Cortese, M. S. & Dunker, A. K., 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

38 Scopus citations

Pacific symposium on biocomputing 2008

Altman, R. B., Dunker, A. K., Hunter, L. & Klein, T. E., Dec 1 2008, In : Pacific Symposium on Biocomputing 2008, PSB 2008. p. v-vi

Research output: Contribution to journalEditorial

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. K. & Mäkinen, K., Aug 1 2008, In : Virology. 377, 2, p. 280-288 9 p.

Research output: Contribution to journalArticle

51 Scopus citations

Protein disorder is positively correlated with gene expression in escherichia coli

Paliy, O., Gargac, S. M., Cheng, Y., Uversky, V. N. & Dunker, A., Jun 1 2008, In : Journal of Proteome Research. 7, 6, p. 2234-2245 12 p.

Research output: Contribution to journalArticle

23 Scopus citations

Protein intrinsic disorder toolbox for comparative analysis of viral proteins

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

Research output: Contribution to journalArticle

28 Scopus citations

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. K. & Obradovic, Z., Sep 16 2008, In : BMC genomics. 9, SUPPL. 2, S26.

Research output: Contribution to journalArticle

43 Scopus citations

Signal transduction via unstructured protein conduits

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

Research output: Contribution to journalShort survey

118 Scopus citations

The unfoldomics decade: An update on intrinsically disordered proteins

Dunker, A. K., 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

375 Scopus citations

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. K., Sep 1 2008, In : Protein and Peptide Letters. 15, 9, p. 956-963 8 p.

Research output: Contribution to journalArticle

216 Scopus citations
2007

A computational investigation of allostery in the catabolite activator protein

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

Research output: Contribution to journalArticle

60 Scopus citations

Another Window into Disordered Protein Function

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

Research output: Contribution to journalShort survey

14 Scopus citations

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. K., Jun 1 2007, In : Journal of Proteome Research. 6, 6, p. 2351-2366 16 p.

Research output: Contribution to journalArticle

318 Scopus citations

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

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

Research output: Contribution to journalArticle

208 Scopus citations

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. K., Jan 1 2007, In : Nucleic acids research. 35, SUPPL. 1, p. D786-D793

Research output: Contribution to journalArticle

595 Scopus citations

Engineering productive enzyme confinement

Dunker, A. K. & Fernández, A., May 1 2007, In : Trends in Biotechnology. 25, 5, p. 189-190 2 p.

Research output: Contribution to journalShort survey

19 Scopus citations

Exploring alternative knowledge representations for protein secondary-structure prediction

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

Research output: Contribution to journalArticle

4 Scopus citations

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. K., Uversky, V. N. & Obradovic, Z., May 1 2007, In : Journal of Proteome Research. 6, 5, p. 1882-1898 17 p.

Research output: Contribution to journalArticle

382 Scopus citations

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. K., Obradovic, Z. & Uversky, V. N., May 1 2007, In : Journal of Proteome Research. 6, 5, p. 1899-1916 18 p.

Research output: Contribution to journalArticle

188 Scopus citations