The importance of intrinsic disorder for protein phosphorylation
Open accessAbstract
Reversible protein phosphorylation provides a major regulatory mechanism in eukaryotic cells. Due to the high variability of amino acid residues flanking a relatively limited number of experimentally identified phosphorylation sites, reliable prediction of such sites still remains an important issue. Here we report the development of a new web-based tool for the prediction of protein phosphorylation sites, DISPHOS (DISorder-enhanced PHOSphorylation predictor, http://www.ist.temple. edu/DISPHOS). We observed that amino acid compositions, sequence complexity, hydrophobicity, charge and other sequence attributes of regions adjacent to phosphorylation sites are very similar to those of intrinsically disordered protein regions. Thus, DISPHOS uses position-specific amino acid frequencies and disorder information to improve the discrimination between phosphorylation and non-phosphorylation sites. Based on the estimates of phosphorylation rates in various protein categories, the outputs of DISPHOS are adjusted in order to reduce the total number of misclassified residues. When tested on an equal number of phosphorylated and non-phosphorylated residues, the accuracy of DISPHOS reaches 76% for serine, 81% for threonine and 83% for tyrosine. The significant enrichment in disorder-promoting residues surrounding phosphorylation sites together with the results obtained by applying DISPHOS to various protein functional classes and proteomes, provide strong support for the hypothesis that protein phosphorylation predominantly occurs within intrinsically disordered protein regions.
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Most protein phosphorylation occurs in IDRs.
“Indeed, most protein phosphorylation occur in IDRs [41].”
From Intrinsically disordered proteins play diverse roles in cell signaling (2022) · cites this paper as [41]
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Cites
An Introduction to the Bootstrap
Efron, B., & Tibshirani, R. J. (1994) · doi:10.1201/9780429246593 · Cited by 40,500 · see citing works
Neural Networks: A Comprehensive Foundation
Haykin, S. (1998) · Cited by 30,070 · see citing works
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970 · see citing works
Neural networks for pattern recognition
Bishop, C. (1994) · Choice Reviews Online · doi:10.5860/choice.31-5500 · Cited by 18,537 · see citing works
The Elements of Statistical Learning: Data Mining, Inference, and Prediction
Lu, Z. Q. J. (2010) · Journal of the Royal Statistical Society Series A (Statistics in Society) · doi:10.1111/j.1467-985x.2010.00646_6.x · Cited by 12,904 · see citing works
Neural Networks for Pattern Recognition
Bishop, C. M. (1995) · doi:10.1093/oso/9780198538493.001.0001 · Cited by 12,287 · see citing works
The protein kinase complement of the human genome
Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002) · Science · doi:10.1126/science.1075762 · Cited by 8,145 · see citing works
Regression Diagnostics: Identifying Influential Data and Sources of Collinearity
Belsley, D. A., Kuh, E., & Welsch, R. E. (1980) · Wiley Series in Probability and Statistics · doi:10.1002/0471725153 · Cited by 7,297 · see citing works
Sequence and structure-based prediction of eukaryotic protein phosphorylation sites
Blom, N., Gammeltoft, S., & Brunak, S. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3310 · Cited by 3,197 · see citing works
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
Wright, P. E., & Dyson, H. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3110 · Cited by 2,968 · see citing works
Addressing the Curse of Imbalanced Training Sets: One-Sided Selection.
Kubát, M., & Matwin, S. (1997) · Cited by 2,161 · see citing works
Satisfying Hydrogen Bonding Potential in Proteins
McDonald, I. K., & Thornton, J. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1334 · Cited by 2,136 · see citing works
Twilight zone of protein sequence alignments
Rost, B. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.2.85 · Cited by 1,833 · see citing works
Intrinsic Disorder and Protein Function
Dunker, A. K., Brown, C. J., Lawson, J. D., Iakoucheva, L. M., & Obradović, Z. (2002) · Biochemistry · doi:10.1021/bi012159+ · Cited by 1,731 · see citing works
Self-citationPEST sequences and regulation by proteolysis
RECHSTEINER, M. C., & Rogers, S. W. (1996) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(96)10031-1 · Cited by 1,645 · see citing works
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
Obenauer, J. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg584 · Cited by 1,602 · see citing works
Coupling of folding and binding for unstructured proteins
Dyson, H. J., & Wright, P. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00289-0 · Cited by 1,327 · see citing works
(1976) · IEEE Transactions on Systems Man and Cybernetics · doi:10.1109/tsmc.1976.4309452 · Cited by 1,295 · see citing works
Machine Learning for the Detection of Oil Spills in Satellite Radar Images
Kubát, M., Holte, R. C., & Matwin, S. (1998) · Machine Learning · doi:10.1023/a:1007452223027 · Cited by 1,255 · see citing works
An Introduction to the Bootstrap.
Kimber, A., Efron, B., & Tibshirani, R. J. (1994) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.2307/2348146 · Cited by 1,246 · see citing works
Predicting the secondary structure of globular proteins using neural network models
Ning Qian, A., & B, T. J. S. A. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90564-5 · Cited by 1,226 · see citing works
Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins
Iakoucheva, L. M., Brown, C. J., Lawson, J. D., Obradović, Z., & Dunker, A. K. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00969-5 · Cited by 1,214 · see citing works
Self-citationThe PROSITE database, its status in 2002
Falquet, L. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.235 · Cited by 1,001 · see citing works
THREE-DIMENSIONAL STRUCTURE OF MEMBRANE AND SURFACE PROTEINS
Eisenberg, D. (1984) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.53.070184.003115 · Cited by 968 · see citing works
Hubbard, S. R. (1997) · The EMBO Journal · doi:10.1093/emboj/16.18.5572 · Cited by 954 · see citing works
The hydrophobic moment detects periodicity in protein hydrophobicity.
Eisenberg, D. S., Weiss, R. M., & Terwilliger, T. C. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.1.140 · Cited by 895 · see citing works
Statistics of local complexity in amino acid sequences and sequence databases
Wootton, J. C., & Federhen, S. (1993) · Computers & Chemistry · doi:10.1016/0097-8485(93)85006-x · Cited by 721 · see citing works
A systematic approach to the analysis of protein phosphorylation
Zhou, H., Watts, J. D., & Aebersold, R. H. (2001) · Nature Biotechnology · doi:10.1038/86777 · Cited by 714 · see citing works
Surface and inside volumes in globular proteins
Janin, J. (1979) · Nature · doi:10.1038/277491a0 · Cited by 714 · see citing works
Use of an oriented peptide library to determine the optimal substrates of protein kinases
Songyang, Z., Blechner, S., Hoagland, N., Hoekstra, M. F., Piwnica-Worms, H. M., & Cantley, L. C. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00221-9 · Cited by 654 · see citing works
Structural Basis for Control by Phosphorylation
Johnson, L. N., & Lewis, R. J. (2001) · Chemical Reviews · doi:10.1021/cr000225s · Cited by 643 · see citing works
Kriwacki, R. W., Hengst, L., Tennant, L. L., Reed, S. I., & Wright, P. E. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11504 · Cited by 576 · see citing works
PHD-an automatic mail server for protein secondary structure prediction
Rost, B., Sander, C., & Schneider, R. (1994) · Computer applications in the biosciences · doi:10.1093/bioinformatics/10.1.53 · Cited by 560 · see citing works
A motif-based profile scanning approach for genome-wide prediction of signaling pathways
Yaffe, M. B., Leparc, G. G., Lai, J., Obata, T., Volinia, S., & Cantley, L. C. (2001) · Nature Biotechnology · doi:10.1038/86737 · Cited by 517 · see citing works
Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure
Sweet, R. M., & Eisenberg, D. S. (1983) · Journal of Molecular Biology · doi:10.1016/0022-2836(83)90041-4 · Cited by 400 · see citing works
Structure of GSK3beta reveals a primed phosphorylation mechanism.
ter Haar, E., Coll, J. T., Austen, D. A., Hsiao, H.-M., Swenson, L. L., & Jain, J. (2001) · Nature Structural Biology · doi:10.1038/89624 · Cited by 394 · see citing works
Bossemeyer, D., Engh, R. A., Kinzel, V., Ponstingl, H., & Huber, R. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb05725.x · Cited by 389 · see citing works
Vučetić, S., Brown, C. J., Dunker, A. K., & Zoran Obradovic, A. (2003) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10437 · Cited by 381 · see citing works
Recognition and specificity in protein tyrosine kinase-mediated signalling
Songyang, Z., & Cantley, L. C. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89103-3 · Cited by 370 · see citing works
Adjusting the Outputs of a Classifier to New a <i>Priori</i> Probabilities: A Simple Procedure
Saerens, M., Latinne, P., & Decaestecker, C. (2002) · Neural Computation · doi:10.1162/089976602753284446 · Cited by 361 · cited 1× · see citing works
“Predictors trained using a specific class distribution are known not to be optimal when applied to unlabeled data with different class priors ( 37 ).”
Protein flexibility and intrinsic disorder
Predrag Radivojac, A., Zoran Obradovic, A., Smith, D. K., Zhu, G., Vučetić, S., Brown, C. J., Lawson, J. D., & Dunker, A. K. (2003) · Protein Science · doi:10.1110/ps.03128904 · Cited by 341 · see citing works
Protein-protein interfaces: Analysis of amino acid conservation in homodimers
Valdar, W. S. J., & Thornton, J. M. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20010101)42:1 · Cited by 322 · see citing works
Leonard, C. J., Aravind, L., & Koonin, E. V. (1998) · Genome Research · doi:10.1101/gr.8.10.1038 · Cited by 318 · see citing works
Accuracy of protein flexibility predictions
Vihinen, M., Torkkila, E., & Riikonen, P. T. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340190207 · Cited by 312 · see citing works
Salamov, A. A., & Solovyev, V. V. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0116 · Cited by 299 · see citing works
PEST sequences and regulation by proteolysis
RECHSTEINER, M. C. (1996) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(96)10031-1 · Cited by 232 · see citing works
Protein histidine kinases and signal tranduction in prokaryotes and eukaryotes
Alex, L. A., & Simon, M. I. (1994) · Trends in Genetics · doi:10.1016/0168-9525(94)90215-1 · Cited by 231 · see citing works
Modeling studies of the change in conformation required for cleavage of limited proteolytic sites
Hubbard, S. J., Eisenmenger, F., & Thornton, J. M. (1994) · Protein Science · doi:10.1002/pro.5560030505 · Cited by 205 · see citing works
Lowe, E. D., Noble, M. E. M., Skamnaki, V. T., Oikonomakos, N. G., Owen, D. J., & Johnson, L. N. (1997) · The EMBO Journal · doi:10.1093/emboj/16.22.6646 · Cited by 200 · see citing works
Probing the conformational state of apomyoglobin by limited proteolysis 1 1Edited by P. E. Wright
Fontana, A., Zambonin, M., de Laureto, P. P., Filippis, V. D., Clementi, A., & Scaramella, E. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0787 · Cited by 194 · see citing works
The apoptotic v-cyclin–CDK6 complex phosphorylates and inactivates Bcl-2
Ojala, P. M., Yamamoto, K., Castaños‐Vélez, E., Biberfeld, P., Korsmeyer, S. J., & Mäkelä, T. P. (2000) · Nature Cell Biology · doi:10.1038/35041064 · Cited by 174 · see citing works
Zor, T., Mayr, B. M., Dyson, H. J., Montminy, M., & Wright, P. E. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207361200 · Cited by 169 · see citing works
Bienkiewicz, E. A., Adkins, J., & Lumb, K. J. (2001) · Biochemistry · doi:10.1021/bi015763t · Cited by 143 · see citing works
Protein secondary structure prediction using local alignments
Salamov, A. A., & Solovyev, V. V. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0958 · Cited by 127 · see citing works
Narayana, N., Cox, S. E., Shaltiel, S., Taylor, S. S., & Xuong, N. (1997) · Biochemistry · doi:10.1021/bi961947+ · Cited by 110 · see citing works
Feng, J., Zhu, M., SCHAUB, M. C., Gehrig, P., Roschitzki, B., Lucchinetti, E., Zaugg, M., & Nucleotide, A. (1996) · Wiley eBooks · doi:10.1002/9783527615032 · Cited by 106 · see citing works
Schulz, G. E. (1979) · MPG.PuRe (Max Planck Society) · Cited by 80 · see citing works
Folding minimal sequences: the lower bound for sequence complexity of globular proteins
Romero, P. R., Obradović, Z., & Dunker, A. K. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)01557-4 · Cited by 75 · see citing works
PREDICTION OF BOUNDARIES BETWEEN INTRINSICALLY ORDERED AND DISORDERED PROTEIN REGIONS
Radivojac, P., Obradović, Z., Brown, C. J., et al. (2002) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812776303_0021 · Cited by 70 · see citing works
The Sequence Attribute Method for Determining Relationships Between Sequence and Protein Disorder.
Xie, Q., Arnold, Romero, P. R., Zoran Obradovic, A., Garner, E. C., & Dunker, K. (1998) · PubMed · Cited by 64 · see citing works
Hay, T., & Meek, D. W. (2000) · FEBS Letters · doi:10.1016/s0014-5793(00)01850-0 · Cited by 61 · see citing works
Molecular Aspects of Proteolysis of Globular Proteins
Fontana, A., de Laureto, P. P., & Filippis, V. D. (1993) · Studies in organic chemistry · doi:10.1016/b978-0-444-89372-7.50017-8 · Cited by 60 · see citing works
The substrates of the cdc2 kinase.
Nigg, E. A. (1991) · PubMed · Cited by 49 · see citing works
Classification on Data with Biased Class Distribution
Vučetić, S., & Obradović, Z. (2001) · Lecture notes in computer science · doi:10.1007/3-540-44795-4_45 · Cited by 48 · see citing works
Three-Dimensional Structure of Membrane and Surface Proteins
Eisenberg, D. (1984) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.53.1.595 · Cited by 33 · see citing works
Binding-Dependent Disorder−Order Transition in PKIα: A Fluorescence Anisotropy Study
Hauer, J. A., Taylor, S. S., & Johnson, D. A. (1999) · Biochemistry · doi:10.1021/bi983074k · Cited by 27 · see citing works
Designing specific protein kinase inhibitors:
Gould, C. M., & Wong, C. F. (2002) · Pharmacology & Therapeutics · doi:10.1016/s0163-7258(02)00186-9 · Cited by 21 · see citing works
Tyrosine protein kinases and their substrates: an overview.
Hunter, T., & Cooper, J. A. (1984) · PubMed · Cited by 20 · see citing works
Vetter, S. W., & Leclerc, E. (2001) · European Journal of Biochemistry · doi:10.1046/j.1432-1327.2001.02347.x · Cited by 16 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- Belsley,D.A., Kuh,E. and Welsch,R.E. (1980) Regression Diagnostics. John Wiley and Sons, New York.
- Tomek,I. (1976) Two modi®cations of CNN. IEEE Trans. Syst. Man Cybern., 6, 769±772.
- Morgan Kaufmann, San Francisco, CA, pp. 179±186.
Cited by
Sorted by citations
Intrinsically unstructured proteins and their functions
Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871 · see citing works
Substrate and Functional Diversity of Lysine Acetylation Revealed by a Proteomics Survey
Kim, S. C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., et al. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.026 · Cited by 1,487 · see citing works
The growing landscape of lysine acetylation links metabolism and cell signalling
Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., & Mann, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3841 · Cited by 1,324 · see citing works
D2P2: database of disordered protein predictions
Oates, M. E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M. J., Xue, B., Dosztányi, Z., Uversky, V. N., Obradovic, Z., Kurgan, L., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1226 · Cited by 705 · see citing works
The interplay between structure and function in intrinsically unstructured proteins
Tompa, P. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.03.072 · Cited by 717 · see citing works
Tight Regulation of Unstructured Proteins: From Transcript Synthesis to Protein Degradation
Gsponer, J., Futschik, M. E., Teichmann, S. A., & Babu, M. M. (2008) · Science · doi:10.1126/science.1163581 · Cited by 466 · see citing works
Pejaver, V., Hsu, W., Xin, F., Dunker, A. K., Uversky, V. N., & Radivojac, P. (2014) · Protein Science · doi:10.1002/pro.2494 · Cited by 349 · see citing works
Disorder and Sequence Repeats in Hub Proteins and Their Implications for Network Evolution
Dosztányi, Z., Chen, J., Dunker, A. K., Simon, I., & Tompa, P. (2006) · Journal of Proteome Research · doi:10.1021/pr060171o · Cited by 341 · see citing works
Minezaki, Y., Homma, K., Kinjo, A. R., & Nishikawa, K. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.04.016 · Cited by 297 · see citing works
Pathological Unfoldomics of Uncontrolled Chaos: Intrinsically Disordered Proteins and Human Diseases
Uversky, V. N., Davé, V., Iakoucheva, L. M., Malaney, P., Metallo, S. J., Pathak, R. R., & Joerger, A. C. (2014) · Chemical Reviews · doi:10.1021/cr400713r · Cited by 288 · see citing works
Self-citationMechanism of adrenergic CaV1.2 stimulation revealed by proximity proteomics
Liu, G., Papa, A., Katchman, A. N., Zakharov, S. I., Roybal, D., Hennessey, J. A., Kushner, J., Yang, L., Chen, B.-X., Kushnir, A., et al. (2020) · Nature · doi:10.1038/s41586-020-1947-z · Cited by 243 · see citing works
Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity
Borg, M., Mittag, T., Pawson, T., Tyers, M., Forman-Kay, J. D., & Chan, H. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702580104 · Cited by 245 · see citing works
Fuzzy Complexes: A More Stochastic View of Protein Function
Fuxreiter, M., & Tompa, P. (2012) · Advances in Experimental Medicine and Biology · doi:10.1007/978-1-4614-0659-4_1 · Cited by 240 · see citing works
Intrinsically disordered proteins play diverse roles in cell signaling
Bondos, S. E., Dunker, A. K., & Uversky, V. N. (2022) · Cell Communication and Signaling · doi:10.1186/s12964-022-00821-7 · Cited by 222 · see citing works
Dynamic protein–DNA recognition: beyond what can be seen
Fuxreiter, M., Simon, I., & Bondos, S. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.04.006 · Cited by 167 · see citing works
Interactions by disorder – A matter of context
Bugge, K., Brakti, I., Fernandes, C. B., Dreier, J. E., Lundsgaard, J. E., Olsen, J. G., Skriver, K., & Kragelund, B. B. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00110 · Cited by 155 · see citing works
Intrinsically disordered proteins and multicellular organisms
Dunker, A. K., Bondos, S. E., Huang, F., & Oldfield, C. J. (2015) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2014.09.025 · Cited by 150 · see citing works
Allosteric Modulators of Steroid Hormone Receptors: Structural Dynamics and Gene Regulation
Kumar, R., & McEwan, I. J. (2012) · Endocrine Reviews · doi:10.1210/er.2011-1033 · Cited by 135 · see citing works
Sigalov, A. B., Zhuravleva, A. V., & Orekhov, V. Y. (2007) · Biochimie · doi:10.1016/j.biochi.2006.11.003 · Cited by 128 · see citing works
A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy
Hu, G., McQuiston, T., Bernard, A., Park, Y.-D., Qiu, J., Vural, A., Zhang, N., Waterman, S. R., Blewett, N. H., Myers, T. G., et al. (2015) · Nature Cell Biology · doi:10.1038/ncb3189 · Cited by 116 · see citing works
Why do eukaryotic proteins contain more intrinsically disordered regions?
Basile, W., Salvatore, M., Bassot, C., & Elofsson, A. (2019) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1007186 · Cited by 113 · see citing works
DDIT4 promotes gastric cancer proliferation and tumorigenesis through the p53 and MAPK pathways
Du, F., Sun, L., Chu, Y., Li, T., Lei, C., Wang, X., Jiang, M., Min, Y., Lu, Y., Zhao, X., et al. (2018) · Cancer Communications · doi:10.1186/s40880-018-0315-y · Cited by 103 · see citing works
Fonin, A. V., Darling, A. L., Kuznetsova, I. M., Turoverov, K. K., & Uversky, V. N. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03276-1 · Cited by 91 · see citing works
Zhou, J., Zhao, S., & Dunker, A. K. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.03.028 · Cited by 90 · see citing works
Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling?
Cornish, J., Chamberlain, S. G., Owen, D., & Mott, H. R. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200467 · Cited by 69 · see citing works
Lee, G. M., Pufall, M. A., Meeker, C. A., Kang, H.-S., Graves, B. J., & McIntosh, L. P. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.07.064 · Cited by 58 · see citing works
Protein intrinsic disorder and oligomericity in cell signaling
Sigalov, A. B. (2009) · Molecular BioSystems · doi:10.1039/b916030m · Cited by 51 · see citing works
Warnet, X. L., Bakke Krog, H., Sevillano‐Quispe, O. G., Poulsen, H., & Kjaergaard, M. (2021) · European Journal of Neuroscience · doi:10.1111/ejn.14842 · Cited by 50 · see citing works
Stochastic machines as a colocalization mechanism for scaffold protein function
Xue, B., Romero, P. R., Noutsou, M., Maurice, M. M., Rüdiger, S. G. D., William, A. M., Mizianty, M. J., Kurgan, L., Uversky, V. N., & Dunker, A. K. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.04.006 · Cited by 47 · see citing works
The roles of MDM2 and MDMX phosphorylation in stress signaling to p53
Chen, J. (2012) · Genes & Cancer · doi:10.1177/1947601912454733 · Cited by 33 · see citing works
A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation
Valverde, J. M., Dubra, G., Phillips, M., Haider, A., Elena-Real, C., Fournet, A., Alghoul, E., Chahar, D., Andrés-Sanchez, N., Paloni, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42049-0 · Cited by 33 · see citing works
Presence and utility of intrinsically disordered regions in kinases
Kathiriya, J. J., Pathak, R. R., Clayman, E., Xue, B., Uversky, V. N., & Davé, V. (2014) · Molecular BioSystems · doi:10.1039/c4mb00224e · Cited by 30 · see citing works
Sigalov, A. B., & Uversky, V. N. (2011) · Self/Nonself · doi:10.4161/self.2.1.14790 · Cited by 23 · see citing works
Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2
Gulsevin, A., Han, B., Porta, J. C., Mchaourab, H. S., Meiler, J., & Kenworthy, A. K. (2023) · Biophysical Journal · doi:10.1016/j.bpj.2022.11.011 · Cited by 16 · see citing works
Hoermann, B., & Köhn, M. (2021) · Biochemical Society Transactions · doi:10.1042/bst20200175 · Cited by 14 · see citing works
- Authors
- Iakoucheva, L. M.
- Affiliations
- Washington State University (US)
- Corresponding author
- Iakoucheva, L. M.
- ORCID
- Iakoucheva, L. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-02-13
- Volume
- 32
- Issue
- 3
- Pages
- 1037-1049
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC373391
- OpenAlex
- W2102025585
- Cited by
- 1,429
- References
- 69
- Citations by year
- 2026: 34 · 2025: 44 · 2024: 53 · 2023: 42 · 2022: 60 · 2021: 71 · 2020: 68 · 2019: 83 · 2018: 77 · 2017: 69 · 2016: 91 · 2015: 90 · 2014: 93 · 2013: 83 · 2012: 88
- FWCI
- 14.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (0196237, 9711532)
- Temple University
- National Institutes of Health
- U.S. National Library of Medicine (1R01 LM07688, R01LM007688)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Tyrosine Phosphatases
- Keywords
- protein phosphorylation, intrinsically disordered proteins, phosphorylation site prediction, sequence complexity, hydrophobicity, protein regulation
- MeSH terms
- Amino Acids, Animals, Phosphorylation, Proteins, Reproducibility of Results, Internet, Sequence Analysis, Protein, Proteome, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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