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Length-dependent prediction of protein intrinsic disorder

Kang Peng, Predrag Radivojac, Slobodan Vucetic, A Keith Dunker, Zoran Obradovic
2006 BMC Bioinformatics  
We proposed two new predictor models, VSL2-M1 and VSL2-M2, to address this length-dependency problem in prediction of intrinsic protein disorder.  ...  Due to the functional importance of intrinsically disordered proteins or protein regions, prediction of intrinsic protein disorder from amino acid sequence has become an area of active research as witnessed  ...  Vladimir Uversky for very helpful discussion regarding the distinction between pre-molten globule and random-coil like disorder.  ... 
doi:10.1186/1471-2105-7-208 pmid:16618368 pmcid:PMC1479845 fatcat:3vey66evznd7nia3xv4xk4s3ae

Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies

Jennifer Atkins, Samuel Boateng, Thomas Sorensen, Liam McGuffin
2015 International Journal of Molecular Sciences  
The role and function of a given protein is dependent on its structure.  ...  As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein.  ...  Dependent upon the composition of the training set, the prediction accuracy for different length regions may be variable.  ... 
doi:10.3390/ijms160819040 pmid:26287166 pmcid:PMC4581285 fatcat:jwo5tfhj6zchdocl5dqn7ef6uu

Utilization of protein intrinsic disorder knowledge in structural proteomics

Christopher J. Oldfield, Bin Xue, Ya-Yue Van, Eldon L. Ulrich, John L. Markley, A. Keith Dunker, Vladimir N. Uversky
2013 Biochimica et Biophysica Acta - Proteins and Proteomics  
Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder.  ...  For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination.  ...  V.N.U.), and the Program of the Russian Academy of Sciences for the "Molecular and Cellular Biology" (to V.N.U.).  ... 
doi:10.1016/j.bbapap.2012.12.003 pmid:23232152 pmcid:PMC3951342 fatcat:m6wicgo3dzb57b6hjb6vnu2htq

NeProc predicts binding segments in intrinsically disordered regions without learning binding region sequences

Hiroto Anbo, Hiroki Amagai, Satoshi Fukuchi
2020 Biophysics and Physicobiology  
Intrinsically disordered proteins are those proteins with intrinsically disordered regions.  ...  One of the unique characteristics of intrinsically disordered proteins is the existence of functional segments in intrinsically dis-ordered regions.  ...  IUPred2A: context-dependent prediction of protein 4 disorder as a function of redox state and protein binding.  ... 
doi:10.2142/biophysico.bsj-2020026 pmid:33304713 pmcid:PMC7692026 fatcat:5cagc7eqnzgzri5omn7h5hwwjy

High GC content causes orphan proteins to be intrinsically disordered

Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson, Roland L. Dunbrack
2017 PLoS Computational Biology  
GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins.  ...  We find that, with the exception of length, there are only small differences in the properties between proteins of different ages.  ...  Predicted properties of proteins Intrinsic disorder content was predicted for all the proteins by using several disorder predictors; short and long disorder predictions by IUPred [24] , three type of  ... 
doi:10.1371/journal.pcbi.1005375 pmid:28355220 pmcid:PMC5389847 fatcat:qjdmwahr4vbullitmqigk3jwwu

Molecular recognition features (MoRFs) in three domains of life

Jing Yan, A. Keith Dunker, Vladimir N. Uversky, Lukasz Kurgan
2016 Molecular Biosystems  
MoRFs are widespread intrinsically disordered protein-binding regions that have similar abundance and amino acid composition across the three domains of life.  ...  Content of MoRF and disordered residues MoRF content Disorder content  ...  The amount of predicted disorder in the bacterial and archaean proteins decreases as protein length increases and reaches a plateau for proteins longer than about 300 residues.  ... 
doi:10.1039/c5mb00640f pmid:26651072 fatcat:j4hit4rlundqtkr3jjrgszybgm

Archaic chaos: intrinsically disordered proteins in Archaea

Bin Xue, Robert W Williams, Christopher J Oldfield, A Dunker, Vladimir N Uversky
2010 BMC Systems Biology  
Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions  ...  With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it  ...  (to A.K.D and V.N.U.) from the National Science Foundation, and the Program of the Russian Academy of Sciences for the "Molecular and Cellular Biology" (to V.N.U.).  ... 
doi:10.1186/1752-0509-4-s1-s1 pmid:20522251 pmcid:PMC2880407 fatcat:b2czo2kbfrajhcsfbr46sli4z4

Direct Prediction of NMR Residual Dipolar Couplings from the Primary Sequence of Unfolded Proteins

Jie-rong Huang, Valéry Ozenne, Malene Ringkjøbing Jensen, Martin Blackledge
2012 Angewandte Chemie International Edition  
characteristics depend on the length of the protein, so that division of the protein into short, uncoupled segments leads to better convergence. [29] It has indeed been demonstrated that a segment length  ...  sequence identity, and compared these to RDCs predicted from the full-length protein (in this case 76 amino acids in length).  ...  [1] [2] [3] [4] The high degree of flexibility inherent to intrinsically disordered proteins (IDPs) bestows distinct properties allowing them to function differently to folded proteins, but this same  ... 
doi:10.1002/anie.201206585 pmid:23192984 fatcat:yfgjjt6onna5pmlz76jrzehbbi

Direct Prediction of NMR Residual Dipolar Couplings from the Primary Sequence of Unfolded Proteins

Jie-rong Huang, Valéry Ozenne, Malene Ringkjøbing Jensen, Martin Blackledge
2012 Angewandte Chemie  
characteristics depend on the length of the protein, so that division of the protein into short, uncoupled segments leads to better convergence. [29] It has indeed been demonstrated that a segment length  ...  sequence identity, and compared these to RDCs predicted from the full-length protein (in this case 76 amino acids in length).  ...  [1] [2] [3] [4] The high degree of flexibility inherent to intrinsically disordered proteins (IDPs) bestows distinct properties allowing them to function differently to folded proteins, but this same  ... 
doi:10.1002/ange.201206585 fatcat:uutf6ieqezdjtedrpghimhgakm

Exploiting heterogeneous sequence properties improves prediction of protein disorder

Zoran Obradovic, Kang Peng, Slobodan Vucetic, Predrag Radivojac, A. Keith Dunker
2005 Proteins: Structure, Function, and Bioinformatics  
During the past few years we have investigated methods to improve predictors of intrinsically disordered regions longer than 30 consecutive residues.  ...  Prediction (CASP5).  ...  with the view that there are several flavors of intrinsic protein disorder.  ... 
doi:10.1002/prot.20735 pmid:16187360 fatcat:x23xill2mnffrpl7au4cipm5xe

Multiple Intrinsically Disordered Sequences Alter DNA Binding by the Homeodomain of theDrosophilaHox Protein Ultrabithorax

Ying Liu, Kathleen S. Matthews, Sarah E. Bondos
2008 Journal of Biological Chemistry  
Binding is restored almost to homeodomain affinity by the mostly disordered N-terminal 174 amino acids (R region) in a length-dependent manner.  ...  Computational and experimental approaches identified several conserved, intrinsically disordered regions outside the homeodomain of Ultrabithorax that impact DNA binding by the homeodomain.  ...  Acknowledgments-We thank the members of the Matthews and  ... 
doi:10.1074/jbc.m800375200 pmid:18508761 pmcid:PMC2475714 fatcat:4peqdeyei5efxm4vtiaxccsdle

Intrinsic Disorder in the Human Spliceosomal Proteome

Iga Korneta, Janusz M. Bujnicki, Lilia M. Iakoucheva
2012 PLoS Computational Biology  
We discovered that almost a half of the combined sequence of proteins abundant in the spliceosome is predicted to be intrinsically disordered, at least when the individual proteins are considered in isolation  ...  The distribution of intrinsic order and disorder throughout the spliceosome is uneven, and is related to the various functions performed by the intrinsic disorder of the spliceosomal proteins in the complex  ...  IK thanks Peter Tompa for the kind gift of his book on protein disorder.  ... 
doi:10.1371/journal.pcbi.1002641 pmid:22912569 pmcid:PMC3415423 fatcat:6cnd5mpd7ffd5lyzqfyfk2xgym

The unfoldomics decade: an update on intrinsically disordered proteins

A Keith Dunker, Christopher J Oldfield, Jingwei Meng, Pedro Romero, Jack Y Yang, Jessica Chen, Vladimir Vacic, Zoran Obradovic, Vladimir N Uversky
2008 BMC Genomics  
On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function.  ...  While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different.  ...  Acknowledgements This work was supported in part by the grants R01 LM007688-01A1 (to A.K.D and V.N.U.) and GM071714-01A2 (to A.K.D and V.N.U.) from the National Institutes of Health and the Programs of  ... 
doi:10.1186/1471-2164-9-s2-s1 pmid:18831774 pmcid:PMC2559873 fatcat:2hhpzzrc3bcxthl4uqimvksnce

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

Bin Xue, Wei-Lun Hsu, Jun-Ho Lee, Hua Lu, A. Keith Dunker, Vladimir N. Uversky
2010 Genes to Cells  
As evident from the data analysis, this method provides more reliable prediction of the intrinsic disorder status of short peptides.  ...  To minimize the influence of these limitations, we developed a method for the prediction of intrinsic disorder in short peptides based on large dataset sampling and statistics.  ...  .), and the Program of the Russian Academy of Sciences for the 'Molecular and Cellular Biology' (to V.N.U.). We gratefully acknowledge the support of the IUPUI Signature Centers Initiative.  ... 
doi:10.1111/j.1365-2443.2010.01407.x pmid:20497238 pmcid:PMC2900848 fatcat:ftxi6ycfqrhelpta3by2dzcyhi

Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins

Lilia M. Iakoucheva, Celeste J. Brown, J.David Lawson, Zoran Obradović, A.Keith Dunker
2002 Journal of Molecular Biology  
at least 75% of their lengths.  ...  The number of intrinsically disordered proteins known to be involved in cell-signaling and regulation is growing rapidly.  ...  Eric Ackerman from Pacific Northwest National Laboratories for useful discussions and critical reading of the manuscript. The anonymous reviewers were especially helpful.  ... 
doi:10.1016/s0022-2836(02)00969-5 pmid:12381310 fatcat:2oemwvzx7zcejpjdvoqdokdolq
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