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OPTIMIZING LONG INTRINSIC DISORDER PREDICTORS WITH PROTEIN EVOLUTIONARY INFORMATION

KANG PENG, SLOBODAN VUCETIC, PREDRAG RADIVOJAC, CELESTE J. BROWN, A. KEITH DUNKER, ZORAN OBRADOVIC
2005 Journal of Bioinformatics and Computational Biology  
PONDR VL3 used several features from a previously introduced PONDR VL2, but benefitted from optimized predictor models and a slightly larger (152 versus 145) set of disordered proteins that were cleaned  ...  The new disorder predictors with the corresponding datasets are freely accessible through the web server at www.ist.temple.edu/disprot.  ...  We also thank Vladimir Vacic for the construction of disorder database and predictor website.  ... 
doi:10.1142/s0219720005000886 pmid:15751111 fatcat:ndeogl654rcvxhvntke52hlfvi

Protein flexibility and intrinsic disorder

P. Radivojac
2004 Protein Science  
Comparisons were made among four categories of protein flexibility: (1) low-B-factor ordered regions, (2) high-B-factor ordered regions, (3) short disordered regions, and (4) long disordered regions.  ...  This predictor achieved an accuracy of 70% and a correlation of 0.43 with experimental data, outperforming the 64% accuracy and 0.32 correlation of predictors based solely on flexibility indices.  ...  This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ... 
doi:10.1110/ps.03128904 pmid:14691223 pmcid:PMC2286519 fatcat:qz4qyxulrvhbxj3c3fncymwca4

Length-dependent prediction of protein intrinsic disorder

Kang Peng, Predrag Radivojac, Slobodan Vucetic, A Keith Dunker, Zoran Obradovic
2006 BMC Bioinformatics  
., 1997), our group has developed several predictors optimized for long disordered regions (>30 residues) with prediction accuracy exceeding 85%.  ...  existing predictors of intrinsic protein disorder.  ...  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

Accurate Ab Initio and Template-Based Prediction of Short Intrinsically-Disordered Regions by Bidirectional Recurrent Neural Networks Trained on Large-Scale Datasets

Viola Volpato, Badr Alshomrani, Gianluca Pollastri
2015 International Journal of Molecular Sciences  
Intrinsically-disordered regions lack a well-defined 3D structure, but play key roles in determining the function of many proteins.  ...  The system exploits sequence and structural information in the forms of frequency profiles, predicted secondary structure and solvent accessibility and direct disorder annotations from homologous protein  ...  This would be more difficult to achieve in the case of the analysis of sequences with long disordered regions that are five-times less than sequences with short disordered segments.  ... 
doi:10.3390/ijms160819868 pmid:26307973 pmcid:PMC4581330 fatcat:ljcycbybbjhrlevooxn44ytxku

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou
2020 Genomics, Proteomics & Bioinformatics  
Here, we employed an ensemble of deep Squeeze-and-Excitation residual inception and long short-term memory (LSTM) networks for predicting protein intrinsic disorder with input from evolutionary information  ...  different ratios of disordered to ordered amino acid residues, and for sequences with either rich or limited evolutionary information.  ...  The discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) in proteins challenged the dogmatic structure-function paradigm, forcing a new perspective where protein  ... 
doi:10.1016/j.gpb.2019.01.004 pmid:32173600 pmcid:PMC7212484 fatcat:q6456u2xfvbwzbd4xefbb6y2jy

DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel

Sumaiya Iqbal, Md Tamjidul Hoque, Alexandre G. de Brevern
2015 PLoS ONE  
Intrinsically disordered proteins or, regions perform important biological functions through their dynamic conformations during binding.  ...  We introduce DisPredict, a disorder predictor that employs a single support vector machine with RBF kernel and novel features for reliable characterization of protein structure.  ...  We also acknowledge the discussion with Md Nasrul Islam, Avdesh Mishra and Denson Smith. Special thanks to Denson Smith for critically reviewing the paper.  ... 
doi:10.1371/journal.pone.0141551 pmid:26517719 pmcid:PMC4627842 fatcat:5elpxt4vwnduziruedxrm54nnq

Predicting intrinsic disorder from amino acid sequence

Zoran Obradovic, Kang Peng, Slobodan Vucetic, Predrag Radivojac, Celeste J. Brown, A. Keith Dunker
2003 Proteins: Structure, Function, and Bioinformatics  
This experiment supports the predictability of intrinsic disorder from amino acid sequence. Proteins 2003;53:566 -572.  ...  Blind predictions of intrinsic order and disorder were made on 42 proteins subsequently revealed to contain 9,044 ordered residues, 284 disordered residues in 26 segments of length 30 residues or less,  ...  VL3-P (profile; id 454-3) The VL3-P predictor uses the evolutionary information both at the stage of training and prediction.  ... 
doi:10.1002/prot.10532 pmid:14579347 fatcat:5a3yhdmm4ndz7epcy3vmfnno5u

Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins

Z. Dosztanyi, B. Meszaros, I. Simon
2009 Briefings in Bioinformatics  
Intrinsically disordered/unstructured proteins exist without a stable three-dimensional (3D) structure as highly flexible conformational ensembles.  ...  In more detail we also discuss approaches that predict disordered regions and specific regions involved in protein binding by modeling the physical background of protein disorder.  ...  The fruitful discussions with Dr Peter Tompa are gratefully acknowledged.  ... 
doi:10.1093/bib/bbp061 pmid:20007729 fatcat:4s65sbwybja5xjp7naue3vqrdy

IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields

Yumeng Liu, Xiaolong Wang, Bin Liu
2018 International Journal of Molecular Sciences  
Accurate prediction of intrinsically disordered proteins/regions is one of the most important tasks in bioinformatics, and some computational predictors have been proposed to solve this problem.  ...  disordered proteins/regions).  ...  The performance of IDP-CRF (intrinsically disordered protein-conditional random field) and three classification-based predictors trained with different ratios of disordered residues and ordered residues  ... 
doi:10.3390/ijms19092483 pmid:30135358 fatcat:qxj7vrelmbaehbqnvaxe2dfwfe

Archaic chaos: intrinsically disordered proteins in Archaea

Bin Xue, Robert W Williams, Christopher J Oldfield, A Dunker, Vladimir N Uversky
2010 BMC Systems Biology  
In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered.  ...  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  ...  We used three measures of intrinsic disorder, overall percentage of intrinsically disordered residues (IDAA), percentage of proteins with long disordered regions (IDP >30 aa), and percentage of wholly  ... 
doi:10.1186/1752-0509-4-s1-s1 pmid:20522251 pmcid:PMC2880407 fatcat:b2czo2kbfrajhcsfbr46sli4z4

MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins

Lukasz P Kozlowski, Janusz M Bujnicki
2012 BMC Bioinformatics  
We have also developed a disorder predictor GSmetaDisorder3D that used no third-party disorder predictors, but alignments to known protein structures, reported by the protein fold-recognition methods,  ...  They are based on different approaches, such as utilizing evolutionary information, energy functions, and various statistical and machine learning methods.  ...  Intrinsic disorder is a common feature of "hub" proteins that interact with multiple other proteins and perform important regulatory roles in the cell [5] .  ... 
doi:10.1186/1471-2105-13-111 pmid:22624656 pmcid:PMC3465245 fatcat:6ywc42vs7nc3nhak6lwxrk4oa4

The Prediction of Intrinsically Disordered Proteins Based on Feature Selection

Hao He, Jiaxiang Zhao, Guiling Sun
2019 Algorithms  
We develop a scheme for predicting intrinsically disordered proteins by employing 35 features including eight structural properties, seven physicochemical properties and 20 pieces of evolutionary information  ...  Intrinsically disordered proteins perform a variety of important biological functions, which makes their accurate prediction useful for a wide range of applications.  ...  Introduction The intrinsically disordered proteins (IDPs) have at least one region lacking a unique 3D structure [1] .  ... 
doi:10.3390/a12020046 fatcat:az6qd3zrhvevxffxffbsbpxj5q

TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

Andrew Campen, Ryan Williams, Celeste Brown, Jingwei Meng, Vladimir Uversky, A. Dunker
2008 Protein Peptide Letters  
Intrinsically disordered proteins carry out various biological functions while lacking ordered secondary and/or tertiary structure.  ...  In order to find general intrinsic properties of amino acid residues that are responsible for the absence of ordered structure in intrinsically disordered proteins we surveyed 517 amino acid scales.  ...  Out of the 710 Swiss-Prot functional keywords that were associated with at least 20 proteins, 238 were found to be strongly positively correlated with predictions of long intrinsically disordered regions  ... 
doi:10.2174/092986608785849164 pmid:18991772 pmcid:PMC2676888 fatcat:sb5tmo3cezghxasrsxaserp3pa

Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

Sebastian Pechmann, Judith Frydman, Lilia M. Iakoucheva
2014 PLoS Computational Biology  
Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered.  ...  Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher l at the  ...  protein families and with available structural information.  ... 
doi:10.1371/journal.pcbi.1003674 pmid:24968255 pmcid:PMC4072544 fatcat:5iv6wgcxozcv3ggwi7juvzpdoi

Prediction of Intrinsic Disorder and Its Use in Functional Proteomics [chapter]

Vladimir N. Uversky, Predrag Radivojac, Lilia M. Iakoucheva, Zoran Obradovic, A. Keith Dunker
2007 Msphere  
A method is provided to utilize intrinsic disorder knowledge to gain structural and functional information related to individual proteins, protein groups, families, classes, and even entire proteomes.  ...  The number of experimentally verified, intrinsically disordered (ID) proteins is rapidly rising.  ...  PONDR VL3 is an ensemble of feed-forward neural networks that uses evolutionary information and is trained on long disordered regions (65).  ... 
doi:10.1007/978-1-59745-547-3_5 pmid:18314578 fatcat:fpbxmi2fmfbafjygbo3zqzbx5q
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