LAIPT: Lysine Acetylation Site Identification with Polynomial Tree

Post-translational modification plays a key role in the field of biology. Experimental identification methods are time-consuming and expensive. Therefore, computational methods to deal with such issues overcome these shortcomings and limitations. In this article, we propose a lysine acetylation site identification with polynomial tree method (LAIPT), making use of the polynomial style to demonstrate amino-acid residue relationships in peptide segments. This polynomial style was enriched by the physical and chemical properties of amino-acid residues. Then, these reconstructed features were input into the employed classification model, named the flexible neural tree. Finally, some effect evaluation measurements were employed to test the model’s performance.

[1]  Wei Chen,et al.  iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition , 2013, Nucleic acids research.

[2]  R. Marmorstein,et al.  Histone acetyltransferases: function, structure, and catalysis. , 2001, Current opinion in genetics & development.

[3]  Junjie Chen,et al.  Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences , 2015, Nucleic Acids Res..

[4]  Kuo-Chen Chou,et al.  iPhosT-PseAAC: Identify phosphothreonine sites by incorporating sequence statistical moments into PseAAC. , 2018, Analytical biochemistry.

[5]  M. Mann,et al.  Proteomic analysis of post-translational modifications , 2003, Nature Biotechnology.

[6]  Dong-Sheng Cao,et al.  propy: a tool to generate various modes of Chou's PseAAC , 2013, Bioinform..

[7]  Jiwen Dong,et al.  Time-series forecasting using flexible neural tree model , 2005, Inf. Sci..

[8]  Thomas A. Milne,et al.  A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling , 2006, Nature.

[9]  K. Chou,et al.  pLoc-mEuk: Predict subcellular localization of multi-label eukaryotic proteins by extracting the key GO information into general PseAAC. , 2018, Genomics.

[10]  Antonio Lavecchia,et al.  Machine-learning approaches in drug discovery: methods and applications. , 2015, Drug discovery today.

[11]  De-Shuang Huang,et al.  Pupylation sites prediction with ensemble classification model , 2017, Int. J. Data Min. Bioinform..

[12]  Chaochun Wei,et al.  LAceP: Lysine Acetylation Site Prediction Using Logistic Regression Classifiers , 2014, PloS one.

[13]  Kuo-Chen Chou,et al.  Quat-2L: a web-server for predicting protein quaternary structural attributes , 2011, Molecular Diversity.

[14]  K. Chou,et al.  iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC. , 2018, Genomics.

[15]  Yu Shyr,et al.  Improved prediction of lysine acetylation by support vector machines. , 2009, Protein and peptide letters.

[16]  K. Chou,et al.  iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model , 2015, Journal of biomolecular structure & dynamics.

[17]  Dinshaw J. Patel,et al.  Multivalent engagement of chromatin modifications by linked binding modules , 2007, Nature Reviews Molecular Cell Biology.

[18]  Kuo-Chen Chou,et al.  pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information , 2018, Bioinform..

[19]  De-Shuang Huang,et al.  iEnhancer‐EL: identifying enhancers and their strength with ensemble learning approach , 2018, Bioinform..

[20]  De-Shuang Huang,et al.  Novel human microbe-disease association prediction using network consistency projection , 2017, BMC Bioinformatics.

[21]  Wei Chen,et al.  iRNA-PseU: Identifying RNA pseudouridine sites , 2016, Molecular therapy. Nucleic acids.

[22]  Xiao Sun,et al.  Sequence-Based Prediction of DNA-Binding Residues in Proteins with Conservation and Correlation Information , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[23]  Shao-Ping Shi,et al.  PLMLA: prediction of lysine methylation and lysine acetylation by combining multiple features. , 2012, Molecular bioSystems.

[24]  Kuo-Chen Chou,et al.  2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function , 2017, Molecular therapy. Nucleic acids.

[25]  Kuo-Chen Chou,et al.  iRNAm5C-PseDNC: identifying RNA 5-methylcytosine sites by incorporating physical-chemical properties into pseudo dinucleotide composition , 2017, Oncotarget.

[26]  Dong Xu,et al.  iPhos‐PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory , 2017, Molecular informatics.

[27]  Kuo-Chen Chou,et al.  iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC. , 2017, Medicinal chemistry (Shariqah (United Arab Emirates)).

[28]  Ren Long,et al.  iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition , 2016, Bioinform..

[29]  Thomas A. Milne,et al.  WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development , 2005, Cell.

[30]  Shu-Yun Huang,et al.  Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features , 2012, PLoS ONE.

[31]  Zhu-Hong You,et al.  CIPPN: computational identification of protein pupylation sites by using neural network , 2017, Oncotarget.

[32]  Kuo-Chen Chou,et al.  pLoc-mGpos: Incorporate Key Gene Ontology Information into General PseAAC for Predicting Subcellular Localization of Gram-Positive Bacterial Proteins , 2017 .

[33]  Wenzheng Bao,et al.  Prediction of protein structure classes with flexible neural tree. , 2014, Bio-medical materials and engineering.

[34]  T. Kouzarides Chromatin Modifications and Their Function , 2007, Cell.

[35]  K. Chou,et al.  Prediction of protein structural classes. , 1995, Critical reviews in biochemistry and molecular biology.

[36]  Jeffrey Skolnick,et al.  Efficient prediction of nucleic acid binding function from low-resolution protein structures. , 2006, Journal of molecular biology.

[37]  Kuo-Chen Chou,et al.  iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier , 2016, Oncotarget.

[38]  Zigang Dong,et al.  Post-translational modification of p53 in tumorigenesis , 2004, Nature Reviews Cancer.

[39]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[40]  Kuo-Chen Chou,et al.  iPTM-mLys: identifying multiple lysine PTM sites and their different types , 2016, Bioinform..

[41]  Bo Yang,et al.  Feature selection and classification using flexible neural tree , 2006, Neurocomputing.

[42]  Florian Gnad,et al.  Predicting post-translational lysine acetylation using support vector machines , 2010, Bioinform..

[43]  K. Chou,et al.  pRNAm-PC: Predicting N(6)-methyladenosine sites in RNA sequences via physical-chemical properties. , 2016, Analytical biochemistry.

[44]  Yuehui Chen,et al.  Classification of Protein Structure Classes on Flexible Neutral Tree , 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[45]  K. Chou,et al.  iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC , 2017, Molecular therapy. Nucleic acids.

[46]  Gary Walsh,et al.  Post-translational modifications in the context of therapeutic proteins , 2006, Nature Biotechnology.

[47]  K. Chou Prediction of signal peptides using scaled window , 2001, Peptides.

[48]  Wei Gu,et al.  p53 post-translational modification: deregulated in tumorigenesis. , 2010, Trends in molecular medicine.

[49]  Geoffrey I. Webb,et al.  Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features , 2014, Scientific Reports.

[50]  K. Chou,et al.  iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier. , 2017, Genomics.

[51]  Kuo-Chen Chou,et al.  An Unprecedented Revolution in Medicinal Chemistry Driven by the Progress of Biological Science. , 2017, Current topics in medicinal chemistry.

[52]  Kyungsook Han,et al.  Mutli-Features Prediction of Protein Translational Modification Sites , 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[53]  K. Chou,et al.  iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins , 2013, PeerJ.

[54]  Kuo-Chen Chou,et al.  pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC , 2016, Bioinform..

[55]  K. Chou,et al.  iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model , 2011, PloS one.

[56]  Kuo-Chen Chou,et al.  Some remarks on predicting multi-label attributes in molecular biosystems. , 2013, Molecular bioSystems.

[57]  Ming-Ming Zhou,et al.  Bromodomain: an acetyl‐lysine binding domain , 2002, FEBS letters.

[58]  Kuo-Chen Chou,et al.  pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC. , 2017, Molecular bioSystems.

[59]  K. Chou,et al.  iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition. , 2015, Analytical biochemistry.

[60]  Fan Yang,et al.  iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC , 2018, Bioinform..

[61]  K. Chou,et al.  iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition , 2014, International journal of molecular sciences.

[62]  Carsten Janke,et al.  Post-translational regulation of the microtubule cytoskeleton: mechanisms and functions , 2011, Nature Reviews Molecular Cell Biology.

[63]  K. Chou,et al.  iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition , 2014, PloS one.

[64]  K. Chou,et al.  iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC , 2016, Oncotarget.

[65]  Bo Yang,et al.  Hybrid flexible neural‐tree‐based intrusion detection systems , 2007, Int. J. Intell. Syst..

[66]  De-Shuang Huang,et al.  iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC , 2018, Bioinform..

[67]  Dong Xu,et al.  Systematic analysis of human lysine acetylation proteins and accurate prediction of human lysine acetylation through bi-relative adapted binomial score Bayes feature representation. , 2012, Molecular bioSystems.

[68]  K. Chou,et al.  Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences. , 2015, Molecular bioSystems.

[69]  Kuo-Chen Chou,et al.  pLoc-mGneg: Predict subcellular localization of Gram-negative bacterial proteins by deep gene ontology learning via general PseAAC. , 2017, Genomics.

[70]  Kuo-Chen Chou,et al.  pLoc‐mAnimal: predict subcellular localization of animal proteins with both single and multiple sites , 2017, Bioinform..

[71]  K. Chou,et al.  iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach , 2014, BioMed research international.