iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets
暂无分享,去创建一个
Kuo-Chen Chou | Xuan Xiao | Zi Liu | Jianhua Jia | Bingxiang Liu | K. Chou | Zi Liu | Jianhua Jia | Bingxiang Liu | Xuan Xiao
[1] J. Chou,et al. Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E. , 1993, Biochemistry.
[2] K. Chou,et al. Recent progress in protein subcellular location prediction. , 2007, Analytical biochemistry.
[3] M. Charton,et al. The structural dependence of amino acid hydrophobicity parameters. , 1982, Journal of theoretical biology.
[4] K. Chou. Prediction of signal peptides using scaled window , 2001, Peptides.
[5] 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.
[6] Dong-Sheng Cao,et al. propy: a tool to generate various modes of Chou's PseAAC , 2013, Bioinform..
[7] K. Chou,et al. iDNA-Methyl: identifying DNA methylation sites via pseudo trinucleotide composition. , 2015, Analytical biochemistry.
[8] Kuo-Chen Chou,et al. Some remarks on predicting multi-label attributes in molecular biosystems. , 2013, Molecular bioSystems.
[9] S. Forsén,et al. Graphical rules for enzyme-catalysed rate laws. , 1980, The Biochemical journal.
[10] Wei Chen,et al. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition , 2014, Nucleic acids research.
[11] K. Chou,et al. Monte Carlo simulation studies on the prediction of protein folding types from amino acid composition. , 1992, Biophysical journal.
[12] K. Chou,et al. iAMP-2L: a two-level multi-label classifier for identifying antimicrobial peptides and their functional types. , 2013, Analytical biochemistry.
[13] Shuigeng Zhou,et al. Prediction of protein-protein interaction sites using an ensemble method , 2009, BMC Bioinformatics.
[14] Wei Chen,et al. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition , 2013, Nucleic acids research.
[15] K. Chou. Prediction of human immunodeficiency virus protease cleavage sites in proteins. , 1996, Analytical biochemistry.
[16] Kuo-Chen Chou,et al. A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. , 2009, Analytical biochemistry.
[17] G M Maggiora,et al. Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth , 1994, Biopolymers.
[18] Pufeng Du,et al. PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets , 2014, International journal of molecular sciences.
[19] K. Chou,et al. 2D-MH: A web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids. , 2010, Journal of theoretical biology.
[20] Dinesh Gupta,et al. Identifying Bacterial Virulent Proteins by Fusing a Set of Classifiers Based on Variants of Chou's Pseudo Amino Acid Composition and on Evolutionary Information , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[21] K. Chou,et al. iLoc-Virus: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites. , 2011, Journal of theoretical biology.
[22] M. Šikić,et al. PSAIA – Protein Structure and Interaction Analyzer , 2008, BMC Structural Biology.
[23] K. Chou,et al. THE BIOLOGICAL FUNCTIONS OF LOW-FREQUENCY PHONONS , 1977 .
[24] K. Chou,et al. Graphic rules in steady and non-steady state enzyme kinetics. , 1989, The Journal of biological chemistry.
[25] G P Zhou,et al. Some insights into protein structural class prediction , 2001, Proteins.
[26] K. Chou,et al. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. , 2007, Journal of proteome research.
[27] Kuo-Chen Chou,et al. Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition. , 2006, Journal of theoretical biology.
[28] P Martel,et al. Biophysical aspects of neutron scattering from vibrational modes of proteins. , 1992, Progress in biophysics and molecular biology.
[29] J. Chou,et al. Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach , 1993, Journal of protein chemistry.
[30] B. Liu,et al. iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition , 2014, PloS one.
[31] K. Chou,et al. Predicting protein-protein interactions from sequences in a hybridization space. , 2006, Journal of proteome research.
[32] H.-B. Shen,et al. Euk-PLoc: an ensemble classifier for large-scale eukaryotic protein subcellular location prediction , 2007, Amino Acids.
[33] Xiaolong Wang,et al. Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach , 2015, Journal of biomolecular structure & dynamics.
[34] 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..
[35] W. Zhong,et al. Molecular Science for Drug Development and Biomedicine , 2014, International journal of molecular sciences.
[36] K. Chou,et al. iGPCR-Drug: A Web Server for Predicting Interaction between GPCRs and Drugs in Cellular Networking , 2013, PloS one.
[37] K. Chou,et al. Low-frequency collective motion in biomacromolecules and its biological functions. , 1988, Biophysical chemistry.
[38] K C Chou,et al. An analysis of protein folding type prediction by seed-propagated sampling and jackknife test , 1995, Journal of protein chemistry.
[39] K. Chou. Structural bioinformatics and its impact to biomedical science. , 2004, Current medicinal chemistry.
[40] K. Chou,et al. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. , 1993, The Journal of biological chemistry.
[41] Xin Wang,et al. PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. , 2012, Analytical biochemistry.
[42] Zaheer Ullah Khan,et al. Discrimination of acidic and alkaline enzyme using Chou's pseudo amino acid composition in conjunction with probabilistic neural network model. , 2015, Journal of theoretical biology.
[43] Dik-Lung Ma,et al. Bioactive luminescent transition-metal complexes for biomedical applications. , 2013, Angewandte Chemie.
[44] Kuo-Chen Chou,et al. Prediction and classification of protein subcellular location—sequence‐order effect and pseudo amino acid composition , 2003, Journal of cellular biochemistry.
[45] Mark J. Shensa,et al. The discrete wavelet transform: wedding the a trous and Mallat algorithms , 1992, IEEE Trans. Signal Process..
[46] Kuo-Chen Chou,et al. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. , 2006, Journal of proteome research.
[47] K. Chou,et al. Prediction of the tertiary structure and substrate binding site of caspase‐8 , 1997, FEBS letters.
[48] 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.
[49] K. Chou,et al. Prediction of the tertiary structure of a caspase‐9/inhibitor complex , 2000, FEBS letters.
[50] B. Liu,et al. Identification of microRNA precursor with the degenerate K-tuple or Kmer strategy. , 2015, Journal of theoretical biology.
[51] K. Chou,et al. Collective motion in DNA and its role in drug intercalation , 1988, Biopolymers.
[52] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[53] Changjun Jiang,et al. A New Strategy for Protein Interface Identification Using Manifold Learning Method , 2014, IEEE Transactions on NanoBioscience.
[54] Dik-Lung Ma,et al. DNA‐Binding Small Molecules as Inhibitors of Transcription Factors , 2013, Medicinal research reviews.
[55] K. Chou,et al. PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition. , 2014, Analytical biochemistry.
[56] K. Chou,et al. Low-frequency resonance and cooperativity of hemoglobin. , 1989, Trends in biochemical sciences.
[57] K. Chou. Graphic rule for drug metabolism systems. , 2010, Current drug metabolism.
[58] Jorma Laurikkala,et al. Improving Identification of Difficult Small Classes by Balancing Class Distribution , 2001, AIME.
[59] Leo Breiman,et al. Random Forests , 2001, Machine Learning.
[60] Kuo-Chen Chou,et al. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS , 2003, Biochemical and Biophysical Research Communications.
[61] Kuo-Chen Chou,et al. Insights from studying the mutation-induced allostery in the M2 proton channel by molecular dynamics. , 2010, Protein engineering, design & selection : PEDS.
[62] K. Chou,et al. The biological functions of low‐frequency vibrations (phonons). VI. A possible dynamic mechanism of allosteric transition in antibody molecules , 1987, Biopolymers.
[63] Kuo-Chen Chou,et al. Insight into the molecular switch mechanism of human Rab5a from molecular dynamics simulations. , 2009, Biochemical and biophysical research communications.
[64] Daqun Zhang,et al. ReviewStance and Voice in Written Academic Genres, Ken Hyland, Carmen Sancho Guinda (Eds.). Palgrave Macmillan, UK (2012), xvi+263 pp., US $ 85.00, hardcover, ISBN: 9780230302839 , 2014 .
[65] K. R. Woods,et al. Prediction of protein antigenic determinants from amino acid sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[66] Nitesh V. Chawla,et al. SMOTE: Synthetic Minority Over-sampling Technique , 2002, J. Artif. Intell. Res..
[67] Kuo-Chen Chou,et al. QuatIdent: a web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information. , 2009, Journal of proteome research.
[68] K. Chou,et al. iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition , 2013, PloS one.
[69] Xiang Cheng,et al. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach , 2015, Journal of biomolecular structure & dynamics.
[70] C. Tanford. Contribution of Hydrophobic Interactions to the Stability of the Globular Conformation of Proteins , 1962 .
[71] Andrew K. C. Wong,et al. Classification of Imbalanced Data: a Review , 2009, Int. J. Pattern Recognit. Artif. Intell..
[72] K. Chou. Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001, Proteins.
[73] Meng Wang,et al. SLLE for predicting membrane protein types. , 2005, Journal of theoretical biology.
[74] G. Rose,et al. Hydrophobicity of amino acid residues in globular proteins. , 1985, Science.
[75] K. Chou,et al. Prediction of protein structural classes. , 1995, Critical reviews in biochemistry and molecular biology.
[76] K. Chou,et al. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale , 2007, Amino Acids.
[77] Stéphane Mallat,et al. A Theory for Multiresolution Signal Decomposition: The Wavelet Representation , 1989, IEEE Trans. Pattern Anal. Mach. Intell..
[78] B. Rost,et al. Predicted protein–protein interaction sites from local sequence information , 2003, FEBS letters.
[79] Kuo-Chen Chou,et al. Molecular dynamics studies on the interactions of PTP1B with inhibitors: from the first phosphate-binding site to the second one. , 2009, Protein engineering, design & selection : PEDS.
[80] Dik-Lung Ma,et al. Luminescent detection of DNA-binding proteins , 2011, Nucleic acids research.
[81] K. Chou. Some remarks on protein attribute prediction and pseudo amino acid composition , 2010, Journal of Theoretical Biology.
[82] Vasant Honavar,et al. A two-stage classifier for identification of protein-protein interface residues , 2004, ISMB/ECCB.
[83] K. Chou. Using subsite coupling to predict signal peptides. , 2001, Protein engineering.
[84] K. Chou,et al. iLoc-Hum: using the accumulation-label scale to predict subcellular locations of human proteins with both single and multiple sites. , 2012, Molecular bioSystems.
[85] Tom Fawcett,et al. An introduction to ROC analysis , 2006, Pattern Recognit. Lett..
[86] Guo-Ping Zhou. The disposition of the LZCC protein residues in wenxiang diagram provides new insights into the protein–protein interaction mechanism , 2011, Journal of Theoretical Biology.
[87] J. Chou,et al. Structure and mechanism of the M2 proton channel of influenza A virus , 2008, Nature.
[88] Kuo-Chen Chou,et al. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes , 2005, Bioinform..
[89] Wu,et al. Genetic algorithm-base virtual screening of combinative mode for peptide/protein , 2006 .
[90] M. Wang,et al. Low-frequency Fourier spectrum for predicting membrane protein types. , 2005, Biochemical and biophysical research communications.
[91] Xue-wen Chen,et al. Sequence-based prediction of protein interaction sites with an integrative method , 2009, Bioinform..
[92] Sarah A. Teichmann,et al. Principles of protein-protein interactions , 2002, ECCB.
[93] H. Mohabatkar,et al. Predicting anticancer peptides with Chou's pseudo amino acid composition and investigating their mutagenicity via Ames test. , 2014, Journal of theoretical biology.
[94] K. Chou,et al. iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components , 2014, International journal of molecular sciences.
[95] K. Chou,et al. iLoc-Animal: a multi-label learning classifier for predicting subcellular localization of animal proteins. , 2013, Molecular bioSystems.
[96] Kuo-Chen Chou,et al. RSARF: prediction of residue solvent accessibility from protein sequence using random forest method. , 2012, Protein and peptide letters.
[97] Dik-Lung Ma,et al. Group 9 organometallic compounds for therapeutic and bioanalytical applications. , 2014, Accounts of chemical research.
[98] Jacques Lapointe,et al. Theoretical and experimental biology in one—A symposium in honour of Professor Kuo-Chen Chou’s 50th anniversary and Professor Richard Giegé’s 40th anniversary of their scientific careers , 2013 .
[99] James G. Lyons,et al. Gram-positive and Gram-negative protein subcellular localization by incorporating evolutionary-based descriptors into Chou׳s general PseAAC. , 2015, Journal of theoretical biology.
[100] K. Chou,et al. iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition. , 2015, Analytical biochemistry.
[101] Wei Chen,et al. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition , 2014, Bioinform..
[102] Xiaolong Wang,et al. repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects , 2015, Bioinform..
[103] K. Chou,et al. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. , 2006, Biochemical and biophysical research communications.
[104] Kuo-Chen Chou,et al. Erratum to “Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS” [Biochem. Biophys. Res. Commun. 308 (2003) 148–151] , 2003, Biochemical and Biophysical Research Communications.
[105] Kuo-Chen Chou,et al. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. , 2007, Biochemical and biophysical research communications.
[106] Wei Chen,et al. iNuc-PhysChem: A Sequence-Based Predictor for Identifying Nucleosomes via Physicochemical Properties , 2012, PloS one.
[107] Sukanta Mondal,et al. Chou's pseudo amino acid composition improves sequence-based antifreeze protein prediction. , 2014, Journal of theoretical biology.
[108] W. R. Krigbaum,et al. Prediction of the amount of secondary structure in a globular protein from its aminoacid composition. , 1973, Proceedings of the National Academy of Sciences of the United States of America.
[109] K. Chou,et al. iMethyl-PseAAC: Identification of Protein Methylation Sites via a Pseudo Amino Acid Composition Approach , 2014, BioMed research international.
[110] P. Suganthan,et al. AFP-Pred: A random forest approach for predicting antifreeze proteins from sequence-derived properties. , 2011, Journal of theoretical biology.
[111] K. Chou,et al. iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition , 2014, PloS one.
[112] Ren Long,et al. iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition , 2016, Bioinform..
[113] K. Chou,et al. Bioinformatical analysis of G-protein-coupled receptors. , 2002, Journal of proteome research.
[114] K. Chou,et al. Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences. , 2015, Molecular bioSystems.
[115] Glen A. Gordon. Extrinsic electromagnetic fields, low frequency (phonon) vibrations, and control of cell function: a non-linear resonance system , 2008 .
[116] A. Esmaeili,et al. Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine. , 2011, Journal of theoretical biology.
[117] Manish Kumar,et al. Prediction of β-lactamase and its class by Chou's pseudo-amino acid composition and support vector machine. , 2015, Journal of theoretical biology.
[118] Kuo-Chen Chou,et al. Steps to the clinic with ELF EMF , 2009 .
[119] K. Chou,et al. iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins , 2013, PeerJ.
[120] R. Grantham. Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.
[121] K. Chou,et al. iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model , 2011, PloS one.
[122] K. Chou,et al. An optimization approach to predicting protein structural class from amino acid composition , 1992, Protein science : a publication of the Protein Society.
[123] Kuo-Chen Chou,et al. Boosting classifier for predicting protein domain structural class. , 2005, Biochemical and biophysical research communications.
[124] Maqsood Hayat,et al. Discriminating outer membrane proteins with Fuzzy K-nearest Neighbor algorithms based on the general form of Chou's PseAAC. , 2012, Protein and peptide letters.
[125] K. Chou,et al. iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels , 2014, BioMed research international.
[126] K. Chou. Pseudo Amino Acid Composition and its Applications in Bioinformatics, Proteomics and System Biology , 2009 .
[127] K. Chou. Impacts of bioinformatics to medicinal chemistry. , 2015, Medicinal chemistry (Shariqah (United Arab Emirates)).