Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble
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Jun Hu | Jing-Yu Yang | Hong-Bin Shen | Hui Yan | Xibei Yang | Dong-Jun Yu | Jing-yu Yang | Xibei Yang | Hongbin Shen | Dong-Jun Yu | Hui Yan | Junda Hu
[1] R. Wade,et al. Computational approaches to identifying and characterizing protein binding sites for ligand design , 2009, Journal of molecular recognition : JMR.
[2] David G. Stork,et al. Pattern classification, 2nd Edition , 2000 .
[3] K. Chou. Some remarks on protein attribute prediction and pseudo amino acid composition , 2010, Journal of Theoretical Biology.
[4] X. Barril,et al. Understanding and predicting druggability. A high-throughput method for detection of drug binding sites. , 2010, Journal of medicinal chemistry.
[5] Bart De Moor,et al. Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks , 2006, ISMB.
[6] M Hendlich,et al. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.
[7] Lukasz Kurgan,et al. ATPsite: sequence-based prediction of ATP-binding residues , 2011, Proteome Science.
[8] Kuo-Chen Chou,et al. Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property , 2011, PloS one.
[9] T. Sterling. Publication Decisions and their Possible Effects on Inferences Drawn from Tests of Significance—or Vice Versa , 1959 .
[10] Michael E Webb,et al. Roles of vitamins B5, B8, B9, B12 and molybdenum cofactor at cellular and organismal levels. , 2007, Natural product reports.
[11] Vincent Le Guilloux,et al. Fpocket: An open source platform for ligand pocket detection , 2009, BMC Bioinformatics.
[12] Concha Bielza,et al. Machine Learning in Bioinformatics , 2008, Encyclopedia of Database Systems.
[13] Richard M. Jackson,et al. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..
[14] Jun Hu,et al. Designing Template-Free Predictor for Targeting Protein-Ligand Binding Sites with Classifier Ensemble and Spatial Clustering , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[15] Lukasz A. Kurgan,et al. Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors , 2012, Bioinform..
[16] Pedro Alexandrino Fernandes,et al. Protein–ligand docking: Current status and future challenges , 2006, Proteins.
[17] Jian Yang,et al. Joint Laplacian feature weights learning , 2014, Pattern Recognit..
[18] Jaime Prilusky,et al. Automated analysis of interatomic contacts in proteins , 1999, Bioinform..
[19] K. Chou,et al. Prediction of protein structural classes. , 1995, Critical reviews in biochemistry and molecular biology.
[20] Deng Cai,et al. Laplacian Score for Feature Selection , 2005, NIPS.
[21] Chih-Jen Lin,et al. Working Set Selection Using Second Order Information for Training Support Vector Machines , 2005, J. Mach. Learn. Res..
[22] F. Rébeillé,et al. Elucidating Biosynthetic Pathways for Vitamins and Cofactors , 2008 .
[23] R. Laskowski. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.
[24] K. Chou,et al. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms , 2008, Nature Protocols.
[25] Anne-Laure Boulesteix,et al. Over-optimism in bioinformatics research , 2010, Bioinform..
[26] BMC Bioinformatics , 2005 .
[27] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[28] Pietro Liò,et al. Identification of DNA regulatory motifs using Bayesian variable selection , 2004, Bioinform..
[29] 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.
[30] A. Emons,et al. Boekbespreking: Molecular biology of the cell, B. Alberts, D. Bray, J. Lewis, M. Raff, K. Robers, D.J. Watson. Garland Publ., New York. 1989. , 1990 .
[31] Thomas L. Madden,et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.
[32] J. Skolnick,et al. FINDSITE‐metal: Integrating evolutionary information and machine learning for structure‐based metal‐binding site prediction at the proteome level , 2011, Proteins.
[33] Yang Zhang,et al. BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions , 2012, Nucleic Acids Res..
[34] Constantin F. Aliferis,et al. A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis , 2004, Bioinform..
[35] C. Sander,et al. A method to predict functional residues in proteins , 1995, Nature Structural Biology.
[36] Thomas Dick,et al. Vitamin B6 biosynthesis is essential for survival and virulence of Mycobacterium tuberculosis , 2010, Molecular microbiology.
[37] Jie Liang,et al. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues , 2006, Nucleic Acids Res..
[38] Vladimir Vapnik,et al. Statistical learning theory , 1998 .
[39] Bruce A. Fenderson,et al. Molecular Biology of the Cell,5th Edition , 2008 .
[40] Pedro Larrañaga,et al. Machine learning: an indispensable tool in bioinformatics. , 2010, Methods in molecular biology.
[41] Jeffrey Skolnick,et al. The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation , 2012, Proceedings of the National Academy of Sciences.
[42] I. Song,et al. Working Set Selection Using Second Order Information for Training Svm, " Complexity-reduced Scheme for Feature Extraction with Linear Discriminant Analysis , 2022 .
[43] Pedro Larrañaga,et al. A review of feature selection techniques in bioinformatics , 2007, Bioinform..
[44] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[45] Yuko Okamoto,et al. Ab Initio prediction of protein–ligand binding structures by replica‐exchange umbrella sampling simulations , 2011, J. Comput. Chem..
[46] M. Michael Gromiha,et al. Development of RNA Stiffness Parameters and Analysis on Protein-RNA Binding Specificity: Comparison with DNA , 2012 .
[47] K. Chou,et al. Cell-PLoc 2.0: an improved package of web-servers for predicting subcellular localization of proteins in various organisms , 2010 .
[48] V. Sobolev,et al. Prediction of transition metal‐binding sites from apo protein structures , 2007, Proteins.
[49] Yvan Saeys,et al. Feature selection for splice site prediction: A new method using EDA-based feature ranking , 2004, BMC Bioinformatics.
[50] Leif E. Peterson,et al. Machine learning in biomedicine and bioinformatics. , 2009, International journal of data mining and bioinformatics.
[51] Jun Hu,et al. TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble , 2013, J. Comput. Chem..
[52] David G. Stork,et al. Pattern Classification , 1973 .
[53] Stefan Günther,et al. SuperSite: dictionary of metabolite and drug binding sites in proteins , 2008, Nucleic Acids Res..
[54] Zhenmin Tang,et al. Enhancing Membrane Protein Subcellular Localization Prediction by Parallel Fusion of Multi-View Features , 2012, IEEE Transactions on NanoBioscience.
[55] Jiangning Song,et al. Improving the accuracy of predicting disulfide connectivity by feature selection , 2010, J. Comput. Chem..
[56] Adeel Malik,et al. Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates , 2011, BMC Biochemistry.
[57] Jian Yang,et al. Improving protein-ATP binding residues prediction by boosting SVMs with random under-sampling , 2013, Neurocomputing.
[58] B. Alberts,et al. Molecular Biology of the Cell 4th edition , 2007 .
[59] Michael Schroeder,et al. MetaDBSite: a meta approach to improve protein DNA-binding sites prediction , 2011, BMC Systems Biology.
[60] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[61] Leif E. Peterson,et al. Logistic ensembles of Random Spherical Linear Oracles for microarray classification , 2009, Int. J. Data Min. Bioinform..
[62] Louette R. Johnson Lutjens. Research , 2006 .
[63] J. Davies,et al. Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.
[64] D. Levitt,et al. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. , 1992, Journal of molecular graphics.
[65] Dario Ghersi,et al. SITEHOUND-web: a server for ligand binding site identification in protein structures , 2009, Nucleic Acids Res..
[66] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[67] Yan Huang,et al. Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features , 2012, BMC Bioinformatics.
[68] Jonathan Knowles,et al. A guide to drug discovery: Target selection in drug discovery , 2003, Nature Reviews Drug Discovery.
[69] Gajendra P. S. Raghava,et al. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information , 2013, BMC Bioinformatics.
[70] Javier De Las Rivas,et al. Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks , 2010, PLoS Comput. Biol..
[71] LarrañagaPedro,et al. A review of feature selection techniques in bioinformatics , 2007 .