A comprehensive review and comparison of different computational methods for protein remote homology detection
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Junjie Chen | Xiaolong Wang | Bin Liu | Mingyue Guo | Xiaolong Wang | Junjie Chen | Mingyue Guo | Bin Liu
[1] Alejandro A. Schäffer,et al. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices , 1999, Bioinform..
[2] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[3] Peter B. McGarvey,et al. UniRef: comprehensive and non-redundant UniProt reference clusters , 2007, Bioinform..
[4] Christopher S. Oehmen,et al. SVM-BALSA: Remote homology detection based on Bayesian sequence alignment , 2005, Comput. Biol. Chem..
[5] David S. Goodsell,et al. The RCSB Protein Data Bank: views of structural biology for basic and applied research and education , 2014, Nucleic Acids Res..
[6] Xugang Ye,et al. An assessment of substitution scores for protein profile-profile comparison , 2011, Bioinform..
[7] Tony Håndstad,et al. Motif kernel generated by genetic programming improves remote homology and fold detection , 2007, BMC Bioinformatics.
[8] Arthur M. Lesk,et al. Introduction to bioinformatics , 2002 .
[9] Christian J. A. Sigrist,et al. Nucleic Acids Research Advance Access published November 14, 2007 The 20 years of PROSITE , 2007 .
[10] Christopher S. Oehmen,et al. Physicochemical property distributions for accurate and rapid pairwise protein homology detection , 2010, BMC Bioinformatics.
[11] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[12] Quan Zou,et al. Exploratory Predicting Protein Folding Model with Random Forest and Hybrid Features , 2014 .
[13] S F Altschul,et al. Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. , 1998, Trends in biochemical sciences.
[14] David C. Jones,et al. CATH--a hierarchic classification of protein domain structures. , 1997, Structure.
[15] O. Chapelle,et al. Semi-Supervised Learning (Chapelle, O. et al., Eds.; 2006) [Book reviews] , 2009, IEEE Transactions on Neural Networks.
[16] Jason Weston,et al. Combining classifiers for improved classification of proteins from sequence or structure , 2008, BMC Bioinformatics.
[17] Jason Weston,et al. Protein ranking: from local to global structure in the protein similarity network. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[18] Hao Lin,et al. Prediction of ketoacyl synthase family using reduced amino acid alphabets , 2012, Journal of Industrial Microbiology & Biotechnology.
[19] K. Chou. Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001 .
[20] Xiaolong Wang,et al. Protein Remote Homology Detection by Combining Chou’s Pseudo Amino Acid Composition and Profile‐Based Protein Representation , 2013, Molecular informatics.
[21] Dominik Gront,et al. BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles , 2012, Nucleic Acids Res..
[22] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[23] David Haussler,et al. A Discriminative Framework for Detecting Remote Protein Homologies , 2000, J. Comput. Biol..
[24] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[25] Hui Ding,et al. The prediction of protein structural class using averaged chemical shifts , 2012, Journal of biomolecular structure & dynamics.
[26] Didier Rognan,et al. IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces , 2015, J. Chem. Inf. Model..
[27] De-Shuang Huang,et al. Human face recognition based on multi-features using neural networks committee , 2004, Pattern Recognit. Lett..
[28] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[29] Amos Bairoch,et al. PROSITE, a protein domain database for functional characterization and annotation , 2009, Nucleic Acids Res..
[30] Byung-Jun Yoon,et al. Hidden Markov Models and their Applications in Biological Sequence Analysis , 2009, Current genomics.
[31] Mindaugas Margelevicius,et al. COMA server for protein distant homology search , 2010, Bioinform..
[32] Jason Weston,et al. Protein Ranking by Semi-Supervised Network Propagation , 2006, BMC Bioinformatics.
[33] Jason Weston,et al. Mismatch string kernels for discriminative protein classification , 2004, Bioinform..
[34] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[35] James E. Bray,et al. The CATH database: an extended protein family resource for structural and functional genomics , 2003, Nucleic Acids Res..
[36] Junjie Chen,et al. Application of learning to rank to protein remote homology detection , 2015, Bioinform..
[37] Vladimir Vapnik,et al. Statistical learning theory , 1998 .
[38] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[39] Gary D Bader,et al. A draft map of the human proteome , 2014, Nature.
[40] Eleazar Eskin,et al. The Spectrum Kernel: A String Kernel for SVM Protein Classification , 2001, Pacific Symposium on Biocomputing.
[41] B. Liu,et al. Protein remote homology detection by combining Chou’s distance-pair pseudo amino acid composition and principal component analysis , 2015, Molecular Genetics and Genomics.
[42] Xiaolong Wang,et al. Using distances between Top-n-gram and residue pairs for protein remote homology detection , 2014, BMC Bioinformatics.
[43] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[44] Michael Gribskov,et al. Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching , 1996, Comput. Chem..
[45] M. Sternberg,et al. Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.
[46] S. B. Needleman,et al. A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.
[47] De-Shuang Huang,et al. A Constructive Hybrid Structure Optimization Methodology for Radial Basis Probabilistic Neural Networks , 2008, IEEE Transactions on Neural Networks.
[48] B. Rost. Twilight zone of protein sequence alignments. , 1999, Protein engineering.
[49] Peng Chen,et al. Predicting protein interaction sites from residue spatial sequence profile and evolution rate , 2006, FEBS Letters.
[50] Frances M. G. Pearl,et al. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution , 2006, Nucleic Acids Res..
[51] Dong Xu,et al. Computational methods for remote homolog identification. , 2005, Current protein & peptide science.
[52] Klaus Obermayer,et al. Fast model-based protein homology detection without alignment , 2007, Bioinform..
[53] Yutaka Akiyama,et al. FORTE: a profile-profile comparison tool for protein fold recognition , 2004, Bioinform..
[54] Erik L. L. Sonnhammer,et al. Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER , 2005, BMC Bioinformatics.
[55] Xiaolong Wang,et al. Sequence analysis Application of latent semantic analysis to protein remote homology detection , 2006 .
[56] Tim J. P. Hubbard,et al. SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..
[57] Li Liao,et al. Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships , 2003, J. Comput. Biol..
[58] Akira R. Kinjo,et al. Protein structure databases with new web services for structural biology and biomedical research , 2008, Briefings Bioinform..
[59] Shanyi Wang,et al. Protein Remote Homology Detection by Combining Pseudo Dimer Composition with an Ensemble Learning Method , 2016 .
[60] Peter Meinicke,et al. Word correlation matrices for protein sequence analysis and remote homology detection , 2008, BMC Bioinformatics.
[61] Yair Neuman. The Definition of Life and the Life of a Definition , 2012, Journal of biomolecular structure & dynamics.
[62] Hasan Ogul,et al. A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets , 2007, Biosyst..
[63] R. Abagyan,et al. Do aligned sequences share the same fold? , 1997, Journal of molecular biology.
[64] Tatsuya Akutsu,et al. Protein homology detection using string alignment kernels , 2004, Bioinform..
[65] N. Grishin,et al. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. , 2003, Journal of molecular biology.
[66] Minoru Kanehisa,et al. AAindex: amino acid index database, progress report 2008 , 2007, Nucleic Acids Res..
[67] Jason Weston,et al. Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding , 2011, PLoS Comput. Biol..
[68] Xiaolong Wang,et al. Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection , 2013, Bioinform..
[69] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[70] Christopher S. Oehmen,et al. SVM-HUSTLE - an iterative semi-supervised machine learning approach for pairwise protein remote homology detection , 2008, Bioinform..
[71] Q. Zou,et al. A Global Characterization and Identification of Multifunctional Enzymes , 2012, PloS one.
[72] Guoli Wang,et al. PISCES: a protein sequence culling server , 2003, Bioinform..
[73] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[74] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[75] Rong Jin,et al. Learning to Rank by Optimizing NDCG Measure , 2009, NIPS.
[76] Jason Weston,et al. Rankprop: a web server for protein remote homology detection , 2008, Bioinform..
[77] Wei Chen,et al. Prediction of thermophilic proteins using feature selection technique. , 2011, Journal of microbiological methods.
[78] Ming Tang,et al. COMPASS server for homology detection: improved statistical accuracy, speed and functionality , 2009, Nucleic Acids Res..
[79] Kuo-Bin Li,et al. Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. , 2008, Journal of theoretical biology.
[80] Jaap Heringa,et al. webPRC: the Profile Comparer for alignment-based searching of public domain databases , 2009, Nucleic Acids Res..
[81] 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.
[82] Piero Fariselli,et al. The WWWH of remote homolog detection: The state of the art , 2006, Briefings Bioinform..
[83] Kuo-Chen Chou,et al. Ensemble classifier for protein fold pattern recognition , 2006, Bioinform..
[84] 陈奕欣. Ongoing and future developments at the Universal Protein Resource , 2011 .
[85] Christoph Weber,et al. FFAS server: novel features and applications , 2011, Nucleic Acids Res..
[86] George Karypis,et al. Profile-based direct kernels for remote homology detection and fold recognition , 2005, Bioinform..
[87] Steven E. Brenner,et al. SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures , 2013, Nucleic Acids Res..
[88] S. Eddy,et al. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.
[89] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[90] 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..
[91] A. Bax,et al. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks , 2013, Journal of Biomolecular NMR.
[92] B. Liu,et al. Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection , 2012, PloS one.
[93] Takashi Ishida,et al. GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics , 2012, PloS one.
[94] María Martín,et al. Ongoing and future developments at the Universal Protein Resource , 2010, Nucleic Acids Res..
[95] Lukasz A. Kurgan,et al. PFRES: protein fold classification by using evolutionary information and predicted secondary structure , 2007, Bioinform..
[96] Theodoros Damoulas,et al. Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection , 2008, Bioinform..
[97] 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..
[98] De-Shuang Huang,et al. A constructive approach for finding arbitrary roots of polynomials by neural networks , 2004, IEEE Transactions on Neural Networks.
[99] D. Mount. Bioinformatics: Sequence and Genome Analysis , 2001 .
[100] Adrian Tsang,et al. Identification of DNA-Binding Proteins by Combining Auto-Cross Covariance Transformation and Ensemble Learning , 2016 .
[101] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[102] A. D. McLachlan,et al. Profile analysis: detection of distantly related proteins. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[103] Xiaolong Wang,et al. A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis , 2008, BMC Bioinformatics.
[104] Yuanzhi Li,et al. A Theoretical Analysis of NDCG Ranking Measures , 2013 .
[105] Nikolaos V. Sahinidis,et al. GPU-BLAST: using graphics processors to accelerate protein sequence alignment , 2010, Bioinform..
[106] Junjie Chen,et al. Protein Remote Homology Detection Based on an Ensemble Learning Approach , 2016, BioMed research international.
[107] Zhenhua Li,et al. Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts , 2014, BMC Bioinformatics.
[108] Xuan Liu,et al. Protein remote homology detection based on auto-cross covariance transformation , 2011, Comput. Biol. Medicine.
[109] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[110] Steven E. Brenner,et al. The value of protein structure classification information—Surveying the scientific literature , 2015, Proteins.
[111] Anders Krogh,et al. SAM: SEQUENCE ALIGNMENT AND MODELING SOFTWARE SYSTEM , 1995 .
[112] Yong Wang,et al. PROCAIN server for remote protein sequence similarity search , 2009, Bioinform..
[113] Peter Meinicke,et al. Remote homology detection based on oligomer distances , 2006, Bioinform..
[114] F E Cohen,et al. Pairwise sequence alignment below the twilight zone. , 2001, Journal of molecular biology.
[115] Mindaugas Margelevicius,et al. Bayesian nonparametrics in protein remote homology search , 2016, Bioinform..
[116] Xiangxiang Zeng,et al. nDNA-prot: identification of DNA-binding proteins based on unbalanced classification , 2014, BMC Bioinformatics.
[117] Andrzej Kloczkowski,et al. GENN: a GEneral Neural Network for learning tabulated data with examples from protein structure prediction. , 2015, Methods in molecular biology.
[118] K. Chou. Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001, Proteins.
[119] Yaoqi Zhou,et al. Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates , 2011, Bioinform..
[120] C. Pál,et al. An integrated view of protein evolution , 2006, Nature Reviews Genetics.
[121] S. Dumais. Latent Semantic Analysis. , 2005 .
[122] Qi Li,et al. A Speculative HMMER Search Implementation on GPU , 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.