Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome
暂无分享,去创建一个
Yuedong Yang | Huiying Zhao | Yaoqi Zhou | Jihua Wang | Yaoqi Zhou | Yuedong Yang | Huiying Zhao | Jihua Wang
[1] Yaoqi Zhou,et al. Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function , 2010, Bioinform..
[2] K Frech,et al. Computer-assisted prediction, classification, and delimitation of protein binding sites in nucleic acids. , 1993, Nucleic acids research.
[3] Yixue Li,et al. Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines. , 2006, Journal of theoretical biology.
[4] Yuedong Yang,et al. Prediction and validation of the unexplored RNA‐binding protein atlas of the human proteome , 2014, Proteins.
[5] S. Harrison,et al. Structure of the NF-kappa B p50 homodimer bound to DNA. , 1995, Nature.
[6] Carmay Lim,et al. DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry , 2012, Nucleic Acids Res..
[7] Jeffrey Skolnick,et al. Efficient prediction of nucleic acid binding function from low-resolution protein structures. , 2006, Journal of molecular biology.
[8] Shandar Ahmad,et al. PSSM-based prediction of DNA binding sites in proteins , 2005, BMC Bioinformatics.
[9] Hong Yan,et al. Prediction of DNA-binding protein based on statistical and geometric features and support vector machines , 2011, Proteome Science.
[10] Shinn-Ying Ho,et al. Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties , 2011, BMC Bioinformatics.
[11] Hongyi Zhou,et al. Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.
[12] Subhash G. Vasudevan,et al. Structure of the Dengue Virus Helicase/Nucleoside Triphosphatase Catalytic Domain at a Resolution of 2.4 Å , 2005, Journal of Virology.
[13] Pinak Chakrabarti,et al. Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters , 2012, Nucleic acids research.
[14] Liangjiang Wang,et al. Prediction of DNA-binding residues from protein sequence information using random forests , 2009, BMC Genomics.
[15] Song Liu,et al. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. , 2005, Journal of medicinal chemistry.
[16] Cathy H. Wu,et al. The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..
[17] Yu-dong Cai,et al. Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. , 2003, Biochimica et biophysica acta.
[18] Frank Dellaert,et al. Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical Fourier Transform , 2009, J. Comput. Biol..
[19] F. Skorpen,et al. Nuclear and mitochondrial uracil-DNA glycosylases are generated by alternative splicing and transcription from different positions in the UNG gene. , 1997, Nucleic acids research.
[20] K. Chou,et al. iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model , 2011, PloS one.
[21] Michael I. Jordan,et al. Genome-scale phylogenetic function annotation of large and diverse protein families. , 2011, Genome research.
[22] Igor B. Kuznetsov,et al. DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins , 2007, Bioinform..
[23] Torsten Schwede,et al. Assessment of template based protein structure predictions in CASP9 , 2011, Proteins.
[24] Jeffrey Skolnick,et al. From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions , 2009, PLoS Comput. Biol..
[25] N. Bhardwaj,et al. Residue‐level prediction of DNA‐binding sites and its application on DNA‐binding protein predictions , 2007, FEBS letters.
[26] J. Skolnick,et al. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm , 2004, Proteins.
[27] Jeffrey Skolnick,et al. DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions , 2008, Nucleic acids research.
[28] Seren Soner,et al. DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues , 2010, Nucleic Acids Res..
[29] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[30] R. Langlois,et al. Boosting the prediction and understanding of DNA-binding domains from sequence , 2010, Nucleic acids research.
[31] Liangjiang Wang,et al. BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences , 2006, Nucleic Acids Res..
[32] Yaoqi Zhou,et al. A new size‐independent score for pairwise protein structure alignment and its application to structure classification and nucleic‐acid binding prediction , 2012, Proteins.
[33] 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..
[34] Gajendra P. S. Raghava,et al. Identification of DNA-binding proteins using support vector machines and evolutionary profiles , 2007, BMC Bioinformatics.
[35] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[36] Kenji Mizuguchi,et al. Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks , 2009, BMC Structural Biology.
[37] Yaoqi Zhou,et al. An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles , 2009, Proteins.
[38] R. Sladek,et al. Chromosomal Mapping of the Human and Murine Orphan Receptors ERRα (ESRRA) and ERRβ (ESRRB) and Identification of a Novel Human ERRα-Related Pseudogene , 1997 .
[39] Kengo Kinoshita,et al. PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces , 2005, Bioinform..
[40] Julio Collado-Vides,et al. Comparative footprinting of DNA-binding proteins , 2006, ISMB.
[41] Yaoqi Zhou,et al. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets , 2010, Nucleic acids research.
[42] Jeffrey Skolnick,et al. A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome , 2009, PLoS Comput. Biol..
[43] P. N. Suganthan,et al. DNA-Prot: Identification of DNA Binding Proteins from Protein Sequence Information using Random Forest , 2009, Journal of biomolecular structure & dynamics.
[44] Yael Mandel-Gutfreund,et al. Annotating nucleic acid-binding function based on protein structure. , 2003, Journal of molecular biology.
[45] Yi Xiong,et al. An accurate feature‐based method for identifying DNA‐binding residues on protein surfaces , 2011, Proteins.
[46] Yuedong Yang,et al. Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction , 2011, RNA biology.
[47] David Liu,et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis , 2007, BMC Bioinformatics.
[48] Xiao Sun,et al. Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature , 2008, Bioinform..
[49] Harianto Tjong,et al. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces , 2007, Nucleic acids research.
[50] Dusanka Janezic,et al. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment , 2010, Bioinform..
[51] Akinori Sarai,et al. Moment-based prediction of DNA-binding proteins. , 2004, Journal of molecular biology.
[52] Wei Yang,et al. Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. , 2007, Molecular cell.
[53] Baris E. Suzek,et al. The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..
[54] Janet M Thornton,et al. Using structural motif templates to identify proteins with DNA binding function. , 2003, Nucleic acids research.
[55] N. Copeland,et al. Chromosomal mapping of the human and murine orphan receptors ERRalpha (ESRRA) and ERRbeta (ESRRB) and identification of a novel human ERRalpha-related pseudogene. , 1997, Genomics.
[56] Hui Lu,et al. NAPS: a residue-level nucleic acid-binding prediction server , 2010, Nucleic Acids Res..
[57] Seungwoo Hwang,et al. Using evolutionary and structural information to predict DNA‐binding sites on DNA‐binding proteins , 2006, Proteins.
[58] M. Sternberg,et al. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. , 2001, Journal of molecular biology.
[59] Jack Y. Yang,et al. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features , 2010, BMC Systems Biology.
[60] N. Bhardwaj,et al. Kernel-based machine learning protocol for predicting DNA-binding proteins , 2005, Nucleic acids research.
[61] Christina S. Leslie,et al. iDBPs: a web server for the identification of DNA binding proteins , 2010, Bioinform..
[62] Vasant Honavar,et al. Predicting DNA-binding sites of proteins from amino acid sequence , 2006, BMC Bioinformatics.
[63] Wolfgang Jahnke,et al. Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein , 2008, The EMBO journal.
[64] Michael Schroeder,et al. MetaDBSite: a meta approach to improve protein DNA-binding sites prediction , 2011, BMC Systems Biology.
[65] Janet M Thornton,et al. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. , 2003, Nucleic acids research.
[66] Lu Xie,et al. A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach , 2010, Molecules and cells.
[67] Guy Nimrod,et al. Identification of DNA-binding proteins using structural, electrostatic and evolutionary features. , 2009, Journal of molecular biology.
[68] Junfeng Xia,et al. Exploiting a Reduced Set of Weighted Average Features to Improve Prediction of DNA-Binding Residues from 3D Structures , 2011, PloS one.
[69] Shandar Ahmad,et al. Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information , 2004, Bioinform..