Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites
暂无分享,去创建一个
Yaoqi Zhou | Yuedong Yang | Ghazaleh Taherzadeh | Huiying Zhao | Yaoqi Zhou | Yuedong Yang | Huiying Zhao | G. Taherzadeh
[1] Elizabeth Yuriev,et al. Challenges and advances in computational docking: 2009 in review , 2011, Journal of molecular recognition : JMR.
[2] M Michael Gromiha,et al. Identification and analysis of binding site residues in protein-carbohydrate complexes using energy based approach. , 2014, Protein and peptide letters.
[3] Milan Mrksich,et al. Carbohydrate arrays for the evaluation of protein binding and enzymatic modification. , 2002, Chemistry & biology.
[4] James G. Lyons,et al. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning , 2015, Scientific Reports.
[5] Xin Chen,et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation , 2012, Nucleic Acids Res..
[6] Yaoqi Zhou,et al. Carbohydrate‐binding protein identification by coupling structural similarity searching with binding affinity prediction , 2014, J. Comput. Chem..
[7] Yang Zhang,et al. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation , 2012, Nucleic Acids Res..
[8] Yuedong Yang,et al. Predicting DNA-Binding Proteins and Binding Residues by Complex Structure Prediction and Application to Human Proteome , 2014, PloS one.
[9] 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.
[10] A. Sali,et al. Structural genomics: beyond the Human Genome Project , 1999, Nature Genetics.
[11] Mark von Itzstein,et al. The war against influenza: discovery and development of sialidase inhibitors. , 2007, Nature reviews. Drug discovery.
[12] Serge Pérez,et al. Glyco3D: a portal for structural glycosciences. , 2015, Methods in molecular biology.
[13] Petety V Balaji,et al. Identification of common structural features of binding sites in galactose‐specific proteins , 2004, Proteins.
[14] Alan Wee-Chung Liew,et al. Sequence‐based prediction of protein–peptide binding sites using support vector machine , 2016, J. Comput. Chem..
[15] Jeffrey Skolnick,et al. PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity , 2015, J. Chem. Inf. Model..
[16] 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..
[17] D. Stuart,et al. More powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules , 2014, Nature Structural &Molecular Biology.
[18] Mark von Itzstein,et al. The war against influenza: discovery and development of sialidase inhibitors , 2007, Nature Reviews Drug Discovery.
[19] Dirk Neumann,et al. BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking , 2008, J. Chem. Inf. Model..
[20] U. Heinemann,et al. High-resolution crystal structures of Caldicellulosiruptor strain Rt8B.4 carbohydrate-binding module CBM27-1 and its complex with mannohexaose. , 2004, Journal of molecular biology.
[21] Sukanta Mondal,et al. MOWGLI: prediction of protein–MannOse interacting residues With ensemble classifiers usinG evoLutionary Information , 2016, Journal of biomolecular structure & dynamics.
[22] 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..
[23] Kuldip K. Paliwal,et al. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? , 2016, Briefings Bioinform..
[24] David F. Smith,et al. Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen , 2012, Nature.
[25] Nitish Kumar Mishra,et al. Identification of Mannose Interacting Residues Using Local Composition , 2011, PloS one.
[26] Wen-Lian Hsu,et al. Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms , 2012, PloS one.
[27] Pedro M. Coutinho,et al. The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..
[28] Jeffrey Skolnick,et al. DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions , 2008, Nucleic acids research.
[29] J M Thornton,et al. Analysis and prediction of carbohydrate binding sites. , 2000, Protein engineering.
[30] J. Skolnick,et al. A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation , 2008, Proceedings of the National Academy of Sciences.
[31] Kuldip K. Paliwal,et al. Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins , 2016, Bioinform..
[32] J. Balzarini,et al. Potential of carbohydrate‐binding agents as therapeutics against enveloped viruses , 2010, Medicinal research reviews.
[33] 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.
[34] Lukasz A. Kurgan,et al. A comprehensive comparative review of sequence-based predictors of DNA- and RNA-binding residues , 2016, Briefings Bioinform..
[35] Yaoqi Zhou,et al. Characterizing the existing and potential structural space of proteins by large-scale multiple loop permutations. , 2011, Journal of molecular biology.
[36] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[37] Yaoqi Zhou,et al. SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity , 2016, J. Comput. Chem..
[38] Hassan Al-Ali,et al. Prediction of protein‐glucose binding sites using support vector machines , 2009, Proteins.
[39] S. Nakahara,et al. Biological modulation by lectins and their ligands in tumor progression and metastasis. , 2008, Anti-cancer agents in medicinal chemistry.
[40] Yaoqi Zhou,et al. Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all‐atom statistical energy functions , 2008, Protein science : a publication of the Protein Society.
[41] M. Heise,et al. A Single-Amino-Acid Polymorphism in Chikungunya Virus E2 Glycoprotein Influences Glycosaminoglycan Utilization , 2013, Journal of Virology.
[42] Petras J. Kundrotas,et al. Template-Based Modeling of Protein-RNA Interactions , 2016, PLoS Comput. Biol..
[43] Shandar Ahmad,et al. PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools , 2010, Adv. Bioinformatics.
[44] Takashi Yamane,et al. An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins. , 2003, Protein engineering.
[45] J. Lowe,et al. Role of glycosylation in development. , 2003, Annual review of biochemistry.
[46] Yaoqi Zhou,et al. SPOT‐ligand 2: improving structure‐based virtual screening by binding‐homology search on an expanded structural template library , 2017, Bioinform..
[47] Nicolai V Bovin,et al. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. , 2015, Biochimica et biophysica acta.
[48] Richard D Cummings,et al. Protein glycosylation in cancer. , 2015, Annual review of pathology.
[49] Alan Wee-Chung Liew,et al. Sequence-Based Prediction of Protein-Carbohydrate Binding Sites Using Support Vector Machines , 2016, J. Chem. Inf. Model..
[50] Mahesh Kulharia,et al. InCa-SiteFinder: a method for structure-based prediction of inositol and carbohydrate binding sites on proteins. , 2009, Journal of molecular graphics & modelling.
[51] S. Hakomori. Tumor malignancy defined by aberrant glycosylation and sphingo(glyco)lipid metabolism. , 1996, Cancer research.
[52] 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.