Determinants of antigenicity and specificity in immune response for protein sequences
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Yulong Wang | Cheng Li | Wenjun Wu | Kevin P. White | Parantu K. Shah | Nicolas N. Negre | K. White | Cheng Li | N. Negre | P. Shah | Wenjun Wu | Yulong Wang | Yulong Wang
[1] 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 .
[2] K. Chou,et al. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale , 2007, Amino Acids.
[3] J. Janin,et al. Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.
[4] Pierre Baldi,et al. SCRATCH: a protein structure and structural feature prediction server , 2005, Nucleic Acids Res..
[5] M. Levitt. A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.
[6] P. Ponnuswamy,et al. Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. , 1980, Biochimica et biophysica acta.
[7] Pierre Baldi,et al. COBEpro: a novel system for predicting continuous B-cell epitopes. , 2009, Protein engineering, design & selection : PEDS.
[8] Irini A. Doytchinova,et al. JenPep: A Novel Computational Information Resource for Immunobiology and Vaccinology , 2003, J. Chem. Inf. Comput. Sci..
[9] P. Karplus,et al. Prediction of chain flexibility in proteins , 1985, Naturwissenschaften.
[10] Gajendra P. S. Raghava,et al. BcePred: Prediction of Continuous B-Cell Epitopes in Antigenic Sequences Using Physico-chemical Properties , 2004, ICARIS.
[11] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[12] M. Gerstein,et al. Unlocking the secrets of the genome , 2009, Nature.
[13] Thorsten Joachims,et al. Making large scale SVM learning practical , 1998 .
[14] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[15] Alessandro Sette,et al. The Immune Epitope Database 2.0 , 2009, Nucleic Acids Res..
[16] P. Tongaonkar,et al. A semi‐empirical method for prediction of antigenic determinants on protein antigens , 1990, FEBS letters.
[17] E. Lundberg,et al. Towards a knowledge-based Human Protein Atlas , 2010, Nature Biotechnology.
[18] Urmila Kulkarni-Kale,et al. CEP: a conformational epitope prediction server , 2005, Nucleic Acids Res..
[19] Irini A. Doytchinova,et al. JenPep: a database of quantitative functional peptide data for immunology , 2002, Bioinform..
[20] Yaoqi Zhou,et al. Achieving 80% ten‐fold cross‐validated accuracy for secondary structure prediction by large‐scale training , 2006, Proteins.
[21] Jean-Luc Pellequer,et al. BEPITOPE: predicting the location of continuous epitopes and patterns in proteins , 2003, Journal of molecular recognition : JMR.
[22] A. Alix,et al. Predictive estimation of protein linear epitopes by using the program PEOPLE. , 1999, Vaccine.
[23] D. Flower,et al. Benchmarking B cell epitope prediction: Underperformance of existing methods , 2005, Protein science : a publication of the Protein Society.
[24] S. Vucetic,et al. Flavors of protein disorder , 2003, Proteins.
[25] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[26] Morten Nielsen,et al. Improved method for predicting linear B-cell epitopes , 2006, Immunome research.
[27] Bernd Mayer,et al. Machine learning approaches for prediction of linear B‐cell epitopes on proteins , 2006, Journal of molecular recognition : JMR.
[28] BMC Bioinformatics , 2005 .
[29] E Westhof,et al. Correlation between the location of antigenic sites and the prediction of turns in proteins. , 1993, Immunology letters.
[30] Sudipto Saha,et al. Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network , 2006, Proteins.
[31] D. Haussler,et al. Hidden Markov models in computational biology. Applications to protein modeling. , 1993, Journal of molecular biology.
[32] D T Jones,et al. Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.
[33] Robert D. Finn,et al. New developments in the InterPro database , 2007, Nucleic Acids Res..
[34] M. Bhasin,et al. Bcipep: A database of B-cell epitopes , 2005, BMC Genomics.
[35] R. Hodges,et al. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. , 1986, Biochemistry.
[36] E. Emini,et al. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide , 1985, Journal of virology.
[37] A. Sali,et al. Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.
[38] R. Doolittle,et al. A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.
[39] O. Lund,et al. Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures , 2006, Protein science : a publication of the Protein Society.
[40] 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.
[41] Vasant Honavar,et al. Recent advances in B-cell epitope prediction methods , 2010, Immunome research.
[42] Vasant G Honavar,et al. Predicting linear B‐cell epitopes using string kernels , 2008, Journal of molecular recognition : JMR.
[43] J. Wootton,et al. Analysis of compositionally biased regions in sequence databases. , 1996, Methods in enzymology.