TY - JOUR AU - Nanni, L. PY - 2006 DA - 2006// TI - Comparison among feature extraction methods for HIV-1 Protease Cleavage Site Prediction JO - Pattern Recognition VL - 39 UR - https://doi.org/10.1016/j.patcog.2005.11.002 DO - 10.1016/j.patcog.2005.11.002 ID - Nanni2006 ER - TY - JOUR AU - Nanni, L. AU - Lumini, A. PY - 2006 DA - 2006// TI - MppS: an ensemble of Support Vector Machine based on multiple physicochemical properties of amino-acids JO - NeuroComputing VL - 69 UR - https://doi.org/10.1016/j.neucom.2006.04.001 DO - 10.1016/j.neucom.2006.04.001 ID - Nanni2006 ER - TY - JOUR AU - Nanni, L. AU - Lumini, A. PY - 2006 DA - 2006// TI - An ensemble of K-Local Hyperplane for predicting Protein-Protein interactions JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl055 DO - 10.1093/bioinformatics/btl055 ID - Nanni2006 ER - TY - JOUR AU - Sarda, D. AU - Chua, G. H. AU - Li, K. AU - Krishnan, A. PY - 2005 DA - 2005// TI - pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-152 DO - 10.1186/1471-2105-6-152 ID - Sarda2005 ER - TY - CHAP AU - Huang, L. AU - Dai, Y. PY - 2005 DA - 2005// TI - A support vector machine approach for prediction of T cell epitopes BT - Proc of the Third Asia-Pacific Bioinformatics Conference ID - Huang2005 ER - TY - CHAP AU - Ogul, H. AU - Mumcuoglu, E. U. PY - 2007 DA - 2007// TI - Subcellular Localization Prediction with New Protein Encoding Schemes BT - IEEE T on Computational Biology and Bioinformatics ID - Ogul2007 ER - TY - JOUR AU - Murphy, L. R. AU - Wallqvist, A. AU - Levy, R. M. PY - 2000 DA - 2000// TI - Simplified amino acid alphabets for protein fold recognition and implications for folding JO - Protein Engineering VL - 13 UR - https://doi.org/10.1093/protein/13.3.149 DO - 10.1093/protein/13.3.149 ID - Murphy2000 ER - TY - BOOK AU - Cristianini, N. AU - Shawe-Taylor, J. PY - 2000 DA - 2000// TI - An introduction to Support vector machines and other kernel-based learning methods PB - Cambridge University Press CY - Cambridge, UK UR - https://doi.org/10.1017/CBO9780511801389 DO - 10.1017/CBO9780511801389 ID - Cristianini2000 ER - TY - CHAP AU - Rögnvaldsson, T. AU - You, L. PY - 2003 DA - 2003// TI - Why Neural Networks Should Not be Used for HIV-1 Protease Cleavage Site Prediction BT - Bioinformatics ID - Rögnvaldsson2003 ER - TY - JOUR AU - Chou, J. J. PY - 1993 DA - 1993// TI - Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach JO - Journal of Protein Chemistry VL - 12 UR - https://doi.org/10.1007/BF01028191 DO - 10.1007/BF01028191 ID - Chou1993 ER - TY - JOUR AU - Chou, J. J. PY - 1993 DA - 1993// TI - A formulation for correlating properties of peptides and its application to predicting human immunodeficiency virus protease-cleavable sites in proteins JO - Biopolymers VL - 33 UR - https://doi.org/10.1002/bip.360330910 DO - 10.1002/bip.360330910 ID - Chou1993 ER - TY - JOUR AU - Chou, K. C. PY - 1993 DA - 1993// TI - A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins JO - J Biol Chem VL - 268 ID - Chou1993 ER - TY - CHAP AU - Liang, G. Z. AU - Li, S. Z. PY - 2007 DA - 2007// TI - A new sequence representation (FASGAI) as applied in better specificity elucidation for human immunodeficiency virus type 1 protease BT - Biopolymers ID - Liang2007 ER - TY - JOUR AU - Cai, Y. D. AU - Chou, K. C. PY - 1998 DA - 1998// TI - Artificial neural network model for predicting HIV protease cleavage sites in protein JO - Advances in Engineering Software VL - 29 UR - https://doi.org/10.1016/S0965-9978(98)00046-5 DO - 10.1016/S0965-9978(98)00046-5 ID - Cai1998 ER - TY - JOUR AU - Narayanan, A. AU - Wu, X. AU - Yang, Z. PY - 2002 DA - 2002// TI - Mining viral protease data to extract cleavage knowledge JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.suppl_1.S5 DO - 10.1093/bioinformatics/18.suppl_1.S5 ID - Narayanan2002 ER - TY - JOUR AU - Rögnvaldsson, T. AU - You, L. AU - Garwicz, D. PY - 2007 DA - 2007// TI - Bioinformatic approaches for modeling the substrate specificity of HIV-1 protease: an overview JO - Expert Rev Mol Diagn VL - 7 UR - https://doi.org/10.1586/14737159.7.4.435 DO - 10.1586/14737159.7.4.435 ID - Rögnvaldsson2007 ER - TY - JOUR AU - Chen, J. AU - Liu, H. AU - Yang, J. AU - Chou, K. C. PY - 2007 DA - 2007// TI - Prediction of linear B-cell epitopes using amino acid pair antigenicity scale JO - Amino Acids VL - 33 UR - https://doi.org/10.1007/s00726-006-0485-9 DO - 10.1007/s00726-006-0485-9 ID - Chen2007 ER - TY - JOUR AU - Madden, D. R. PY - 1995 DA - 1995// TI - The three-dimensional structure of peptide-MHC complexes JO - Annual Review of Immunology VL - 13 UR - https://doi.org/10.1146/annurev.iy.13.040195.003103 DO - 10.1146/annurev.iy.13.040195.003103 ID - Madden1995 ER - TY - JOUR AU - Hammer, J. PY - 1995 DA - 1995// TI - New methods to predict MHC-binding sequences within protein antigens JO - Current Opinion Immunology VL - 7 UR - https://doi.org/10.1016/0952-7915(95)80013-1 DO - 10.1016/0952-7915(95)80013-1 ID - Hammer1995 ER - TY - JOUR AU - Sturniolo, T. AU - Bono, E. AU - Ding, J. AU - Raddrizzani, L. AU - Tuereci, O. AU - Sahin, U. AU - Braxenthaler, M. AU - Gallazzi, F. AU - Protti, M. P. AU - Sinigaglia, F. AU - Hammer, J. PY - 1999 DA - 1999// TI - Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices JO - Nature Biotechnology VL - 17 UR - https://doi.org/10.1038/9858 DO - 10.1038/9858 ID - Sturniolo1999 ER - TY - JOUR AU - Honeyman, M. C. AU - Brusic, V. AU - Stone, N. L. AU - Harrison, L. C. PY - 1998 DA - 1998// TI - Neural network-based prediction of candidate T-cell epitopes JO - Nature Biotechnology VL - 16 UR - https://doi.org/10.1038/nbt1098-966 DO - 10.1038/nbt1098-966 ID - Honeyman1998 ER - TY - JOUR AU - Milik, M. AU - Sauer, D. AU - Brunmark, A. P. AU - Yuan, L. AU - Vitiello, A. AU - Jackson, M. R. AU - Peterson, P. A. AU - Skolnick, J. AU - Glass, C. A. PY - 1998 DA - 1998// TI - Application of an artificial neural network to predict specific class I MHC binding peptide sequences JO - Nature Biotechnology VL - 16 UR - https://doi.org/10.1038/nbt0898-753 DO - 10.1038/nbt0898-753 ID - Milik1998 ER - TY - JOUR AU - Zhao, Y. AU - Pinilla, C. AU - Valmori, D. AU - Roland Martin, R. AU - Simon, R. PY - 2003 DA - 2003// TI - Application of support vector machines for T-cell epitopes prediction JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg255 DO - 10.1093/bioinformatics/btg255 ID - Zhao2003 ER - TY - JOUR AU - Brusic, V. AU - Petrovsky, N. AU - Zhang, G. AU - Bajic, V. B. PY - 2002 DA - 2002// TI - Prediction of promiscuous peptides that bind HLA class I molecules JO - Immunol Cell Biol VL - 80 UR - https://doi.org/10.1046/j.1440-1711.2002.01088.x DO - 10.1046/j.1440-1711.2002.01088.x ID - Brusic2002 ER - TY - JOUR AU - Zhang, G. L. AU - Khan, A. M. AU - Srinivasan, K. N. AU - August, J. T. AU - Brusic, V. PY - 2005 DA - 2005// TI - Neural Models for predicting viral vaccine targets JO - Journal Bioinform Comp Biol VL - 3 UR - https://doi.org/10.1142/S0219720005001466 DO - 10.1142/S0219720005001466 ID - Zhang2005 ER - TY - CHAP AU - Bozic, I. AU - Zhang, G. L. AU - Brusic, V. PY - 2005 DA - 2005// TI - Predictive Vaccinology: Optimization of Predictions using Support Vector Machine Classifiers BT - IDEAL ID - Bozic2005 ER - TY - JOUR AU - Chou, K. C. AU - Zhang, C. T. PY - 1995 DA - 1995// TI - Review: Prediction of protein structural classes JO - Critical Reviews in Biochemistry and Molecular Biology VL - 30 UR - https://doi.org/10.3109/10409239509083488 DO - 10.3109/10409239509083488 ID - Chou1995 ER - TY - JOUR AU - Shen, H. B. AU - Chou, K. C. PY - 2006 DA - 2006// TI - Ensemble classifier for protein fold pattern recognition JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl170 DO - 10.1093/bioinformatics/btl170 ID - Shen2006 ER - TY - JOUR AU - Huang, J. AU - Ling, C. X. PY - 2005 DA - 2005// TI - Using AUC and Accuracy in Evaluating Learning Algorithms JO - IEEE Trans Knowl Data Eng VL - 17 UR - https://doi.org/10.1109/TKDE.2005.50 DO - 10.1109/TKDE.2005.50 ID - Huang2005 ER - TY - CHAP AU - Fawcett, T. PY - 2003 DA - 2003// TI - ROC graphs: Notes and practical considerations for researchers BT - Tech Report HPL-2003-4, HP Laboratories ID - Fawcett2003 ER - TY - JOUR AU - Halkidi, M. AU - Batistakis, Y. AU - Vazirgiannis, M. PY - 2002 DA - 2002// TI - Cluster validity methods: Part I JO - SIGMOD Rec VL - 31 UR - https://doi.org/10.1145/565117.565124 DO - 10.1145/565117.565124 ID - Halkidi2002 ER - TY - CHAP AU - Martin, A. AU - Doddington, G. AU - Kamm, T. AU - Ordowski, M. AU - Przybocki, M. PY - 1997 DA - 1997// TI - The DET curve in assessment of decision task performance BT - Proc of EuroSpeech ID - Martin1997 ER - TY - JOUR AU - Kontijevskis, A. AU - Wikberg, J. E. S. AU - Komorowski, J. PY - 2007 DA - 2007// TI - Computational proteomics analysis of HIV-1 protease interactome JO - Proteins: Structure, Function, and Bioinformatics VL - 68 UR - https://doi.org/10.1002/prot.21415 DO - 10.1002/prot.21415 ID - Kontijevskis2007 ER - TY - BOOK AU - Duda, R. AU - Hart, P. AU - Stork, D. PY - 2001 DA - 2001// TI - Pattern Classification PB - Wiley CY - New York ID - Duda2001 ER -