TY - JOUR AU - Langlois, R. E. AU - Lu, H. PY - 2010 DA - 2010// TI - Boosting the prediction and understanding of DNA-binding domains from sequence JO - Nucleic Acids Res VL - 15 ID - Langlois2010 ER - TY - JOUR AU - Sarai, A. AU - Kono, H. PY - 2005 DA - 2005// TI - Protein-DNA recognition patterns and predictions JO - Annu Rev Biophys Biomol Struct VL - 34 UR - https://doi.org/10.1146/annurev.biophys.34.040204.144537 DO - 10.1146/annurev.biophys.34.040204.144537 ID - Sarai2005 ER - TY - JOUR AU - Parola, M. AU - Bellomo, G. AU - Robino, G. AU - Barrera, G. AU - Dianzani, M. U. PY - 1999 DA - 1999// TI - 4-Hydroxynonenal as a biological signal: molecular basis and pathophysiological implications JO - Antioxid Redox Signal VL - 1 UR - https://doi.org/10.1089/ars.1999.1.3-255 DO - 10.1089/ars.1999.1.3-255 ID - Parola1999 ER - TY - JOUR AU - Chou, C. C. AU - Lin, T. W. AU - Chen, C. Y. AU - Wang, A. H. PY - 2003 DA - 2003// TI - Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms JO - J Bacteriol VL - 185 UR - https://doi.org/10.1128/JB.185.14.4066-4073.2003 DO - 10.1128/JB.185.14.4066-4073.2003 ID - Chou2003 ER - TY - JOUR AU - Freeman, K. AU - Gwadz, M. AU - Shore, D. PY - 1995 DA - 1995// TI - Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast JO - Genetics VL - 141 ID - Freeman1995 ER - TY - JOUR AU - Gao, M. AU - Skolnick, J. PY - 2008 DA - 2008// TI - DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn332 DO - 10.1093/nar/gkn332 ID - Gao2008 ER - TY - JOUR AU - Zhao, H. AU - Yang, Y. AU - Zhou, Y. PY - 2010 DA - 2010// TI - Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq295 DO - 10.1093/bioinformatics/btq295 ID - Zhao2010 ER - TY - JOUR AU - Nimrod, G. AU - Szilágyi, A. AU - Leslie, C. AU - Ben-Tal, N. PY - 2009 DA - 2009// TI - Identification of DNA-binding proteins using structural, electrostatic and evolutionary features JO - J Mol Biol VL - 387 UR - https://doi.org/10.1016/j.jmb.2009.02.023 DO - 10.1016/j.jmb.2009.02.023 ID - Nimrod2009 ER - TY - JOUR AU - Kumar, M. AU - Gromiha, M. M. AU - Raghava, G. P. PY - 2007 DA - 2007// TI - Identification of DNA-binding proteins using support vector machines and evolutionary profiles JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-463 DO - 10.1186/1471-2105-8-463 ID - Kumar2007 ER - TY - JOUR AU - Kumar, K. K. AU - Pugalenthi, G. AU - Suganthan, P. N. PY - 2009 DA - 2009// TI - DNA-Prot: identification of DNA binding proteins from protein sequence information using random forest JO - J Biomol Struct Dynam VL - 26 UR - https://doi.org/10.1080/07391102.2009.10507281 DO - 10.1080/07391102.2009.10507281 ID - Kumar2009 ER - TY - JOUR AU - Lin, W. Z. AU - Fang, J. A. AU - Xiao, X. AU - Chou, K. C. PY - 2011 DA - 2011// TI - iDNA-Prot: identification of DNA binding proteins using random forest with grey model JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0024756 DO - 10.1371/journal.pone.0024756 ID - Lin2011 ER - TY - JOUR AU - Song, L. AU - Li, D. AU - Zeng, X. AU - Wu, Y. AU - Guo, L. AU - Zou, Q. PY - 2014 DA - 2014// TI - nDNA-prot: identification of DNA-binding proteins based on unbalanced classification JO - BMC Bioinformatics VL - 15 UR - https://doi.org/10.1186/1471-2105-15-298 DO - 10.1186/1471-2105-15-298 ID - Song2014 ER - TY - STD TI - Xu R, Zhou J, Liu B, Yao L, He Y, Zou Q, Wang X. enDNA-Prot: identification of DNA-binding proteins by applying ensemble learning. BioMed Res Int. 2014. ID - ref13 ER - TY - JOUR AU - Zou, C. AU - Gong, J. AU - Li, H. PY - 2013 DA - 2013// TI - An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis JO - BMC Bioinformatics VL - 14 UR - https://doi.org/10.1155/2013/191586 DO - 10.1155/2013/191586 ID - Zou2013 ER - TY - JOUR AU - Lou, W. AU - Wang, X. AU - Chen, F. AU - Chen, Y. AU - Jiang, B. AU - Zhang, H. PY - 2014 DA - 2014// TI - Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naive Bayes JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0086703 DO - 10.1371/journal.pone.0086703 ID - Lou2014 ER - TY - JOUR AU - Rohs, R. AU - Jin, X. AU - West, S. M. AU - Joshi, R. AU - Honig, B. AU - Mann, R. S. PY - 2010 DA - 2010// TI - Origins of specificity in protein-DNA recognition JO - Annu Rev Biochem VL - 79 UR - https://doi.org/10.1146/annurev-biochem-060408-091030 DO - 10.1146/annurev-biochem-060408-091030 ID - Rohs2010 ER - TY - JOUR AU - Chou, K. C. AU - Shen, H. B. PY - 2007 DA - 2007// TI - Recent progress in protein subcellular location prediction JO - Anal Biochem VL - 370 UR - https://doi.org/10.1016/j.ab.2007.07.006 DO - 10.1016/j.ab.2007.07.006 ID - Chou2007 ER - TY - JOUR AU - Wang, G. AU - Dunbrack, R. L. PY - 2005 DA - 2005// TI - PISCES: recent improvements to a PDB sequence culling server JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki402 DO - 10.1093/nar/gki402 ID - Wang2005 ER - TY - JOUR AU - Zhang, J. AU - Chen, W. AU - Sun, P. AU - Zhao, X. AU - Ma, Z. PY - 2015 DA - 2015// TI - Prediction of protein solvent accessibility using PSO-SVR with multiple sequence-derived features and weighted sliding window scheme JO - BioData Min VL - 8 UR - https://doi.org/10.1186/s13040-014-0034-0 DO - 10.1186/s13040-014-0034-0 ID - Zhang2015 ER - TY - STD TI - Zhang J, Zhao X, Sun P, Gao B, Ma Z. Conformational B-cell epitopes prediction from sequences using cost-sensitive ensemble classifiers and spatial clustering. BioMed Res Int. 2014. ID - ref20 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Bochman, M. L. AU - Paeschke, K. AU - Zakian, V. A. PY - 2012 DA - 2012// TI - DNA secondary structures: stability and function of G-quadruplex structures JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3296 DO - 10.1038/nrg3296 ID - Bochman2012 ER - TY - STD TI - Greive SJ, Fung HK, Chechik M, Jenkins HT, Weitzel SE, Aguiar PM, Brentnall AS, Glousieau M, Gladyshev GV, Potts JR, Antson AA. DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif. Nucleic Acids Res. 2016;44(2):776-789. ID - ref23 ER - TY - JOUR AU - Jones, D. T. PY - 1999 DA - 1999// TI - Protein secondary structure prediction based on position-specific scoring matrices JO - J Mol Biol VL - 292 UR - https://doi.org/10.1006/jmbi.1999.3091 DO - 10.1006/jmbi.1999.3091 ID - Jones1999 ER - TY - JOUR AU - Liu, Z. P. AU - Wu, L. Y. AU - Wang, Y. AU - Zhang, X. S. AU - Chen, L. PY - 2010 DA - 2010// TI - Prediction of protein–RNA binding sites by a random forest method with combined features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq253 DO - 10.1093/bioinformatics/btq253 ID - Liu2010 ER - TY - JOUR AU - Bordner, A. J. AU - Abagyan, R. PY - 2005 DA - 2005// TI - Statistical analysis and prediction of protein–protein interfaces JO - Proteins Struct Funct Bioinf VL - 60 UR - https://doi.org/10.1002/prot.20433 DO - 10.1002/prot.20433 ID - Bordner2005 ER - TY - JOUR AU - Jayaram, B. AU - McConnell, K. J. AU - Dixit, S. B. AU - Beveridge, D. L. PY - 1999 DA - 1999// TI - Free energy analysis of protein–DNA binding: the EcoRI endonuclease–DNA complex JO - J Comput Phys VL - 151 UR - https://doi.org/10.1006/jcph.1998.6173 DO - 10.1006/jcph.1998.6173 ID - Jayaram1999 ER - TY - JOUR AU - Chaires, J. B. AU - Satyanarayana, S. AU - Suh, D. AU - Fokt, I. AU - Przewloka, T. AU - Priebe, W. PY - 1996 DA - 1996// TI - Parsing the free energy of anthracycline antibiotic binding to DNA JO - Biochemistry VL - 35 UR - https://doi.org/10.1021/bi952812r DO - 10.1021/bi952812r ID - Chaires1996 ER - TY - JOUR AU - Liu, S. AU - Liu, S. AU - Zhu, X. AU - Liang, H. AU - Cao, A. AU - Chang, Z. AU - Lai, L. PY - 2007 DA - 2007// TI - Nonnatural protein–protein interaction-pair design by key residues grafting JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0606198104 DO - 10.1073/pnas.0606198104 ID - Liu2007 ER - TY - JOUR AU - Ahmad, S. AU - Sarai, A. PY - 2004 DA - 2004// TI - Moment-based prediction of DNA-binding proteins JO - J Mol Biol VL - 341 UR - https://doi.org/10.1016/j.jmb.2004.05.058 DO - 10.1016/j.jmb.2004.05.058 ID - Ahmad2004 ER - TY - JOUR AU - Landschulz, W. H. AU - Johnson, P. F. AU - McKnight, S. L. PY - 1988 DA - 1988// TI - The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins JO - Science VL - 240 UR - https://doi.org/10.1126/science.3289117 DO - 10.1126/science.3289117 ID - Landschulz1988 ER - TY - JOUR AU - Ip, Y. T. AU - Kraut, R. AU - Levine, M. AU - Rushlow, C. A. PY - 1991 DA - 1991// TI - The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in Drosophila JO - Cell VL - 64 UR - https://doi.org/10.1016/0092-8674(91)90651-E DO - 10.1016/0092-8674(91)90651-E ID - Ip1991 ER - TY - JOUR AU - Yu, X. AU - Cao, J. AU - Cai, Y. AU - Shi, T. AU - Li, Y. PY - 2016 DA - 2016// TI - Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines JO - J Theor Biol VL - 240 UR - https://doi.org/10.1016/j.jtbi.2005.09.018 DO - 10.1016/j.jtbi.2005.09.018 ID - Yu2016 ER - TY - JOUR AU - Slattery, M. AU - Riley, T. AU - Liu, P. AU - Abe, N. AU - Gomez-Alcala, P. AU - Dror, I. AU - Zhou, T. AU - Rohs, R. AU - Honig, B. AU - Bussemaker, H. J. AU - Mann, R. S. PY - 2011 DA - 2011// TI - Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins JO - Cell VL - 147 UR - https://doi.org/10.1016/j.cell.2011.10.053 DO - 10.1016/j.cell.2011.10.053 ID - Slattery2011 ER - TY - JOUR AU - PSORT, I. PY - 1997 DA - 1997// TI - PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization JO - J Mol Biol VL - 266 UR - https://doi.org/10.1006/jmbi.1996.0804 DO - 10.1006/jmbi.1996.0804 ID - PSORT1997 ER - TY - JOUR AU - Mukherjee, S. AU - Berger, M. F. AU - Jona, G. AU - Wang, X. S. AU - Muzzey, D. AU - Snyder, M. AU - Young, R. A. AU - Bulyk, M. L. PY - 2004 DA - 2004// TI - Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1473 DO - 10.1038/ng1473 ID - Mukherjee2004 ER - TY - JOUR AU - Ahmad, S. AU - Gromiha, M. M. AU - Sarai, A. PY - 2004 DA - 2004// TI - Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg432 DO - 10.1093/bioinformatics/btg432 ID - Ahmad2004 ER - TY - JOUR AU - Goodsell, D. AU - Dickerson, R. E. PY - 2004 DA - 2004// TI - Isohelical analysis of DNA groove-binding drugs JO - J Med Chem VL - 29 UR - https://doi.org/10.1021/jm00155a023 DO - 10.1021/jm00155a023 ID - Goodsell2004 ER - TY - JOUR AU - Chaires, J. B. PY - 2006 DA - 2006// TI - A thermodynamic signature for drug–DNA binding mode JO - Arch Biochem Biophys VL - 453 UR - https://doi.org/10.1016/j.abb.2006.03.027 DO - 10.1016/j.abb.2006.03.027 ID - Chaires2006 ER - TY - JOUR AU - Nowak, M. W. AU - Kearney, P. C. AU - Saks, M. E. AU - Labarca, C. G. AU - Silverman, S. K. AU - Zhong, W. AU - Thorson, J. AU - Abelson, J. N. AU - Davidson, N. PY - 1995 DA - 1995// TI - Nicotinic receptor binding site probed with unnatural amino acid incorporation in intact cells JO - Science VL - 268 UR - https://doi.org/10.1126/science.7716551 DO - 10.1126/science.7716551 ID - Nowak1995 ER - TY - JOUR AU - Zhang, J. AU - Sun, P. AU - Zhao, X. AU - Ma, Z. PY - 2014 DA - 2014// TI - PECM: Prediction of extracellular matrix proteins using the concept of Chou’s pseudo amino acid composition JO - J Theor Biol VL - 363 UR - https://doi.org/10.1016/j.jtbi.2014.08.002 DO - 10.1016/j.jtbi.2014.08.002 ID - Zhang2014 ER - TY - BOOK AU - Vapnik, V. PY - 2013 DA - 2013// TI - The nature of statistical learning theory ID - Vapnik2013 ER - TY - JOUR AU - Chang, C. C. AU - Lin, C. J. PY - 2011 DA - 2011// TI - LIBSVM: a library for support vector machines JO - ACM Trans Intell Syst Technol VL - 2 UR - https://doi.org/10.1145/1961189.1961199 DO - 10.1145/1961189.1961199 ID - Chang2011 ER - TY - STD TI - Yang XS. Firefly algorithms for multimodal optimization. In Stochastic algorithms: foundations and applications. Springer Berlin Heidelberg; 2009: 169–178. ID - ref44 ER - TY - JOUR AU - Hashmi, A. AU - Goel, N. AU - Goel, S. AU - Gupta, D. PY - 2013 DA - 2013// TI - Firefly algorithm for unconstrained optimization JO - IOSR J Comput Eng VL - 11 UR - https://doi.org/10.9790/0661-1117578 DO - 10.9790/0661-1117578 ID - Hashmi2013 ER - TY - JOUR AU - Yang, X. S. AU - He, X. PY - 2013 DA - 2013// TI - Firefly algorithm: recent advances and applications JO - Int J Swarm Intell VL - 1 UR - https://doi.org/10.1504/IJSI.2013.055801 DO - 10.1504/IJSI.2013.055801 ID - Yang2013 ER - TY - JOUR AU - Palit, S. AU - Sinha, S. N. AU - Molla, M. A. AU - Khanra, A. AU - Kule, M. PY - 2011 DA - 2011// TI - A cryptanalytic attack on the knapsack cryptosystem using binary firefly algorithm JO - In Int Conf Comput Commun Technol (ICCCT) VL - 2 ID - Palit2011 ER - TY - JOUR AU - Sayadi, M. K. AU - Hafezalkotob, A. AU - Naini, S. G. J. PY - 2013 DA - 2013// TI - Firefly-inspired algorithm for discrete optimization problems: an application to manufacturing cell formation JO - J Manuf Syst VL - 32 UR - https://doi.org/10.1016/j.jmsy.2012.06.004 DO - 10.1016/j.jmsy.2012.06.004 ID - Sayadi2013 ER - TY - JOUR AU - Poursalehi, N. AU - Zolfaghari, A. AU - Minuchehr, A. PY - 2015 DA - 2015// TI - A novel optimization method, Effective Discrete Firefly Algorithm, for fuel reload design of nuclear reactors JO - Ann Nuclear Energy VL - 81 UR - https://doi.org/10.1016/j.anucene.2015.02.047 DO - 10.1016/j.anucene.2015.02.047 ID - Poursalehi2015 ER - TY - JOUR AU - Chuang, L. Y. AU - Chang, H. W. AU - Tu, C. J. AU - Yang, C. H. PY - 2008 DA - 2008// TI - Improved binary PSO for feature selection using gene expression data JO - Comput Biol Chem VL - 32 UR - https://doi.org/10.1016/j.compbiolchem.2007.09.005 DO - 10.1016/j.compbiolchem.2007.09.005 ID - Chuang2008 ER - TY - JOUR AU - Chandrashekar, G. AU - Sahin, F. PY - 2014 DA - 2014// TI - A survey on feature selection methods JO - Comput Electr Eng VL - 40 UR - https://doi.org/10.1016/j.compeleceng.2013.11.024 DO - 10.1016/j.compeleceng.2013.11.024 ID - Chandrashekar2014 ER - TY - JOUR AU - Ding, C. AU - Peng, H. PY - 2005 DA - 2005// TI - Minimum redundancy feature selection from microarray gene expression data JO - J Bioinform Comput Biol VL - 3 UR - https://doi.org/10.1142/S0219720005001004 DO - 10.1142/S0219720005001004 ID - Ding2005 ER - TY - JOUR AU - Gao, M. AU - Skolnick, J. PY - 2009 DA - 2009// TI - A threading-based method for the prediction of DNA-binding proteins with application to the human genome JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000567 DO - 10.1371/journal.pcbi.1000567 ID - Gao2009 ER -