TY - JOUR AU - Gohlke, H. AU - Hendlich, M. AU - Klebe, G. PY - 2000 DA - 2000// TI - Knowledge-based scoring function to predict protein-ligand interactions JO - J Mol Biol VL - 295 UR - https://doi.org/10.1006/jmbi.1999.3371 DO - 10.1006/jmbi.1999.3371 ID - Gohlke2000 ER - TY - JOUR AU - Zhu, S. AU - Okuno, Y. AU - Tsujimoto, G. AU - Mamitsuka, H. PY - 2005 DA - 2005// TI - A probabilistic model for mining implicit ‘chemical compound-gene’ relations from literature JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1141 DO - 10.1093/bioinformatics/bti1141 ID - Zhu2005 ER - TY - JOUR AU - Tabei, Y. AU - Pauwels, E. AU - Stoven, V. AU - Takemoto, K. AU - Yamanishi, Y. PY - 2012 DA - 2012// TI - Identification of chemogenomic features from drug–target interaction networks using interpretable classifiers JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts412 DO - 10.1093/bioinformatics/bts412 ID - Tabei2012 ER - TY - JOUR AU - Rognan, D. PY - 2007 DA - 2007// TI - Chemogenomic approaches to rational drug design JO - Br J Pharmacol VL - 152 UR - https://doi.org/10.1038/sj.bjp.0707307 DO - 10.1038/sj.bjp.0707307 ID - Rognan2007 ER - TY - JOUR AU - Yamanishi, Y. AU - Araki, M. AU - Gutteridge, A. AU - Honda, W. AU - Kanehisa, M. PY - 2008 DA - 2008// TI - Prediction of drug-target interaction networks from the integration of chemical and genomic spaces JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn162 DO - 10.1093/bioinformatics/btn162 ID - Yamanishi2008 ER - TY - JOUR AU - Jacob, L. AU - Vert, J. P. PY - 2008 DA - 2008// TI - Protein-ligand interaction prediction: An improved chemogenomics approach JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn409 DO - 10.1093/bioinformatics/btn409 ID - Jacob2008 ER - TY - JOUR AU - Campillos, M. AU - Kuhn, M. AU - Gavin, A. C. AU - Jensen, L. J. AU - Bork, P. PY - 2008 DA - 2008// TI - Drug target identification using side-effect similarity JO - Science VL - 321 UR - https://doi.org/10.1126/science.1158140 DO - 10.1126/science.1158140 ID - Campillos2008 ER - TY - CHAP AU - Fernandez, M. AU - Sarai, A. AU - Ahmad, S. PY - 2009 DA - 2009// TI - Recognition of drug-target interaction patterns using genetic algorithm-optimized bayesian-regularized neural networks and support vector machines BT - Proceedings of the 2009 IEEE International Conference on Systems, Man and Cybernetics. SMC’09 PB - IEEE Press CY - San Antonio, TX, USA ID - Fernandez2009 ER - TY - JOUR AU - Geppert, H. AU - Humrich, J. AU - Stumpfe, D. AU - Gartner, T. AU - Bajorath, J. PY - 2009 DA - 2009// TI - Ligand prediction from protein sequence and small molecule information using support vector machines and fingerprint descriptors JO - J Chem Inf Model VL - 49 UR - https://doi.org/10.1021/ci900004a DO - 10.1021/ci900004a ID - Geppert2009 ER - TY - JOUR AU - Keiser, M. J. AU - Setola, V. AU - Irwin, J. J. AU - Laggner, C. AU - Abbas, A. I. AU - Hufeisen, S. J. AU - Jensen, N. H. AU - Kuijer, M. B. AU - Matos, R. C. AU - Tran, T. B. PY - 2009 DA - 2009// TI - Predicting new molecular targets for known drugs JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08506 DO - 10.1038/nature08506 ID - Keiser2009 ER - TY - JOUR AU - Bleakley, K. AU - Yamanishi, Y. PY - 2009 DA - 2009// TI - Supervised prediction of drug-target interactions using bipartite local models JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp433 DO - 10.1093/bioinformatics/btp433 ID - Bleakley2009 ER - TY - JOUR AU - He, Z. AU - Zhang, J. AU - Shi, X. H. AU - Hu, L. L. AU - Kong, X. AU - Cai, Y. D. AU - Chou, K. C. PY - 2010 DA - 2010// TI - Predicting drug-target interaction networks based on functional groups and biological features JO - PLoS ONE VL - 5 UR - https://doi.org/10.1371/journal.pone.0009603 DO - 10.1371/journal.pone.0009603 ID - He2010 ER - TY - JOUR AU - Yamanishi, Y. AU - Kotera, M. AU - Kanehisa, M. AU - Goto, S. PY - 2010 DA - 2010// TI - Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq176 DO - 10.1093/bioinformatics/btq176 ID - Yamanishi2010 ER - TY - JOUR AU - Takarabe, M. AU - Kotera, M. AU - Nishimura, Y. AU - Goto, S. AU - Yamanishi, Y. PY - 2012 DA - 2012// TI - Drug target prediction using adverse event report systems: a pharmacogenomic approach JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts413 DO - 10.1093/bioinformatics/bts413 ID - Takarabe2012 ER - TY - JOUR AU - Gonen, M. PY - 2012 DA - 2012// TI - Predicting drug-target interactions from chemical and genomic kernels using bayesian matrix factorization JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts360 DO - 10.1093/bioinformatics/bts360 ID - Gonen2012 ER - TY - STD TI - van Laarhoven T, Nabuurs SB, Marchiori E. Gaussian interaction profile kernels for predicting drug-target interaction. Bioinforma. 2011. doi:10.1093/bioinformatics/btr500, http://bioinformatics.oxfordjournals.org/content/early/2011/09/04/bioinformatics.btr500.full.pdf+html. UR - http://bioinformatics.oxfordjournals.org/content/early/2011/09/04/bioinformatics.btr500.full.pdf+html ID - ref16 ER - TY - JOUR AU - van Laarhoven, T. AU - Marchiori, E. PY - 2013 DA - 2013// TI - Predicting drug-target interactions for new drug compounds using a weighted nearest neighbor profile JO - PLoS ONE VL - 8 UR - https://doi.org/10.1371/journal.pone.0066952 DO - 10.1371/journal.pone.0066952 ID - van Laarhoven2013 ER - TY - JOUR AU - Willett, P. AU - Barnard, J. M. AU - Downs, G. M. PY - 1998 DA - 1998// TI - Chemical similarity searching JO - J Chem Inf Comput Sci VL - 38 UR - https://doi.org/10.1021/ci9800211 DO - 10.1021/ci9800211 ID - Willett1998 ER - TY - JOUR AU - Schuffenhauer, A. AU - Gillet, V. J. AU - Willett, P. PY - 2000 DA - 2000// TI - Similarity searching in files of three-dimensional chemical structures: analysis of the bioster database using two-dimensional fingerprints and molecular field descriptors JO - J Chem Inf Comput Sci VL - 40 UR - https://doi.org/10.1021/ci990263g DO - 10.1021/ci990263g ID - Schuffenhauer2000 ER - TY - JOUR AU - Helguera, A. M. AU - Combes, R. D. AU - González, M. P. AU - Cordeiro, M. PY - 2008 DA - 2008// TI - Applications of 2d descriptors in drug design: a dragon tale JO - Curr Top Med Chem VL - 8 UR - https://doi.org/10.2174/156802608786786598 DO - 10.2174/156802608786786598 ID - Helguera2008 ER - TY - JOUR AU - Hong, H. AU - Xie, Q. AU - Ge, W. AU - Qian, F. AU - Fang, H. AU - Shi, L. AU - Su, Z. AU - Perkins, R. AU - Tong, W. PY - 2008 DA - 2008// TI - Mold2, molecular descriptors from 2d structures for chemoinformatics and toxicoinformatics JO - J Chem Inf Model VL - 48 UR - https://doi.org/10.1021/ci800038f DO - 10.1021/ci800038f ID - Hong2008 ER - TY - JOUR AU - Kombo, D. C. AU - Tallapragada, K. AU - Jain, R. AU - Chewning, J. AU - Mazurov, A. A. AU - Speake, J. D. AU - Hauser, T. A. AU - Toler, S. PY - 2013 DA - 2013// TI - 3d molecular descriptors important for clinical success JO - J Chem Inf Model VL - 53 UR - https://doi.org/10.1021/ci300445e DO - 10.1021/ci300445e ID - Kombo2013 ER - TY - JOUR AU - Sawada, R. AU - Kotera, M. AU - Yamanishi, Y. PY - 2014 DA - 2014// TI - Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach JO - Mol Inf VL - 33 ID - Sawada2014 ER - TY - JOUR AU - Weininger, D. PY - 1988 DA - 1988// TI - Smiles, a chemical language and information system. 1. introduction to methodology and encoding rules JO - J Chem Inf Comput Sci VL - 28 UR - https://doi.org/10.1021/ci00057a005 DO - 10.1021/ci00057a005 ID - Weininger1988 ER - TY - JOUR AU - Weininger, D. AU - Weininger, A. AU - Weininger, J. L. PY - 1989 DA - 1989// TI - Smiles. 2. algorithm for generation of unique smiles notation JO - J Chem Inf Comput Sci VL - 29 UR - https://doi.org/10.1021/ci00062a008 DO - 10.1021/ci00062a008 ID - Weininger1989 ER - TY - JOUR AU - Vidal, D. AU - Thormann, M. AU - Pons, M. PY - 2005 DA - 2005// TI - Lingo, an efficient holographic text based method to calculate biophysical properties and intermolecular similarities JO - J Chem Inf Model VL - 45 UR - https://doi.org/10.1021/ci0496797 DO - 10.1021/ci0496797 ID - Vidal2005 ER - TY - JOUR AU - Cao, D. S. AU - Zhao, J. C. AU - Yang, Y. N. AU - Zhao, C. X. AU - Yan, J. AU - Liu, S. AU - Hu, Q. N. AU - Xu, Q. S. AU - Liang, Y. Z. PY - 2012 DA - 2012// TI - In silico toxicity prediction by support vector machine and smiles representation-based string kernel JO - SAR QSAR Environ Res VL - 23 UR - https://doi.org/10.1080/1062936X.2011.645874 DO - 10.1080/1062936X.2011.645874 ID - Cao2012 ER - TY - JOUR AU - Schwartz, J. AU - Awale, M. AU - Reymond, J. L. PY - 2013 DA - 2013// TI - Smifp (smiles fingerprint) chemical space for virtual screening and visualization of large databases of organic molecules JO - J Chem Inf Model VL - 53 UR - https://doi.org/10.1021/ci400206h DO - 10.1021/ci400206h ID - Schwartz2013 ER - TY - JOUR AU - Toropov, A. A. AU - Toropova, A. P. AU - Benfenati, E. PY - 2010 DA - 2010// TI - Smiles-based optimal descriptors: {QSAR} modeling of carcinogenicity by balance of correlations with ideal slopes JO - Eur J Med Chem VL - 45 UR - https://doi.org/10.1016/j.ejmech.2010.05.002 DO - 10.1016/j.ejmech.2010.05.002 ID - Toropov2010 ER - TY - JOUR AU - Toropov, A. A. AU - Toropova, A. P. AU - Benfenati, E. AU - Leszczynska, D. AU - Leszczynski, J. PY - 2010 DA - 2010// TI - Smiles-based optimal descriptors: Qsar analysis of fullerene-based hiv-1 pr inhibitors by means of balance of correlations JO - J Comput Chem VL - 31 ID - Toropov2010 ER - TY - JOUR AU - Hattori, M. AU - Tanaka, N. AU - Kanehisa, M. AU - Goto, S. PY - 2010 DA - 2010// TI - SIMCOMP/SUBCOMP: chemical structure search servers for network analyses JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq367 DO - 10.1093/nar/gkq367 ID - Hattori2010 ER - TY - JOUR AU - Wagner, R. A. AU - Fischer, M. J. PY - 1974 DA - 1974// TI - The string-to-string correction problem JO - J ACM VL - 21 UR - https://doi.org/10.1145/321796.321811 DO - 10.1145/321796.321811 ID - Wagner1974 ER - TY - JOUR AU - Islam, A. AU - Inkpen, D. PY - 2008 DA - 2008// TI - Semantic text similarity using corpus-based word similarity and string similarity JO - ACM Trans Knowl Discov Data VL - 2 UR - https://doi.org/10.1145/1376815.1376819 DO - 10.1145/1376815.1376819 ID - Islam2008 ER - TY - STD TI - Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in kegg. 2006; 34(suppl 1):354–57. doi:10.1093/nar/gkj102. UR - http://dx.doi.org/10.1093/nar/gkj102 ID - ref34 ER - TY - JOUR AU - Schomburg, I. AU - Chang, A. AU - Ebeling, C. AU - Gremse, M. AU - Heldt, C. AU - Huhn, G. AU - Schomburg, D. PY - 2004 DA - 2004// TI - Brenda, the enzyme database: updates and major new developments JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh081 DO - 10.1093/nar/gkh081 ID - Schomburg2004 ER - TY - JOUR AU - Gunther, S. AU - Kuhn, M. AU - Dunkel, M. AU - Campillos, M. AU - Senger, C. AU - Petsalaki, E. AU - Ahmed, J. AU - Urdiales, E. G. AU - Gewiess, A. AU - Jensen, L. J. AU - Schneider, R. AU - Skoblo, R. AU - Russell, R. B. AU - Bourne, P. E. AU - Bork, P. AU - Preissner, R. PY - 2008 DA - 2008// TI - Supertarget and matador: resources for exploring drug-target relationships JO - Nucleic Acids Res VL - 36 ID - Gunther2008 ER - TY - JOUR AU - Wishart, D. S. AU - Knox, C. AU - Guo, A. C. AU - Cheng, D. AU - Shrivastava, S. AU - Tzur, D. AU - Gautam, B. AU - Hassanali, M. PY - 2008 DA - 2008// TI - Drugbank: a knowledgebase for drugs, drug actions and drug targets JO - Nucleic Acids Res VL - 36 ID - Wishart2008 ER - TY - JOUR AU - Hattori, M. AU - Okuno, Y. AU - Goto, S. AU - Kanehisa, M. PY - 2003 DA - 2003// TI - Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways JO - J Am Chem Soc VL - 125 UR - https://doi.org/10.1021/ja036030u DO - 10.1021/ja036030u ID - Hattori2003 ER - TY - JOUR AU - Levenshtein, V. I. PY - 1966 DA - 1966// TI - Binary Codes Capable of Correcting Deletions, Insertions, and Reversals JO - Sov Phys Doklady VL - 10 ID - Levenshtein1966 ER - TY - JOUR AU - Hirschberg, D. S. PY - 1975 DA - 1975// TI - A linear space algorithm for computing maximal common subsequences JO - Commun ACM VL - 18 UR - https://doi.org/10.1145/360825.360861 DO - 10.1145/360825.360861 ID - Hirschberg1975 ER - TY - STD TI - Krause EF. 1986. An Adventure in Non-Euclidean Geometry. New York: Dover Publication. ID - ref41 ER - TY - STD TI - James CA, Weininger D, Delany J. Fingerprints - Screening and Similarity. 2000. Daylight Theory Manual. Irvine, CA and Santa Fe, NM, Daylight Chemical Information Systems, Inc., www.daylight.com/dayhtml/doc/theory/theory.finger.html. UR - http://www.daylight.com/dayhtml/doc/theory/theory.finger.html ID - ref42 ER - TY - JOUR AU - Luhn, H. P. PY - 1957 DA - 1957// TI - A statistical approach to mechanized encoding and searching of literary information JO - IBM J Res Dev VL - 1 UR - https://doi.org/10.1147/rd.14.0309 DO - 10.1147/rd.14.0309 ID - Luhn1957 ER - TY - CHAP AU - Bilenko, M. AU - Mooney, R. J. PY - 2003 DA - 2003// TI - Adaptive duplicate detection using learnable string similarity measures BT - Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD ’03 PB - ACM CY - Washington, DC, U.S.A ID - Bilenko2003 ER - TY - JOUR AU - Jones, K. S. PY - 1972 DA - 1972// TI - A statistical interpretation of term specificity and its application in retrieval JO - J Doc VL - 28 UR - https://doi.org/10.1108/eb026526 DO - 10.1108/eb026526 ID - Jones1972 ER - TY - STD TI - Davis J, Goadrich M. The relationship between precision-recall and roc curves. In: Proceedings of the 23rd International Conference on Machine Learning. ACM: 2006. p. 233–40. ID - ref46 ER -