Computational Methods in Drug Discovery
Tóm tắt
Từ khóa
Tài liệu tham khảo
Accelrys (2013) Accelrys metabolite. Available from http://accelrys.com/products/databases/bioactivity/metabolite.html.
Bajorath, 2001, Selected concepts and investigations in compound classification, molecular descriptor analysis, and virtual screening, J Chem Inf Comput Sci, 41, 233, 10.1021/ci0001482
Barnard, 1997, Chemical fragment generation and clustering software, J Chem Inf Comput Sci, 37, 141, 10.1021/ci960090k
Bauerschmidt, 1997, Overcoming the limitations of a connection table description: a universal representation of chemical species, J Chem Inf Comput Sci, 37, 705, 10.1021/ci9704423
Boser BE, Guyon IM, and Vapnik VN (1992) A training algorithm for optimal margin classifiers, in Proceedings of the Fifth Annual Workshop on Computational Learning Theory; Association for Computing Machinery; 27--29 July 1992; Pittsburgh, PA, pp. 144–152.
Boyle BH (2011) Support Vector Machines: Data Analysis, Machine Learning, and Applications, Nova Science Publishers, New York.
Broto, 1984, Molecular-structures—perception, auto-correlation descriptor, and SAR studies—perception of molecule-topological structure and 3-dimensional structure, Eur J Med Chem, 19, 71
Brown, 2004, A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules, J Chem Inf Comput Sci, 44, 1079, 10.1021/ci034290p
Chen Y-W and Lin C-J (2006) Combining SVMs with various feature selection strategies. Studies in Fuzziness and Soft Computing 207:315–324.
Chiosis, 2006, Emerging Hsp90 inhibitors: from discovery to clinic, Anticancer Agents Med Chem, 6, 1, 10.2174/187152006774755483
Cristianini N Shawe-Taylor J (2000) An Introduction to Support Vector Machines: and Other Kernel-Based Learning Methods, Cambridge University Press, Cambridge, New York.
Davis L (1991) Handbook of Genetic Algorithms, Van Nostrand Reinhold, New York.
Daylight Chemical Information Systems (2008) Daylight Theory: SMARTS—A language for describing molecular patterns. Available from http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html#RTFToC35.
Daylight Chemical Information Systems (2013) Daylight theory manual. Available from http://www.daylight.com/dayhtml/doc/theory/.
Devillers J Balaban AT (1999) Topological Indices and Related Descriptors in QSAR and QSPR, Gordon and Breach, Amsterdam.
Dimitropoulos D, Ionides J, and Henrick K (2006) Using PDBeChem to Search the PDB Ligand Dictionary, in Current Protocols in Bioinformatics; John Wiley & Sons, 14.13.11-14.13.13.
Durrant, 2010, Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1, PLoS Negl Trop Dis, 4, 1, 10.1371/journal.pntd.0000803
Ekonomiuk, 2009, Discovery of a non-peptidic inhibitor of West Nile virus NS3 protease by high-throughput docking, PLoS Negl Trop Dis, 3, 1, 10.1371/journal.pntd.0000356
Erickson, 2010, Structure-guided expansion of kinase fragment libraries driven by support vector machine models, Biochim Biophys Acta, 1804, 642, 10.1016/j.bbapap.2009.12.002
Euer, 2002, Identification of genes associated with metastasis of mammary carcinoma in metastatic versus non-metastatic cell lines, Anticancer Res, 22, 733
Fedorov VV (1972) Theory of Optimal Experiments, Academic Press, New York.
Frimurer, 2000, Improving the odds in discriminating “drug-like” from “non drug-like” compounds, J Chem Inf Comput Sci, 40, 1315, 10.1021/ci0003810
Galvez, 1994, Charge indexes. New topological descriptors, J Chem Inf Comput Sci, 34, 520, 10.1021/ci00019a008
Gasparini, 2008, mGluR5 antagonists: discovery, characterization and drug development, Curr Opin Drug Discov Devel, 11, 655
Gasteiger, 1979, A representation of π systems for efficient computer manipulation, J Chem Inf Comput Sci, 19, 111, 10.1021/ci60018a015
Goldstein A (1974) Principles of Drug Action; the Basis of Pharmacology, Wiley, New York.
Grubmüller, 1995, Predicting slow structural transitions in macromolecular systems: Conformational flooding, Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 52, 2893
Güner OF (2000) Pharmacophore Perception, Development, and Use in Drug Ddesign, International University Line, LaJolla, CA.
Han J and Kamber M (2006) Data mining: concepts and techniques. Amsterdam; Boston
Hansch, 1962, Correlation of biological activity of phenoxyacetic acids with Hammett substituent constants and partition coefficients, Nature, 194, 178, 10.1038/194178b0
Henrich, 2010, Computational approaches to identifying and characterizing protein binding sites for ligand design, J Mol Recognit, 23, 209, 10.1002/jmr.984
Howells, 2002, Indole-3-carbinol inhibits protein kinase B/Akt and induces apoptosis in the human breast tumor cell line MDA MB468 but not in the nontumorigenic HBL100 line, Mol Cancer Ther, 1, 1161
Huguenard, 1992, A novel T-type current underlies prolonged Ca(2+)-dependent burst firing in GABAergic neurons of rat thalamic reticular nucleus, J Neurosci, 12, 3804, 10.1523/JNEUROSCI.12-10-03804.1992
Ijjaali, 2007, Ligand-based virtual screening to identify new T-type calcium channel blockers, Channels (Austin), 1, 300, 10.4161/chan.4999
InChITRUST (2013) InChI FAQ. Available from http://www.inchi-trust.org/fileadmin/user_upload/html/inchifaq/inchi-faq.html.
Ivanciuc O (2007) Applications of support vector machines in chemistry, in Reviews in Computational Chemistry pp 291–400, John Wiley & Sons, Inc., Hoboken, NJ.
Jilek, 2004, Topomers: a validated protocol for their self-consistent generation, J Chem Inf Comput Sci, 44, 1221, 10.1021/ci049961d
Joffe, 1991, Complication during root canal therapy following accidental extrusion of sodium hypochlorite through the apical foramen, Gen Dent, 39, 460
Johnson MA Maggiora GM (1990) Concepts and Applications of Molecular Similarity, Wiley, New York.
Kawagoe, 1997, Expression and transcriptional regulation of the PD-Ialpha/autotaxin gene in neuroblastoma, Cancer Res, 57, 2516
Khatib, 2012, Crystal structure of a monomeric retroviral protease solved by protein folding game players, Nat Struct Mol Biol, 18, 1175, 10.1038/nsmb.2119
Kulkarni, 2002, Predicting Caco-2 cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis, J Chem Inf Comput Sci, 42, 331, 10.1021/ci010108d
Lajiness, 2004, Molecular properties that influence oral drug-like behavior, Curr Opin Drug Discov Devel, 7, 470
Le Fèvre RJW (1965) Molecular refractivity and polarizability, in Advances in Physical Organic Chemistry ( Gold V ed.), Academic Press, New York.
Lewell, 1998, RECAP—retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry, J Chem Inf Comput Sci, 38, 511, 10.1021/ci970429i
Liang Y (2011) Support Vector Machines and Their Application in Chemistry and Biotechnology, CRC Press, Boca Raton.
Livingstone D (2008) Artificial Neural Networks: Methods and Applications, Humana Press, Totowa, NJ.
March J (1977) Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, McGraw-Hill, New York.
Marshall GR, Barry CD, Bosshard H, Dammkoehler R, and Dunn D (1979) Conformational parameter in drug design - active analog approach. in Computer Assisted Drug Design. pp. 205–226, ACS Publications, Washington DC.
McGregor, 1997, Clustering of large databases of compounds: Using the MDL ''keys'' as structural descriptors, J Chem Inf Comput Sci, 37, 443, 10.1021/ci960151e
Mitchell TM (1997) Machine Learning, McGraw-Hill, New York.
Mitcheson, 2003, Molecular determinants of high-affinity drug binding to HERG channels, Curr Opin Drug Discov Devel, 6, 667
Moreau, 1980, The auto-correlation of a topological-structure - a new Molecular Descriptor, Nouveau Journal De Chimie-New Journal of Chemistry, 4, 359
Olah M Mracec M Ostopouici L Rad R Bora A Hadaruga N Olah I Banda M Simon Z Mracec M (2005) WOMBAT: World of Molecular Bioactivity, in Chemoinformatics in Drug Discovery, pp 221–239, Wiley-VCH Verlag GmbH, Weinheim, Germany.
Ortiz de Montellano PR (2005) Cytochrome P450: Structure, Mechanism, and Biochemistry. Springer Publishing, New York.
Pan, 2003, Quantitative structure-based design: formalism and application of receptor-dependent RD-4D-QSAR analysis to a set of glucose analogue inhibitors of glycogen phosphorylase, J Chem Inf Comput Sci, 43, 1591, 10.1021/ci0340714
Pastor M (2006) Alignment-independent descriptors from molecular interaction fields, in Molecular Interaction Fields, pp 117–143, Wiley-VCH Verlag GmbH, Weinheim, Germany.
Pimentel GC McClellan AL (1960) The Hydrogen Bond, W.H. Freeman, San Francisco, CA.
Platt JC (1999) Fast training of support vector machines using sequential minimal optimization, in Advances in Kernel Methods, pp 185–208, MIT Press, Cambridge, MA.
Poptodorov K Luu T Hoffmann R (2006) Pharmacophore model generation software tools, in Pharmacophores and Pharmacophore Searches, pp 15–47, Wiley-VCH Verlag GmbH & Co, Weinheim, Germany.
Quinlan JR (1993) C4.5: Programs for Machine Learning, Morgan Kaufmann Publishers, San Mateo, CA.
Randić, 2001, Characterization of DNA primary sequences based on the average distances between bases, J Chem Inf Comput Sci, 41, 561, 10.1021/ci0000981
Raval, 2012, Refinement of protein structure homology models via long, all-atom molecular dynamics simulations, Proteins-Structure Function and Genetics, 80, 2071, 10.1002/prot.24098
RCSB (2013) RCSB protein data bank. Available from http://www.rcsb.org/pdb/home/home.do.
Rekker RF Mannhold R (1992) Calculation of Drug Lipophilicity: The Hydrophobic Fragmental Constant Approach, VCH, Weinheim, New York.
Roberto Todeschini VC (2010) Molecular Descriptors for Chemoinformatics Wiley-VCH Verlag GmbH & Co, Weinheim, Germany .
Rogers, 1994, Application of genetic function approximation to quantitative structure-activity-relationships and quantitative structure-property relationships, J Chem Inf Comput Sci, 34, 854, 10.1021/ci00020a020
RosettaCommons (2013) Rosetta–The premier software suite for macromolecular modeling. Available from http://www.rosettacommons.org/.
Roughley, 2012, Hsp90 inhibitors and drugs from fragment and virtual screening, Top Curr Chem, 317, 61, 10.1007/128_2011_181
Sanderson RT (1960) Chemical Periodicity, Reinhold Pub. Corp., New York.
Schuur, 1996, The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity, J Chem Inf Comput Sci, 36, 334, 10.1021/ci950164c
Shaw, 2008, Anton, a special-purpose machine for molecular dynamics simulation, Commun ACM, 51, 91, 10.1145/1364782.1364802
Shimada, 2000, Analysis of knowledge-based protein-ligand potentials using a self-consistent method, Protein Sci, 9, 765, 10.1110/ps.9.4.765
Totrov M Abagyan R (1997) Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins (Suppl 1):215–220.
Trinajstić N (1992) Chemical Graph Theory, CRC Press, Boca Raton.
Vapnik VN (2006) Estimation of Dependences Based on Empirical Data; Empirical Inference Science: Afterword of 2006, Springer, New York.
Vapnik, 1963, Pattern recognition using generalized portrait method, Autom Remote Control, 24, 774
Vedani, 2007, VirtualToxLab - in silico prediction of the toxic potential of drugs and environmental chemicals: evaluation status and internet access protocol, ALTEX, 24, 153, 10.14573/altex.2007.3.153
Vinogradov SN Linnell RH (1971) Hydrogen Bonding, Van Nostrand Reinhold, New York.
Weininger SJ Stermitz FR (1984) Organic Chemistry, Academic Press, Orlando.
Wermuth CG (2006) Pharmacophores: historical perspective and viewpoint from a medicinal chemist, in Pharmacophores and Pharmacophore Searches pp 1–13, Wiley-VCH Verlag GmbH & Co, Weinheim, Germany.
Wiswesser WJ (1954) A Line-Formula Chemical Notation, Crowell, New York.
Wiswesser, 1985, Historic development of chemical notations, J Chem Inf Comput Sci, 25, 258, 10.1021/ci00047a023
Xing, 2002, Novel methods for the prediction of logP, pK(a), and logD, J Chem Inf Comput Sci, 42, 796, 10.1021/ci010315d
Yarnitzky, 2010, Homology modeling of G-protein-coupled receptors with X-ray structures on the rise, Curr Opin Drug Discov Devel, 13, 317
Yuan, 2011, LigBuilder 2: A Practical de Novo Drug Design Approach, J Chem Inf Model, 51, 1083, 10.1021/ci100350u
Zhou, 2012, Ant colony optimization with combining Gaussian eliminations for matrix multiplication, IEEE Trans Syst Man Cybern B Cybern, 43, 347