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Publications
References
1999
Filimonov D., Poroikov V., Borodina Yu., Gloriozova T. Chemical similarity assessment through multilevel neighborhoods of atoms: definition and comparison with the other descriptors. Journal of Chemical Information and Computational Sciences, 1999, 39: 666-670.
2000
Lagunin A., Stepanchikova A., Filimonov D., Poroikov V. PASS: prediction of activity spectra for biologically active substances. Bioinformatics, 2000, 16: 747-748.
2001
Poroikov V., Akimov D., Shabelnikova E., Filimonov D. Top 200 medicines: can new actions be discovered through computer-aided prediction? SAR and QSAR in Environmental Research, 2001, 12: 327-344.
2003
Borodina Yu., Sadym A., Filimonov D., Blinova V., Dmitriev A., Poroikov V. Predicting biotransformation potential from molecular structure. J. Chem. Inform. Comput. Sci., 2003, 43: 1636-1646.
Sadym A., Lagunin A., Filimonov D., Poroikov V. Prediction of biological activity spectra via Internet. SAR and QSAR in Environmental Research, 2003, 14: 339-347.
Van de Waterbeemd H. and Gifford E. ADMET in silico modelling: towards prediction paradise? Nature Reviews Drug Discovery, 2003, 2: 192-204.
2004
Borodina Yu., Rudik A., Filimonov D., Kharchevnikova N., Dmitriev A., Blinova V., Poroikov V. A new statistical approach to predicting aromatic hydroxylation sites. Comparison with model-based approaches. J. Chem. Inform. Comput. Sci., 2004, 44: 1998-2009.
2005
Cronin M. Report on the "Review of the Status of the Development of Alternatives to using Animals in Chemical Safety Testing and Identification of New Areas for Development or Research in the Context of the Proposed REACH Regulation". Liverpool John Moores University and The Fund for the Replacement of Animals in Medical Experiments, May 2005.
2007
Bender A., Young D.W., Jenkins J.L., Serrano M., Mikhailov D., Clemons P.A., Davies J.W. Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprints. Combinatorial Chemistry & High Throughput Screening, 2007, 10: 719-731.
Dix D.J., Houck K.A., Martin M.T., Richard A.M., Setzer R.W., Kavlock R.J. The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicological Sciences, 2007, 95: 5–12.
Ekins S., Mestres J., Testa B. In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling. British Journal of Pharmacology, 2007, 152: 9–20.
2008
Geronikaki A., Druzhilovsky D., Zakharov A., Poroikov V. Computer-aided predictions for medicinal chemistry via Internet. SAR and QSAR in Environ. Res., 2008, 19: 27-38.
2011
Filimonov D.A., Zakharov A.V., Lagunin A.A., Poroikov V.V. QNA based “Star Track” QSAR approach. SAR and QSAR in Environmental Research, 2009, 20: 679-709.
Ekins S., Williams5 A.J., Krasowski M.D., Freundlich J.S. In silico repositioning of approved drugs for rare and neglected diseases. Drug Discovery Today, 2011, 16: 298-310.
Kokurkina G.V., Dutov M.D., Shevelev S.A., Popkov S.V., Zakharov A.V., Poroikov V.V. Synthesis, antifungal activity and QSAR study of 2-arylhydroxynitroindoles. Eur. J. Med. Chem., 2011, 46: 4374-4382.
Lagunin A., Zakharov A., Filimonov D., Poroikov V. QSAR Modelling of Rat Acute Toxicity on the Basis of PASS Prediction. Molecular Informatics, 2011, 30: 241–250.
2012
Kryzhanovskii S.A., Salimov R.M., Lagunin A.A., Filimonov D.A., Gloriozova T.A., Poroikov V.V. Nootropic action of some antihypertensive drugs: computer predicting and experimental testing. Pharmaceutical Chemistry Journal, 2012, 45: 605-611.
Zakharov A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. Quantitative prediction of antitarget interaction profiles for chemical compounds. Chemical Research in Toxicology, 2012: 25: 2378-2385.
2013
Lagunin A., Ivanov S., Rudik A., Filimonov D., Poroikov V. DIGEP-Pred: web-service for in-silico prediction of drug-induced expression profiles based on structural formula. Bioinformatics, 2013, 29: 2062-2063.
2014
Fedorova E.V., Buryakina A.V., Zakharov A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V. Design, synthesis and pharmacological evaluation of novel vanadium-containing complexes as antidiabetic agents. PLoS ONE, 2014, 9 (7): e100386.
Filimonov D.A., Lagunin A.A., Gloriozova T.A., Rudik A.V., Druzhilovskii D.S., Pogodin P.V., Poroikov V.V. Prediction of the biological activity spectra of organic compounds using the PASS online web resource. Chemistry of Heterocyclic Compounds, 2014, 50: 444-457.
Rudik A.V., Dmitriev A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. Metabolism sites prediction based on xenobiotics structural formulae and PASS prediction algorithm. Journal of Chemical Information and Modeling, 2014, 54: 498–507.
Zakharov A.V., Peach M.L., Sitzmann M., Nicklaus M.C. A new approach to radial basis function approximation and its application to QSAR, Journal of Chemical Information and Modeling, 2014, 54: 713-719.
2015
Guasch L., Zakharov A.V., Tarasova O.A., Poroikov V.V., Liao C., Nicklaus M.C. (2015). Novel HIV-1 integrase inhibitor development by virtual screening based on QSAR models. Current Topics in Medicinal Chemistry, 16 (4), 441-448. DOI: 10.2174/1568026615666150813150433.
Tarasova O.A., Urusova A.F., Filimonov D.A., Nicklaus M.C., Zakharov A.V., Poroikov V.V. (2015). QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors. Journal of Chemical Information and Modeling, 55 (7), 1388-1399, DOI: 10.1021/acs.jcim.5b00019.
Ivanov S.M., Lagunin A.A., Pogodin P.V., Filimonov D.A., Poroikov V.V. (2015). Identification of drug targets related to the induction of ventricular tachyarrhythmia through systems chemical biology approach. Toxicological Sciences, 145 (2): 321-336. DOI: 10.1093/toxsci/kfv054.
Rudik A., Dmitriev A., Lagunin A., Filimonov D., Poroikov V. (2015). SOMP: web-service for in silico prediction of sites of metabolism for drug-like compounds. Bioinformatics, 31 (12), 2046-2048. DOI: 10.1093/bioinformatics/btv087.
Poroikov V. (2015). 20th EuroQSAR: Understanding Chemical-Biological Interactions. Molecular Informatics, 34 (6-7), 340. DOI: 10.1002/minf.201580631.
Konova V., Lagunin A., Pogodin P., Kolotova E., Shtil A., Poroikov V. (2015). Virtual screening of chemical compounds active against breast cancer cell lines based on cell cycle modeling, prediction of cytotoxicity and interaction with targets. SAR and QSAR in Environmental Research, 26 (7-9), 595-604. DOI: 10.1080/1062936X.2015.1076516.
Pogodin P.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. (2015) PASS Targets: ligand-based multi-target computational system based on public data and naïve bayes approach. SAR and QSAR in Environmental Research, 26 (10), 783-793. DOI: 10.1080/1062936X.2015.1078407.
Goel R.K., Poroikov V., Gawande D., Lagunin A., Randhawa P., Mishra A. (2015). Revealing medicinal plants useful for comprehensive management of epilepsy and associated co-morbidities through in silico mining of their phytochemical diversity. Planta Medica, 81 (6), 495-506. DOI: 10.1055/s-0035-1545884.
Anusevicius K., Mickevicius V., Stasevych M., Zvarych V., Komarovska-Porokhnyavets O., Novikov V., Tarasova O., Gloriozova T., Poroikov V. (2015). Design, synthesis, in vitro antimicrobial activity evaluation and computational studies of new N-(4-iodophenyl)-β-alanine derivatives. Research on Chemical Intermediates. 41 (10), 7517-7540. DOI: 10.1007/s11164-014-1841-0.
2016
Ivanov S.M., Lagunin A.A., Poroikov V.V. (2016). In silico assessment of adverse drug reactions and associated mechanisms. Drug Discovery Today, 21 (1), 58-71. DOI: 10.1016/j.drudis.2015.07.018.
Zakharov A.V., Varlamova E.V., Lagunin A.A., Dmitriev A.V., Muratov E.N., Fourches D., Kuz'min V.E., Poroikov V.V., Tropsha A., Nicklaus M.C. (2016). QSAR Modeling and Prediction of Drug-Drug Interactions. Molecular Pharmaceutics, 13 (2), 545–556. DOI 10.1021/acs.molpharmaceut.5b00762.
Karasev D.A., Veselovsky A.V., Oparina N.Yu., Filimonov D.A., Sobolev B.N. (2016). Prediction of amino acid positions specific for functional groups in a protein family based on local sequence similarity. Journal of Molecular Recognition, 29 (4), 159-169. DOI: 10.1002/jmr.2515.
Bezhentsev V.M., Tarasova O.A., Dmitriev A.V., Rudik A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. Computer-aided prediction of xenobiotics metabolism in the human organism. Russ. Chem. Rev., 2016, 85 (8) 854-879. DOI: 10.1070/RCR4614.
Geronikaki A., Eleftheriou P., Poroikov V. (2016). Anti-HIV Agents: Current Status and Recent Trends. Topics in Medicinal Chemistry. 1-59. DOI: 10.1007/7355_2015_5001.