XXXII Symposium on Bioinformatics and Computer-Aided Drug Discovery (BCADD-2026) Visit Now
Schimunek J., Seidl P., Elez K., et al. A community effort in SARS-CoV-2 drug discovery, Molecular Informatics, 2024, 43(1), e202300262, doi: 10.1002/minf.202300262.
Bitencourt-Ferreira G., Villarreal M.A., Quiroga R., Biziukova N., Poroikov V., Tarasova O., de Azevedo Junior W.F., Exploring Scoring Function Space: Developing Computational Models for Drug Discovery, Current Medicinal Chemistry, 2024, 31(17), 2361-2377, doi: 10.2174/0929867330666230321103731.
de Azevedo W.F. Jr, Quiroga R., Villarreal M.A., da Silveira N.J.F., Bitencourt-Ferreira G., da Silva A.D., Veit-Acosta M., Oliveira P.R., Tutone M., Biziukova N., Poroikov V., Tarasova O., Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space, Journal of Computational Chemistry, 2024, 45(27), 2333-2346, doi: 10.1002/jcc.27449.
Ivanov S.M., Rudik A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V., DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes, Molecular Informatics, 2024, 43(00), 00-00, doi: 10.1002/minf.202400032.
Lagunin A.A., Rudik A.V., Pogodin P.V., Savosina P.I., Tarasova O.A., Dmitriev A.V., Ivanov S.M., Biziukova N.Y., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V., CLC-Pred 2.0: A Freely Available Web Application for In Silico Prediction of Human Cell Line Cytotoxicity and Molecular Mechanisms of Action for Druglike Compounds, International Journal of Molecular Sciences, 2023, 24(2), 1689, doi: 10.3390/ijms24021689.
Muratov E.N., Amaro R., Andrade C.H., Brown N., Ekins S., Fourches D., Isayev O., Kozakov D., Medina-Franco J., Merz K.M., Oprea T.I., Poroikov V., Schneider G., Todd M.H., Varnek A., Winkler D.A., Zakharov A., Cherkasov A., Tropsha A., A critical overview of computational approaches employed for COVID-19 drug discovery, Chemical Society Reviews, 2021, 50(16), 9121-9151, doi: 10.1039/d0cs01065k.
Madugula S.S., John L., Nagamani S., Gaur A.S., Poroikov V.V., Sastry G.N., Molecular Descriptor Analysis of Approved Drugs Using Unsupervised Learning for Drug Repurposing, Computers in Biology and Medicine, 2021, 138, 104856, doi: 10.1016/j.compbiomed.2021.104856.
Tarasova O.A., Rudik A.V., Ivanov S.M., Lagunin A.A., Poroikov V.V., Filimonov D.A., Machine Learning Methods in Antiviral Drug Discovery, Topics in Medicinal Chemistry, 2021, 37, 245-279, doi: 10.1007/7355_2021_121.
Muratov E.N., Bajorath J., Sheridan R.P., Tetko I.V., Filimonov D., Poroikov V., Oprea T.I., Baskin I.I., Varnek A., Roitberg A., Isayev O., Curtarolo S., Fourches D., Cohen Y., Aspuru-Guzik A., Winkler D.A., Agrafiotis D., Cherkasov A., Tropsha A. (2020). QSAR without borders, Chemical Society Reviews, 49, p. 3525-3564, doi: 10.1039/d0cs00098a.
Gaur A.S., Nagamani S., Tanneeru K., Druzhilovskiy D., Rudik A., Poroikov V., Sastry G.N. (2018). Molecular Property Diagnostic Suite for Diabetes Mellitus (MPDSDM): An Integrated Web platform for Drug Discovery and Drug Repurposing, Journal of Biomedical Informatics, 85, 114-125. doi: 10.1016/j.jbi.2018.08.003.
Malakhov G.S., Karasev D.A., Sobolev B.N. (2025). Comparative efficiency of structure activity relationship and proteochemometric modelling, Journal of Molecular Graphics and Modelling, 2025, 141, 109137, doi: 10.1016/j.jmgm.2025.109134.
Dmitriev A.V., Lagunin A.A., Rudik A.V., Savosina P.I., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V. , (2025). SAR Modeling to Predict Ames Mutagenicity Across Different Salmonella typhimurium Strains, Pharmaceuticals, 18(12), 1853, doi: 10.3390/ph18121853.
Lagunin A.A., Lisitsa E.Yu, Rudik A.V., Ivanov S.M., Dmitriev A.V., Muraviova E.S., Filimonov D.A., Poroikov V.V., QSAR modeling for predicting IC50 and GI50 values for human cell lines used in toxicological studies, International Journal of Molecular Sciences, 2025, 26(24), 12063, doi: 10.3390/ijms262412063.
Pogodin P.V., Salina E.G., Semenov V.V., Raihstat M.M., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V. (2024). Ligand-based virtual screening and biological evaluation of inhibitors of Mycobacterium tuberculosis H37Rv, SAR and QSAR in Environmental Research, 2024, 35(1), 53-69, doi: 10.1080/1062936X.2024.2304803.
Karasev D.A., Sobolev B.N., Filimonov D.A., Lagunin A, (2024). Prediction of viral protease inhibitors using proteochemometrics approach, Computational Biology and Chemistry, 110, 108061, doi: 10.1016/j.compbiolchem.2024.108061.
de Azevedo W.F. Jr, Quiroga R., Villarreal M.A., da Silveira N.J.F., Bitencourt-Ferreira G., da Silva A.D., Veit-Acosta M., Oliveira P.R., Tutone M., Biziukova N., Poroikov V., Tarasova O., Baud S. SAnDReS 2.0: Development of machine-learning models to explore the scoring function space, Journal of Computational Chemistry, 2024, 45(27), 2333-2346, doi: 10.1002/jcc.27449.
Medvedeva S.M., Shikhaliev K.S., Geronikaki A.A., Savosina P.I., Druzhilovsky D.S., Poroikov V.V. (2022). Computer-aided discovery of pleiotropic effects: Anti-inflammatory action of dithioloquinolinethiones as a case study, SAR and QSAR in Environmental Research, 33(4), 273-287, doi: 10.1080/1062936X.2022.2064547.
Rudik A., Dmitriev A., Lagunin A., Filimonov D., Poroikov V.(2022). Computational prediction of inhibitors and inducers of the major isoforms of cytochrome P450, Molecules, 2022(27), 5875-5875, doi: 10.3390/molecules27185875.
Stolbov L.A., Filimonov D.A., Poroikov V.V. (2022). SAR based on Self Consistent Classifier, SAR and QSAR in Environmental Research, 33(10), 793-804, doi: 10.1080/1062936X.2022.2139751.
Madugula S.S., John L., Nagamani S., Gaur A.S., Poroikov V.V., Sastry G.N., Molecular Descriptor Analysis of Approved Drugs Using Unsupervised Learning for Drug Repurposing, Computers in Biology and Medicine, 2021, 138, 104856, doi: 10.1016/j.compbiomed.2021.104856.
Muratov E.N., Bajorath J., Sheridan R.P., Tetko I.V., Filimonov D., Poroikov V., Oprea T.I., Baskin I.I., Varnek A., Roitberg A., Isayev O., Curtarolo S., Fourches D., Cohen Y., Aspuru-Guzik A., Winkler D.A., Agrafiotis D., Cherkasov A., Tropsha A. (2020). QSAR without borders, Chemical Society Reviews, 49, p. 3525-3564, doi: 10.1039/d0cs00098a.
Lagunin A.A., Romanova M.A., Zadorozhny A.D., Kurilenko N.S., Shilov B.V., Pogodin P.V., Ivanov S.M., Filimonov D.A., Poroikov V.V. (2018). Comparison of Quantitative and Qualitative (Q)SAR Models Created for the Prediction of Ki and IC50 Values of Antitarget Inhibitors, Frontiers in Pharmacology, Vol 9, 1136-1147.doi: 10.3389/fphar.2018.01136.
Savosina P.I., Poroikov V.V., Druzhilovskiy D.S. Open-Access Adverse Drug Reaction Databases: Applicability for Safety Assessment of the Developed Drugs (Review), Safety and Risk of Pharmacotherapy, 2025, doi: 10.30895/2312-7821-2025-535.
Savosina, P. I., Filimonov, D. A., Druzhilovskiy, D. S. (2025). Prediction of potential adverse drug reactions utilizing highly specific structural fragments, Biomeditsinskaya Khimiya, 71(6), 454-459, doi: 10.18097/PBMCR1634.
Savosina, P., Druzhilovskiy, D., Filimonov, D., & Poroikov, V. (2025). Design of Highly Specific Structural Fragments for Filtering Compounds with Undesirable Activities, Biomedical Chemistry: Research and Methods, 8(4), e00303, doi: 10.18097/BMCRM00303.
Dmitriev A.V., Lagunin A.A., Rudik A.V., Savosina P.I., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V. , (2025). SAR Modeling to Predict Ames Mutagenicity Across Different Salmonella typhimurium Strains, Pharmaceuticals, 18(12), 1853, doi: 10.3390/ph18121853.
Lagunin A.A., Lisitsa E.Yu, Rudik A.V., Ivanov S.M., Dmitriev A.V., Muraviova E.S., Filimonov D.A., Poroikov V.V., QSAR modeling for predicting IC50 and GI50 values for human cell lines used in toxicological studies, International Journal of Molecular Sciences, 2025, 26(24), 12063, doi: 10.3390/ijms262412063.
Suhachov V.S., Dmitriev A.V., Ivanov S.M., Savosina P.I., Druzhilovskij D.S., Filimonov D.A., Porojkov V.V., Assessment of the Efficiency of Selecting Promising Compounds During Virtual Screening Based on Various Estimations of Drug-Likeness, Pharmaceutical Chemistry Journal, 2025, 58(9), 1388-1396, doi: 10.1007/s11094-025-03286-3.
Poroikov V.V., Dmitriev A.V., Druzhilovskiy D.S., Ivanov S.M., Lagunin A.A., Pogodin P.V., Rudik A.V., Savosina P.I., Tarasova O.A., Filimonov D.A. In Silico Estimation of the Safety of Pharmacologically Active Substances Using Machine Learning Methods: A Review, Safety and Risk of Pharmacotherapy. 2023;11(4):372-389, doi: 10.30895/2312-7821-2023-11-4-372-389.
Ivanov S.M., Lagunin A.A., Filimonov D.A., Poroikov V.V..(2022). Relationships between the Structure and Severe Drug-Induced Liver Injury for Low, Medium, and High Doses of Drugs, Chemical Research in Toxicology, 35(3), 402-411, doi: 10.1021/acs.chemrestox.1c00307.
Koroleva P.I., Kuzikov A.V., A.V., Masamrekh R.A., Filimonov D.A., Dmitriev A.V., Zaviyalova M.G., Rikova S.M., Shich E.V., Makhova A.A., Bulko T.V., Gilep A.A., Shumyantseva V.V., Modeling of Drug-Drug Interactions between Omeprazole and Erythromycin in the Cytochrome P450-Dependent System in vitro, Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 2021, 15(1), 62-70. doi: 10.1134/S1990750821010030.
Stasevich M.V., Zvarich V.I., Novikov V.P., Zagorodnyaya S.D., Povnitsa O.Yu., Chaika M.A., Nesterkina M.V., Kravchenko I.A., Druzhilovskii D.S., Poroikov V.V., (2020). 9,10-Anthraquinone Dithiocarbamates as Potential Pharmaceutical Substances with Pleiotropic Actions: Computerized Prediction of Biological Activity and Experimental Validation, Pharmaceutical Chemistry Journal, 53(10), 905-913, doi: 10.1007/s11094-020-02098-x.
Daneman V.R., Meika B., Tjahjono E., Revtovich A.V., Stolbov K.A., Gilbertson S.R., Poroikov V.V., Kirienko N.V. (2025). Cheminformatic identification of small molecules targeting acute myeloid leukemia, BioRxiv, 00(00), 1-50, doi: 10.1101/2025.05.20.655224.
Lagunin A.A., Sezganova A.S., Muraviova E.S., Rudik A.V., Filimonov D.A., (2024). BC CLC-Pred: a freely available web-application for quantitative and qualitative predictions of substance cytotoxicity in relation to human breast cancer cell lines, SAR and QSAR in Environmental Research, 2024, 35(1), 1-9, doi: 10.1080/1062936X.2023.2289050.
Ilyin N.P., Nabiullin A.D., Kozlova A.D., Kupriyanova O.V., Shevyrin V.A., Gloriozova T., Filimonov D., Lagunin A., Galstyan D.S., Kolesnikova T.O., Mor M.S., Efimova E.V., Poroikov V., Yenkoyan K.B., de Abreu M.S., Demin K.A., Kalueff A.V. (2024). Chronic behavioral and neurochemical effects of four novel N-benzyl-2-phenylethylamine derivatives recently identified as ‘psychoactive’ in adult zebrafish screens, ACS Chemical Neuroscience, 15(10), 2006-2017, , doi: 10.1021/acschemneuro.4c00017.
Ivanov S.M., Zgoda V.G., Isakova V.A., Trukhanova L.S., Poroikov V.V., Shtil A.A., Proteomic Analysis Identifies Multiple Mechanisms of 5-Fluorouracil-Induced Gut Mucositis in Mice, Cancers, 2024, 16(23), 4025-4025, doi: 10.3390/cancers16234025.
Bocharova O.A., Kazeev I.V., Shevchenko V.E., Ionov N.S., Sheichenko O.P., Bocharov E.V., Karpova R.V., Kucheryanu V.G., Lagunin A.A., Filimonov D.A., Kosorukov V.S., Poroikov V.V., Tutelyan V.A., Pyatigorskaya N.V. Schisandrin and Schisantherin A in Multiphytoadaptogen for Preventive Oncology, Russian Journal of Biotherapy, 2023, Vol. 22, n.3, P. 51-63, doi: 10.17650/1726-9784-2023-22-3-51-63.
Bocharova O.A., Karpova R.V., Bocharov E.V., Aksyonov A.A., Chekalina T.L., Chulkova S.V., Ionov N.S., Kazeev I.V., Lyzhenkova M.A., Vershinskaya A.A., Kucheryanu V.G., Kosorukov V.S. (2023). Adhesive phytoadaptogens-geroprotectors in preventive oncology, Cardiometry, (26), 55-64, doi: 10.18137/cardiometry.2023.26.5568.
Bocharova O.A., Kazeev I.V., Shevchenko V.E., Ionov N.S. , Sheichenko O.P., Bocharov E.V., Karpova R.V., Kucheryanu V.G., Lagunin A.A., Filimonov D.A., Kosorukov V.B., Poroikov V.V., Tutelyan V.A., Pyatigorskaya N.V. (2023). Secondary metabolites of Schisandra chinensis in homeostasis regulator adaptogen herbal formula for preventive oncology, Cardiometry, (27), 63-74, doi: 10.18137/cardiometry.2023.27.6374.
Panina S.B., Pei J., Baran N., Tjahjono E., Patel S., Alatrash G., Konoplev S.N., Stolbov L.A., Poroikov V.V., Konopleva M., Kirienko N.V. (2022). Novel mitochondria-targeting compounds selectively kill human leukemia cells, Leukemia, 36(7), 2009-2021, doi: 10.1038/s41375-022-01614-0.
Ionov, N.S., Baryshnikova, M.A., Bocharov, E.V., Pogodin, P.V., Lagunin, A.A., Filimonov, D.A., Karpova, R.V., Kosorukov, V.S., Stilidi, I.S., Matveev, V.B., Bocharova, O.A., Poroikov, V.V. (2021). Possibilities of in silico estimations for the development of pharmaceutical composition phytoladaptogene cytotoxic for bladder cancer cells, Biomeditsinskaya Khimiya, 67(3), 278-288, doi: 10.18097/PBMC20216703278.
Zawacka-Pankau J., Grinkevich V.V., Burmakin M., Vema A., Ridderstrale K., Issaeva N., Andreotti V., Dickinson E.R., Hedstrom E., Spinnler C., Inga A., Larsson K.-G., Karlen A., Tarasova O., Poroikov V., Lavrenov S., Preobrazhenskaya M., Wilhelm M., Barran P.E., Okorokov A.L., Selivanova G. (2018). Novel allosteric mechanism of p53 activation by small molecules for targeted anticancer therapy bioRxiv, 384248, doi: 10.1101/384248.
Biziukova N., Rudik A., Dmitriev A., Tarasova O., Filimonov D., Poroikov V., XenoMet: A corpus of texts to extract data on metabolites of xenobiotics, ACS Omega, 2025, 10(3), 2459-2471, doi: 10.1021/acsomega.4c05723.
Rudik, A., Pogodin, P., Lagunin, A., Filimonov, D., & Poroikov, V. (2025). MetaPASS 2024: Visualization of Biological Activity Spectra of Organic Compounds Taking into Account Their Biotransformation, Biomedical Chemistry: Research and Methods, 8(2), e00243, doi: 10.18097/BMCRM00243.
Kolodnitsky A.S., Ionov N.S., Rudik A.V., Filimonov D.A., Poroikov V.V. (2023). HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database, Journal of Chemical Information and Modeling, 63(21), 6463-6468, doi: 10.1021/acs.jcim.3c00837.
Rudik A.V., Dmitriev A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V. (2023). MetaTox 2.0: Estimating the Biological Activity Spectra of Drug-Like Compounds Taking into Account Probable Biotransformations, ACS Omega, 8(48), 45774-45778, doi: 10.1021/acsomega.3c06119.
Tarasova O.A., Biziukova N.Y., Rudik A.V., Dmitriev A.V., Filimonov D.A., Poroikov V.V., Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts, Journal of Chemical Information and Modeling, 2021, 61(4), 1683-1690, doi: 10.1021/acs.jcim.0c01054.
Korotkevich, E.I., Rudik, A.V., Dmitriev, A.V. et al. Prediction of Metabolic Stability of Xenobiotics by the Pass and Gusar Programs, Biochem. Moscow Suppl. Ser. B 15, 301–305 (2021), doi: 10.1134/S1990750821040089.
Stolbov L., Rudik A., Lagunin A., Druzhilovskiy D., Filimonov D., Poroikov V., (2025). In Silico Assessment of Potential Geroprotectors: From Separate Endpoints to Complex Pharmacotherapeutic Effects, International Journal of Molecular Sciences, 2025, 26(18), 8858, doi: 10.3390/ijms26188858.
Porfireva E.S., Zadorozhny A.D., Rudik A.V., Filimonov D.A., Lagunin A.A., Sequence-structure based prediction of pathogenicity for amino acid substitutions in proteins associated with primary immunodeficiencies, Frontiers in Immunology, 2025, 16, 1492751, doi: 10.3389/fimmu.2025.1492751.
Stolbova E.A., Pokrovskaya A.V., Shemshura A.B., Kireev D.E., Lagunin A.A., Sobolev B.N., Ivanov S.M., Tarasova O.A., Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients, International Journal of Molecular Sciences, 2025, 26(21), 10678, doi: 10.3390/ijms262110678.
Tarasova O., Petrou A., Ivanov S.M., Geronikaki A., Poroikov V., Viral Factors in Modulation of Host Immune Response: A Route to Novel Antiviral Agents and New Therapeutic Approaches, International Journal of Molecular Sciences, 2024, 25(17), 9408, , doi: 10.3390/ijms25179408 10.3390/ijms25179408.
Ivanov S.M., Tarasova O.A., Poroikov V.V. (2023). Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections, Frontiers in Immunology, 14, 1199482, doi: 10.3389/fimmu.2023.1199482.
Smirnov A.S., Rudik A.V., Filimonov D.A., Lagunin A.A. (2023). TCR-Pred: A new web-application for prediction of epitope and MHC specificity for CDR3 TCR sequences using molecular fragment descriptors, Immunology, 169(4), 447-453, doi: 10.1111/imm.13641.
Ivanov S, Filimonov D, Tarasova O., A Computational Approach for the Prediction of HIV Resistance Based o(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression, Computational and structural biotechnology journal, 2021, 19, 2447-2459, doi: 10.1016/j.csbj.2021.04.056.
Ivanov S.M., Sukhachev V.S., Tarasova O.A., Lagunin A.A., Poroikov V.V. (2025). Analysis of Genomic and Transcriptomic Data Revealed Key Genes and Processes in the Development of Major Depressive Disorder, International Journal of Molecular Sciences, 2025, 26(19), 9557-9557, doi: 10.3390/ijms26199557.
Galiakberova A., Ivanov S., Golov A., Artyuhov A., Zolkin A., Kondratyev N., Lagunin A., Golimbet V., Dashinimaev E., (2025). Transcriptomic profiling of neural cultures from the KYOU iPSC line via alternative differentiation protocols, Frontiers in Molecular Neuroscience, 18, 1661986, doi: 10.3389/fnmol.2025.1661986.
Stolbova E.A., Pokrovskaya A.V., Shemshura A.B., Kireev D.E., Lagunin A.A., Sobolev B.N., Ivanov S.M., Tarasova O.A., Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients, International Journal of Molecular Sciences, 2025, 26(21), 10678, doi: 10.3390/ijms262110678.
Ivanov S.M., Lagunin A.A., Tarasova O.A., Analysis of transcription profiles for the identification of master regulators as the key players in glioblastoma, Computational and Structural Biotechnology Journal, 2024, 23, 3559-3574, doi: 10.1016/j.csbj.2024.09.022.
Ivanov S.M., Tarasova O.A., Poroikov V.V. (2023). Transcriptome-based analysis of human peripheral blood reveals regulators of immune response in different viral infections, Frontiers in Immunology, 14, 1199482, doi: 10.3389/fimmu.2023.1199482.
Ivanov S, Filimonov D, Tarasova O., A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression, Computational and structural biotechnology journal, 2021, 19, 2447-2459, doi: 10.1016/j.csbj.2021.04.056.
Shapovalova, V., Radko, S., Ptitsyn, K., Krasnov, G., Nakhod, K., Konash, O., Vinogradina, M., Ponomarenko, E., Druzhilovskiy, D., & Lisitsa, A. (2020). Processing Oxford Nanopore Long Reads Using Amazon Web Services, Biomedical Chemistry: Research and Methods, 3(4), e00131., doi: 10.18097/bmcrm00131.
Savosina P.I., Poroikov V.V., Druzhilovskiy D.S. Open-Access Adverse Drug Reaction Databases: Applicability for Safety Assessment of the Developed Drugs (Review), Safety and Risk of Pharmacotherapy, 2025, doi: 10.30895/2312-7821-2025-535.
Lagunin A.A., Sezganova A.S., Muraviova E.S., Rudik A.V., Filimonov D.A., (2024). BC CLC-Pred: a freely available web-application for quantitative and qualitative predictions of substance cytotoxicity in relation to human breast cancer cell lines, SAR and QSAR in Environmental Research, 2024, 35(1), 1-9, doi: 10.1080/1062936X.2023.2289050.
Ivanov S.M., Rudik A.V., Lagunin A.A., Filimonov D.A., Poroikov V.V., DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes, Molecular Informatics, 2024, 43(00), 00-00, doi: 10.1002/minf.202400032.
Savosina P., Druzhilovskiy D., Filimonov D., Poroikov V., WWAD: the most comprehensive small molecule World Wide Approved Drug database of therapeutics, Frontiers in Pharmacology, 2024, 15, 1473279, doi: 10.3389/fphar.2024.1473279.
Savosina, P., Druzhilovskiy, D., Filimonov, D., & Poroikov, V. (2024). Bigdata of National Medicine Registers, Biomedical Chemistry: Research and Methods, 7(3), e00230, doi: 10.18097/BMCRM00230.
Lagunin A.A., Rudik A.V., Pogodin P.V., Savosina P.I., Tarasova O.A., Dmitriev A.V., Ivanov S.M., Biziukova N.Y., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V., CLC-Pred 2.0: A Freely Available Web Application for In Silico Prediction of Human Cell Line Cytotoxicity and Molecular Mechanisms of Action for Druglike Compounds, International Journal of Molecular Sciences, 2023, 24(2), 1689, doi: 10.3390/ijms24021689.
Ionov N., Druzhilovskiy D., Filimonov D., Poroikov V. (2023). Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants, Journal of Chemical Information and Modeling, 63(7), 1847-1851, doi: 10.1021/acs.jcim.2c01567.
Paremskaia A.I., Rudik A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V., Tarasova O.A. (2023). Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets, Viruses, 15(11), 2245, doi: 10.3390/v15112245.
Kolodnitsky A.S., Ionov N.S., Rudik A.V., Filimonov D.A., Poroikov V.V. (2023). HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database, Journal of Chemical Information and Modeling, 63(21), 6463-6468, doi: 10.1021/acs.jcim.3c00837.
Tarasova O., Rudik A., Kireev D., Poroikov V. , RHIVDB: A freely accessible database of HIV amino acid sequences and clinical data of infected patients, Frontiers in Genetics, 2021, 12, 679029, doi: 10.3389/fgene.2021.679029.
Ionov, N., Pogodin, P., & Poroikov, V. (2020). Assessing the Prediction Quality of the Anti-SARS-CoV-2 Activity Using the D3Targets-2019-nCoV Web Service, Biomedical Chemistry: Research and Methods, 3(4), e00140., doi: 10.18097/bmcrm00140.
Stolbov L., Druzhilovskiy D., Rudik A., Filimonov D., Poroikov V., Nicklaus M. (2020). AntiHIV-Pred: Web-resource for in silico prediction of anti-HIV/AIDS activity, Bioinformatics. 36 (3), 978–979. DOI: 10.1093/bioinformatics/btz638.
Biziukova N., Rudik A., Dmitriev A., Tarasova O., Filimonov D., Poroikov V., XenoMet: A corpus of texts to extract data on metabolites of xenobiotics, ACS Omega, 2025, 10(3), 2459-2471, doi: 10.1021/acsomega.4c05723.
Bitencourt-Ferreira G., Villarreal M.A., Quiroga R., Biziukova N., Poroikov V., Tarasova O., de Azevedo Junior W.F., Exploring Scoring Function Space: Developing Computational Models for Drug Discovery, Current Medicinal Chemistry, 2024, 31(17), 2361-2377, doi: 10.2174/0929867330666230321103731.
Biziukova N.Yu., Ivanov S.M., Tarasova O.A. (2024). Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach, Big Data Mining and Analytics, 7(1), 107-130, doi: 10.26599/BDMA.2023.9020007.
Tarasova, O. A., Biziukova, N. Yu., Stolbova, E. A., Stolbov, L. A., Taktashov, R. R., Karasev, D. A., Ionov, N. S., Ivanov, S. M., Dmitriev, A. V., Rudik, A. V., Druzhilovskiy, D. S., Sobolev, B. N., Filimonov, D. A., Poroikov, V. V. (2024). Extracting information on virus-human interactions and on antiviral compounds based on automated analysis of large text collections, Biomeditsinskaya Khimiya, 70(6), 469-474, doi: 10.18097/PBMC20247006469.
Tarasova O.A., Biziukova N.Yu., Shemshura A.B., Filimonov D.A., Kireev D.E., Pokrovskaya A.V., Poroikov V.V., Identification of molecular mechanisms involved into viral in-fection progression based on text-mining: case study for HIV-infection, International Journal of Molecular Sciences, 2023, 24(2), 1465, doi: 10.3390/ijms24021465.
Pogodin P.V., Kiseleva O.I., Ilgisonis E.V. (2023). Identification of Potential Therapeutic Targets on the Level of DNA/mRNAs, Proteins and Metabolites: A Systematic Mapping Review of Scientific Texts’ Fragments from Open Targets, Current Issues in Molecular Biology, 45(4), 3406-3418, doi: 10.3390/cimb45040223.
Tarasova O.A., Rudik A.V., Biziukova N.Yu., Filimonov D.A., Poroikov V.V., (2022). Chemical named entity recognition in the texts of scientific publications using the naïve Bayes classifier approach, Journal of Cheminformatics, 14 (1), 55, doi: 10.1186/s13321-022-00633-4.
Tarasova O.A., Biziukova N.Y., Rudik A.V., Dmitriev A.V., Filimonov D.A., Poroikov V.V., Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts, Journal of Chemical Information and Modeling, 2021, 61(4), 1683-1690, doi: 10.1021/acs.jcim.0c01054.
Lagunin A.A., Lisitsa E.Yu, Rudik A.V., Ivanov S.M., Dmitriev A.V., Muraviova E.S., Filimonov D.A., Poroikov V.V., QSAR modeling for predicting IC50 and GI50 values for human cell lines used in toxicological studies, International Journal of Molecular Sciences, 2025, 26(24), 12063, doi: 10.3390/ijms262412063.
Lagunin A.A., Sezganova A.S., Muraviova E.S., Rudik A.V., Filimonov D.A., (2024). BC CLC-Pred: a freely available web-application for quantitative and qualitative predictions of substance cytotoxicity in relation to human breast cancer cell lines, SAR and QSAR in Environmental Research, 2024, 35(1), 1-9, doi: 10.1080/1062936X.2023.2289050.
Lagunin A.A., Rudik A.V., Pogodin P.V., Savosina P.I., Tarasova O.A., Dmitriev A.V., Ivanov S.M., Biziukova N.Y., Druzhilovskiy D.S., Filimonov D.A., Poroikov V.V., CLC-Pred 2.0: A Freely Available Web Application for In Silico Prediction of Human Cell Line Cytotoxicity and Molecular Mechanisms of Action for Druglike Compounds, International Journal of Molecular Sciences, 2023, 24(2), 1689, doi: 10.3390/ijms24021689.
Ionov N.S., Baryshnikova M.A., Bocharov E.V., Pogodin P.V., Lagunin A.A., Filimonov D.A., Karpova R.V., Kosorukov V.S., Stilidi I.S., Matveev V.B., Bocharova O.A., Poroikov V.V., Possibilities of in Silico Estimations for the Development of the Pharmaceutical Composition Phytoladaptogene Cytotoxic for Bladder Cancer Cells, Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 2021, 15(4), 290-300, doi: 10.1134/S1990750821040041.
Lebedev N.V., Filimonov D.A., Poroikov V.V., Lagunin A.A. (2025). Prediction of New Nε-Acetylation Sites in the Human Proteome Based on Molecular Multilevel Neighborhoods of Atom Descriptors, Molecular Biology, 2025, 59(5), 836-848, doi: 10.1134/S0026893325700311.
Zakharov O.S., Rudik A.V., Filimonov D.A., Lagunin A.A., Prediction of Protein Secondary Structures Based on Substructural Descriptors of Molecular Fragments, International Journal of Molecular Sciences, 2024, 25(23), 12525 , doi: 10.3390/ijms252312525.
Ivanov S.M., Sukhachev V.S., Tarasova O.A., Lagunin A.A., Poroikov V.V. (2025). Analysis of Genomic and Transcriptomic Data Revealed Key Genes and Processes in the Development of Major Depressive Disorder, International Journal of Molecular Sciences, 2025, 26(19), 9557-9557, doi: 10.3390/ijms26199557.
Galiakberova A., Ivanov S., Golov A., Artyuhov A., Zolkin A., Kondratyev N., Lagunin A., Golimbet V., Dashinimaev E., (2025). Transcriptomic profiling of neural cultures from the KYOU iPSC line via alternative differentiation protocols, Frontiers in Molecular Neuroscience, 18, 1661986, doi: 10.3389/fnmol.2025.1661986.
Ivanov, S. M., Lagunin, A. A., Poroikov, V. V. (2024). Repositioning of drugs for the treatment of major depressive disorder based on prediction of drug-induced gene expression changes, Biomeditsinskaya Khimiya, 70(6), 403-412, doi: 10.18097/PBMC20247006403.
Kositsyn Y.M., de Abreu M.S., Kolesnikova T.O., Lagunin A.A., Poroikov V.V., Harutyunyan H.S., Yenkoyan K.B., Kalueff A.V. Towards Novel Potential Molecular Targets for Antidepressant and Antipsychotic Pharmacotherapies, International Journal of Molecular Sciences, 2023, 24(11), 9482, doi: 10.3390/ijms24119482.
Kumar S., Ivanov S., Lagunin A., Goel R.K., (2022). Bioinformatics guided rotenone adjuvant kindling in mice as a new animal model of drug-resistant epilepsy, Computers in Biology and Medicine, 147, 105754, doi: 10.1016/j.compbiomed.2022.105754.
Borozdenko D.A., Ezdoglian A.A., Shmigol T.A., Gonchar D.I., Lyakhmun D.N., Tarasenko D.V., Golubev Ya.V., Cherkashova E.A., Namestnikova D.D., Gubskiy I.L., Lagunin A.A., Gubsky L.V., Chekhonin V.P., Borisevich S.S., Gureev M.A., Shagina A.D., Kiseleva N.M., Negrebetsky V.V., Baukov Yu.I., A Novel Phenylpyrrolidine Derivative: Synthesis and Effect on Cognitive Functions in Rats with Experimental Ishemic Stroke, Molecules, 2021, 26(20), 6124, doi: 10.3390/molecules26206124.
Dembitsky V.M., Terent`ev A.O., Stolbov L.A., Pogodin P.V., Filimonov D.A., Poroikov V.V., Salicylic Acid and Its Boron Complexes as Quorum Sensing Molecules, Molecular Pharmaceutics, 2025, 22(11), 6499-6509, doi: 10.1021/acs.molpharmaceut.5c00848.
Bocharova O.A., Ionov N.S., Kazeev I.V., Shevchenko V.E., Bocharov E.V., Karpova R.V., Sheychenko O.P., Aksenov A.A., Chulkova S.V., Kucheryanu V.G., Revishchin A.V., Pavlova G.V., Kosorukov V.S., Filimonov D.A., Lagunin A.A., Matveev V.B., Pyatigorskaya N.V., Stilidi I.S., Poroikov V.V., Computer-Aided Evaluation of Polyvalent Medications’ Pharmacological Potential. Multiphytoadaptogen as a Case Study, Molecular Informatics, 2023, 42(1), 2200176, doi: 10.1002/minf.202200176.
Kazeev I.V., Ionov N.S., Shevchenko V.E., Bocharov E.V., Karpova R.V., Aksenov A.A., Sheichenko O.P., Kucheryanu V.G., Kosorukov V.S., Filimonov D.A., Lagunin A.A., Poroikov V.V., Pyatigorskaya N.V., Bocharova O.A., Secondary metabolites of oplopanax elatus: possibilities of standardization of the multi-phytoadaptogen for preventive oncology, Pharmaceutical Chemistry Journal, 2023, 57(2), 75-82,doi: 10.1007/s11094-023-02853-w.
Ionov N., Druzhilovskiy D., Filimonov D., Poroikov V. (2023). Phyto4Health: Database of Phytocomponents from Russian Pharmacopoeia Plants, Journal of Chemical Information and Modeling, 63(7), 1847-1851, doi: 10.1021/acs.jcim.2c01567.
Bocharova O.A., Karpova R.V., Bocharov E.V., Aksyonov A.A., Chekalina T.L., Chulkova S.V., Ionov N.S., Kazeev I.V., Lyzhenkova M.A., Vershinskaya A.A., Kucheryanu V.G., Kosorukov V.S. (2023). Adhesive phytoadaptogens-geroprotectors in preventive oncology, Cardiometry, (26), 55-64, doi: 10.18137/cardiometry.2023.26.5568.
Bocharova O.A., Kazeev I.V., Shevchenko V.E., Ionov N.S. , Sheichenko O.P., Bocharov E.V., Karpova R.V., Kucheryanu V.G., Lagunin A.A., Filimonov D.A., Kosorukov V.B., Poroikov V.V., Tutelyan V.A., Pyatigorskaya N.V. (2023). Secondary metabolites of Schisandra chinensis in homeostasis regulator adaptogen herbal formula for preventive oncology, Cardiometry, (27), 63-74, doi: 10.18137/cardiometry.2023.27.6374.
Bocharova O.A., Shevchenko V.E., Kazeev I.V., Sheichenko O.P., Ionov N.S., Bocharov E.V., Karpova R.V., Aksenov A.A., Poroikov V.V., Kucheryanu V.G., Kosorukov V.S., Analysis of Eleutherosides by Tandem Mass Spectrometry: Possibilities of Standardizing Multi-Phytoadaptogen Formulation for Preventive Oncology, Pharmaceutical Chemistry Journal, 2022, 56, 806-814, doi: 10.1007/s11094-022-02712-0.
Bocharova O.A., Kazeev I.V., Shevchenko V.E., Sheichenko O.P., Poroikov V.V., Bocharov E.V., Karpova R.V., Ionov N.S., Kucheryanu V.G., Kosorukov V.S., Matveev V.B., Stilidi I.S., (2022). A potential method for standardization of multiphytoadaptogen: Tandem mass spectrometry for analysis of biologically active substances from Rhodiola rosea, Pharmaceutical Chemistry Journal, 56(1), 78-84, doi: 10.1007/s11094-022-02607-0.
Lupanova I.A., Mizina P.G., Ionov N.S., Poroikov V.V., Khlebnikov A.I., Martynchik I.A. (2022). Effect of chicoric and chlorogenic acids of Cichorium intybus L. on cytochrome P450 and glutathione transferase activities, Russian Journal of Biopharmaceuticals, Vol 14(5), 8-18, doi: 10.30906/2073-8099-2022-14-5-8-18.
Whaley A.K., Ponkratova A.O., Orlova A.A., Serebryakov E.B., Smirnov S.N., Proksh P., Ionov N.S., Poroikov V.V., Luzhanin V.G., Phytochemical Analysis of Polyphenol Secondary Metabolites in Cloudberry (Rubus Chamaemorus L.) Leaves, Pharmaceutical Chemistry Journal, 2021, 55(3), 253-258, doi: 10.1007/s11094-021-02407-y.
Stolbova E.A., Pokrovskaya A.V., Shemshura A.B., Kireev D.E., Lagunin A.A., Sobolev B.N., Ivanov S.M., Tarasova O.A., Early Transcriptomic Signatures of Immune Response Modulation Following Antiretroviral Therapy in HIV-Infected Patients, International Journal of Molecular Sciences, 2025, 26(21), 10678, doi: 10.3390/ijms262110678.
Stolbova E.A., Stolbov L.A., Filimonov D.A., Poroikov V.V., Tarasova O.A., Quantitative Prediction of Human Immunodeficiency Virus Drug Resistance, Viruses, 2024, 16(7), 1132, doi: 10.3390/v16071132.
Paremskaia A.I., Rudik A.V., Filimonov D.A., Lagunin A.A., Poroikov V.V., Tarasova O.A. (2023). Web Service for HIV Drug Resistance Prediction Based on Analysis of Amino Acid Substitutions in Main Drug Targets, Viruses, 15(11), 2245, doi: 10.3390/v15112245.
Kumar S., Ivanov S., Lagunin A., Goel R.K., Rhee S.-Y., Boehm M., Tarasova O., Di Teodoro G., Abecasis A.B., Sönnerborg A., Bailey A.J., Kireev D., Zazzi M., the EuResist Network Study Group, Shafer R.W., Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations, Pathogens, 2022, 11(5), 546, doi: 10.3390/pathogens11050546.
Pikalyova K., Orlov A., Lin A., Tarasova O., Marcou G., Horvath D., Poroikov V., Varnek A., HIV-1 drug resistance profiling using amino acid sequence space cartography, Bioinformatics, 2022, 38(8), 2306-2314, doi: 10.1093/bioinformatics/btac090.
Rhee S., Boehm M., Tarasova O., Di Teodoro G., Abecasis A.B., Sönnerborg A., Bailey A.J., Kireev D., Zazzi M., The EuResist Network Study Group, Shafer R.W., Spectrum of Atazanavir-Selected Protease Inhibitor-Resistance Mutations, Pathogens, 11(5), 546, doi: 10.3390/pathogens11050546.
Ivanov S, Filimonov D, Tarasova O., A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression, Computational and structural biotechnology journal, 2021, 19, 2447-2459, doi: 10.1016/j.csbj.2021.04.056.
Tarasova O., Rudik A., Kireev D., Poroikov V., RHIVDB: A freely accessible database of HIV amino acid sequences and clinical data of infected patients, Frontiers in Genetics, 2021, 12, 679029, doi: 10.3389/fgene.2021.679029.
Tarasova O.A., Rudik A.V., Ivanov S.M., Lagunin A.A., Poroikov V.V., Filimonov D.A., Machine Learning Methods in Antiviral Drug Discovery, Topics in Medicinal Chemistry, 2021, 37, 245-279, doi: 10.1007/7355_2021_121.
Khandazhinskaya A.L., Maslova A.A., Matyugina E.S., Kukhanova M.K., Kochetkov S.N., Mercurio V., Ñahui Palomino R.A., Margolis L., Vanpouille C., Novikov M.S., Paramonova M.P., Fedorova N.E., Yurlov K.I., Kushch A.A., Tarasova O., Dual-targeted anti-CMV/anti-HIV-1 heterodimers, Biochimie, 2021, 189, 169-180, doi: 10.1016/j.biochi.2021.06.011.
Tarasova O., Poroikov V., Machine learning in discovery of new antivirals and optimization of viral infections therapy, Current Medicinal Chemistry, 2021, 28(38), 7840-7861, doi: 10.2174/0929867328666210504114351.
Tarasova O., Biziukova N., Kireev D., Lagunin A., Ivanov S., Filimonov D., Poroikov V., A Computational Approach for the Prediction of Treatment History and the Effectiveness or Failure of Antiretroviral Therapy, International Journal of Molecular Sciences, 2020, 21(3), 748, doi: 10.3390/ijms21030748.
Ivanov S., Lagunin A., Filimonov D., Tarasova O., Network-Based Analysis of OMICs Data to Understand the HIV–Host Interaction, Frontiers in Microbiology, 2020, 11, 1314, doi: 10.3389/fmicb.2020.01314.
Tarasova O., Biziukova N., Filimonov D., Poroikov V., A Computational Approach for the Prediction of HIV Resistance Based on Amino Acid and Nucleotide Descriptors, Molecules, 2018, 23(11), 2751-2764, doi: 10.3390/molecules23112751.
Ivanov S.M., Zgoda V.G., Isakova V.A., Trukhanova L.S., Poroikov V.V., Shtil A.A., Proteomic Analysis Identifies Multiple Mechanisms of 5-Fluorouracil-Induced Gut Mucositis in Mice, Cancers, 2024, 16(23), 4025-4025, doi: 10.3390/cancers16234025.
Kliuchnikova A.A., Novikova S.E., Ilgisonis E.V., Kiseleva O.I., Poverennaya E.V., Zgoda V.G., Moshkovskii S.A., Poroikov V.V., Lisitsa A.V., Archakov A.I., Ponomarenko E.A., Blood Plasma Proteome: A Meta-Analysis of the Results of Protein Quantification in Human Blood by Targeted Mass Spectrometry, International Journal of Molecular Sciences, 2023, 24(1), 769, doi: 10.3390/ijms24010769.
Pogodin P.V., Kiseleva O.I., Ilgisonis E.V. (2023). Identification of Potential Therapeutic Targets on the Level of DNA/mRNAs, Proteins and Metabolites: A Systematic Mapping Review of Scientific Texts’ Fragments from Open Targets, Current Issues in Molecular Biology, 45(4), 3406-3418, doi: 10.3390/cimb45040223.
Shkrigunov T., Pogodin P., Zgoda V., Larina O., Kisrieva Y., Klimenko M., Latyshkevich O., Klimenko P., Lisitsa A., Petushkova N. (2022). Protocol for Increasing the Sensitivity of MS-Based Protein Detection in Human Chorionic Villi, Current Issues in Molecular Biology, 44(5), 2069-2088, doi: 10.3390/cimb44050140.
Ilgisonis E.V., Pogodin P.V., Kiseleva O.I., Tarbeeva S.N., Ponomarenko E.A. (2022). Evolution of Protein Functional Annotation: Text Mining Study, Journal of Personalized Medicine, 12(3), 479, doi: 10.3390/jpm12030479.
Gomazkov O.A., Neuroproteomics: How a Multitude of Proteins Reflect Brain Functions, Biology Bulletin, 2021, 11(2), 143-153, doi: 10.1134/S2079086421020043.
Schimunek J., Seidl P., Elez K., et al., A community effort in SARS-CoV-2 drug discovery, Molecular Informatics, 2024, 43(1), e202300262, doi: 10.1002/minf.202300262.
Karasev D.A., Sobolev B.N., Filimonov D.A., Lagunin A, (2024). Prediction of viral protease inhibitors using proteochemometrics approach, Computational Biology and Chemistry, 110, 108061, doi: 10.1016/j.compbiolchem.2024.108061.
Stolbova E.A., Stolbov L.A., Filimonov D.A., Poroikov V.V., Tarasova O.A., Quantitative Prediction of Human Immunodeficiency Virus Drug Resistance, Viruses, 2024, 16(7), 1132, doi: 10.3390/v16071132.
Tarasova O., Petrou A., Ivanov S.M., Geronikaki A., Poroikov V., Viral Factors in Modulation of Host Immune Response: A Route to Novel Antiviral Agents and New Therapeutic Approaches, International Journal of Molecular Sciences, 2024, 25(17), 9408, , doi: 10.3390/ijms25179408.
Tarasova, O. A., Biziukova, N. Yu., Stolbova, E. A., Stolbov, L. A., Taktashov, R. R., Karasev, D. A., Ionov, N. S., Ivanov, S. M., Dmitriev, A. V., Rudik, A. V., Druzhilovskiy, D. S., Sobolev, B. N., Filimonov, D. A., Poroikov, V. V. (2024). Extracting information on virus-human interactions and on antiviral compounds based on automated analysis of large text collections, Biomeditsinskaya Khimiya, 70(6), 469-474, doi: 10.18097/PBMC20247006469.
Kolodnitsky A., Ionov N., Gravel I., Poroikov V. (2023). Natural compounds from medicinal plants against COVID-19. Exploration of Drug Science, 2023(1), 253-275, doi: 10.37349/eds.2023.00017.
Muratov E.N., Amaro R., Andrade C.H., Brown N., Ekins S., Fourches D., Isayev O., Kozakov D., Medina-Franco J., Merz K.M., Oprea T.I., Poroikov V., Schneider G., Todd M.H., Varnek A., Winkler D.A., Zakharov A., Cherkasov A., Tropsha A., A critical overview of computational approaches employed for COVID-19 drug discovery, Chemical Society Reviews, 2021, 50(16), 9121-9151, doi: 10.1039/d0cs01065k.
Tarasova O.A., Rudik A.V., Ivanov S.M., Lagunin A.A., Poroikov V.V., Filimonov D.A., Machine Learning Methods in Antiviral Drug Discovery, Topics in Medicinal Chemistry, 2021, 37, 245-279, doi: 10.1007/7355_2021_121.
Khandazhinskaya A.L., Maslova A.A., Matyugina E.S., Kukhanova M.K., Kochetkov S.N., Mercurio V., Ñahui Palomino R.A., Margolis L., Vanpouille C., Novikov M.S., Paramonova M.P., Fedorova N.E., Yurlov K.I., Kushch A.A., Tarasova O., Dual-targeted anti-CMV/anti-HIV-1 heterodimers, Biochimie, 2021, 189, 169-180, doi: 10.1016/j.biochi.2021.06.011.
Tarasova O., Poroikov V., Machine learning in discovery of new antivirals and optimization of viral infections therapy, Current Medicinal Chemistry, 2021, 28(38), 7840-7861, doi: 10.2174/0929867328666210504114351.
Sukhachev V.S., Ivanov S.M., Dmitriev A.V., (2023). Prediction of Adverse Effects of Drug–Drug Interactions on Cardiovascular System Based on the Analysis of Structure–Activity Relationships, Biochemistry (Moscow), 88, 630-639, doi: 10.1134/s0006297923050061.
Rudik A., Dmitriev A., Lagunin A., Filimonov D., Poroikov V.(2022). Computational prediction of inhibitors and inducers of the major isoforms of cytochrome P450, Molecules, 2022(27), 5875-5875, doi: 10.3390/molecules27185875.
Koroleva P.I., Kuzikov A.V., A.V., Masamrekh R.A., Filimonov D.A., Dmitriev A.V., Zaviyalova M.G., Rikova S.M., Shich E.V., Makhova A.A., Bulko T.V., Gilep A.A., Shumyantseva V.V., Modeling of Drug-Drug Interactions between Omeprazole and Erythromycin in the Cytochrome P450-Dependent System in vitro, Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 2021, 15(1), 62-70. doi: 10.1134/S1990750821010030.
Dmitriev A.V., Rudik A.V., Karasev D.A., Pogodin P.V., Lagunin A.A., Filimonov D.A., Poroikov V.V., In Silico Prediction of Drug–Drug Interactions Mediated by Cytochrome P450 Isoforms, Pharmaceutics, 2021, 13(4), 538, doi: 10.3390/pharmaceutics13040538.
Dmitriev A.V., Lagunin A.A., Karasev D.A., Rudik A.V., Pogodin P.V., Filimonov D.A., Poroikov V.V. (2019). Prediction of Drug-Drug Interactions Related to Inhibition or Induction of Drug-Metabolizing Enzymes, Current Topics in Medicinal Chemistry, 19 (5) 319-336. DOI: 10.2174/1568026619666190123160406.
Ivanov S.M.,Lagunin A.A., Filimonov D.A., Poroikov V.V. (2018). Computer Prediction of Adverse Drug Effects on the Cardiovascular System, Pharmaceutical Chemistry Journal, 52(9), 758-762, doi: 10.1007/s11094-018-1895-1.
Bitencourt-Ferreira G., Villarreal M.A., Quiroga R., Biziukova N., Poroikov V., Tarasova O., de Azevedo Junior W.F., Exploring Scoring Function Space: Developing Computational Models for Drug Discovery, Current Medicinal Chemistry, 2024, 31(17), 2361-2377, doi: 10.2174/0929867330666230321103731.
Karasev D.A., Sobolev B.N., Filimonov D.A., Lagunin A, (2024). Prediction of viral protease inhibitors using proteochemometrics approach, Computational Biology and Chemistry, 110, 108061, doi: 10.1016/j.compbiolchem.2024.108061.
de Azevedo W.F. Jr, Quiroga R., Villarreal M.A., da Silveira N.J.F., Bitencourt-Ferreira G., da Silva A.D., Veit-Acosta M., Oliveira P.R., Tutone M., Biziukova N., Poroikov V., Tarasova O., Baud S., (2024). SAnDReS 2.0: Development of machine-learning models to explore the scoring function space, Journal of Computational Chemistry, 45(27), 2333-2346, doi: 10.1002/jcc.27449.
Karasev D.A., Sobolev B.N., Lagunin A.A., Filimonov D.A., Poroikov V.V.,(2022). The method predicting interaction between protein targets and small-molecular ligands with the wide applicability domain, Computational Biology and Chemistry, 98, 107674, doi: 10.1016/j.compbiolchem.2022.107674.
Horishny М., Geronikaki A., Kartsev V., Matiychuk V., Petrou A., Pogodin P., Poroikov V., Papadopoulou T.A., Vizirianakis I.S., Kostic M., IvanovM., Sokovic M. (2022). Synthesis, biological evaluation and molecular docking studies of 5-indolylmethylen-4-oxo-2-thioxothiazolidine derivatives, Molecules, 27(3), 1068, doi: 10.3390/molecules27031068.
Kamoutsis C., Fesatidou M., Petrou A., Geronikaki A., Poroikov V., Ivanov M., Sokovic M., Ciric A., Carazo A., Mladenka P., Triazolo based-thiadiazole derivatives. Synthesis, biological evaluation and molecular docking studies, Antibiotics, 2021, 2021(10), 804, doi: 10.3390/antibiotics10070804.
Zveaghintseva M., Stingaci E., Pogrebnoi S., Smetanscaia A., Valica V., Uncu L., Kravtsov V., Melnik E., Petrou A., Glamočlija J., Soković M., Carazo A., Mladěnka P., Poroikov V., Geronikaki A., Macaev F., Chromenol derivatives as novel antifungal agents. Synthesis, in silico and in vitro evaluation, Molecules, 2021, 26(14), 4304, doi: 10.3390/molecules26144304.
Tarasova O., Poroikov V., Veselovsky A., Molecular docking studies of HIV-1 resistance to reverse transcriptase inhibitors: mini-review, Molecules, 2018, Vol 23(5), 1233, doi: 10.3390/molecules23051233.
Schimunek J., Seidl P., Elez K., et al., A community effort in SARS-CoV-2 drug discovery, Molecular Informatics, 2024, 43(1), e202300262, doi: 10.1002/minf.202300262.
Gomazkov O.A. (2024) Pathogenesis of Post-COVID Syndrome: The Key Role of the Immune System, Advances in Current Biology, Vol 144(2), 171-177, doi: 10.31857/S0042132424020046.
Gomazkov O.A. (2023) Post-Covid Syndrome: Pathophysiology of Systemic Disregulations, Vol 143(3), 229-238, doi: 10.31857/S0042132423030067.
Kolodnitsky A., Ionov N., Gravel I., Poroikov V. (2023). Natural compounds from medicinal plants against COVID-19, Exploration of Drug Science, 2023(1), 253-275, doi: 10.37349/eds.2023.00017.
Gomazkov O.A. (2022) Neuropilin Is a New Player in the Pathogenesis of COVID-19, Neurochemical Journal, Vol 16(2), 130–135, doi: 10.1134/S1819712422020064.
Gomazkov, O.A. (2022) COVID-19: Cellular and Molecular Mechanisms of Brain Damage, Biology Bulletin Reviews, 12, 131–139, doi: 10.1134/S2079086422020037.
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