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List of Publucations

Dr. Igor I. Baskin

Complete list of publications
(book chapters and peer-reviewed journals)

 

Book Chapters

  1. Baskin I.I., Varnek A. Chapter 1. Fragment Descriptors in SAR/QSAR/QSPR Studies, Molecular Similarity Analysis and in Virtual Screening. // In: Chemoinformatics Approaches to Virtual Screening / Varnek A., Tropsha A., Ed. – RCS Publishing. - 2008. – P. 1-43.
  2. Baskin I.I., Palyulin V.A., Zefirov N.S. Chapter 8. Neural Networks in Building QSAR Models // In: Artificial Neural Networks: Methods and Protocols / Livingstone D.S., Ed. – Humana Press, a part of Springer Science + Business Media - 2008. – P. 139-160.
  3. Baskin I.I. Chapter 9. Formal-Logical Approach of N.S. Zefirov and S.S. Tratch to Organic Reactions and Its Application to Solving Problems in Organic Chemistry // In: Organic Chemistry in Publications of N.S. Zefirov. Collection of Reviews / Zlotsky S.S., Proskurnina M.V., Eds. - GILEM: Ufa – 2012. - P. 219-238 (Russ.).
  4. Marcou G., Baskin I.I. Chapter 8. Using Chemoinformatics Tools from R // In: Data Mining in Drug Discovery / R.D. Hoffmann, A. Gohier, P. Pospisil, Eds. - Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany. – 2013. – P. 177-207.
  5. Baskin I.I., Varnek A. Building a chemical space based on fragment descriptors // In:Advances in Combinatorial Chemistry & High Throughput Screening / Chaguturu R., Ed. - Bentham Science Publishers - 2013. - Vol. 1, P. 36–59..

Articles in Journals

  1. Yaroslavtsev, A.B.; Chuvaev, V.F.; Prozorovskaya, Z.N.; Baskin, I.I. Broadband PMR Study of Hydrates of Inorganic Acids. Zh. Neorg. Khim. 1983, v.28, No.11, p.2746-2749 (Russ.).
  2. Levina, O.I.; Potekhin, K.A.; Kurkutova, E.N.; Struchkov, Yu.T.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Crystal and Molecular Structure of 3,7-Diacetyl-1,5-diphenyl-3,7- diazobicyclo[3.3.1]nonane-9-one. Dokl. Akad. Nauk. SSSR. 1985, v.281, No.6, p.1367-1370 (Russ.).
  3. Zefirov, N.S.; Baskin, I.I.; Trach, S.S. Universal Computer Graphics Program for Organic Chemistry Purposes. Zh. Vses. Khim. O-va im. D.I.Mendeleeva. 1987, v.32, No.1, p.112-113 (Russ.).
  4. Stankevich, M.I.; Baskin, I.I.; Zefirov, N.S. Automation of Structural-Fragment Searches. Algorithm and Computer Programs. Zh. Strukt. Khim. 1987, v.28, No.6, p.136-137 (Russ.).
  5. Trach, S.S.; Baskin, I.I.; Zefirov, N.S. Computers and Molecular Design Problems. XIII. Systematic Analysis of Organic Processes Characterized by Open Topologies of Bond Redistributions. Journal of Organic Chemistry of the USSR 1988, v.24, No.6, p.1011-1020.
  6. Trach, S.S.; Baskin, I.I.; Zefirov, N.S. Problems of Molecular Design and the Computer. XIV. Systematic Analysis of Organic Processes Characterized by Linear-Cyclic Topology of Bond Redistribution. Journal of Organic Chemistry of the USSR 1989, v.25, No.8, p.1431-1449.
  7. Baskin, I.I.; Gordeeva, E.V.; Devdariani, R.O.; Zefirov, N.S.; Palyulin, V.A.; Stankevich, M.I. Solving the Inverse Problem of Structure-Property Relations for the Case of Topological Indexes. Doklady Chemistry 1989, v.307, No.3, p.217-220.
  8. Baskin, I.I.; Stankevich, M.I.; Devdariani, R.O.; Zefirov, N.S. Program Set for Finding Structure-Property Correlations Using Topological Indices. Journal of Structural Chemistry 1989, v.30, No.6, p.995.
  9. Zefirov, N.S.; Baskin, I.I. Moby. Version 1.41. J. Chem. Inf. Comput. Sci. 1992, v.32, No.3, p.260-261.
  10. Skvortsova, M.I.; Baskin, I.I.; Slovokhotova, O.L.; Palyulin, V.A.; Zefirov, N.S. The Inverse Problem in QSAR/QSPR Studies for the Case of Topological Indexes Characterizing Molecular Shape (Kier Indexes). Doklady Chemistry 1992, v.324, No.2, p.103-107.
  11. Baskin, I.I.; Burstein, K.Ya.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. Molecular Modeling of Conformations and Electronic Absorption Speactra of Crown-Containing Styryl Dyes and Their Complexes with Metal Cations. Doklady Physical Chemistry 1992, Vol. 325, No. 1/3, p.369.
  12. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Methodology for Obtaining the Complete Set of Canonical Types of Conformations for Cyclic Molecules. Dokl. Akad. Nauk 1992, v.326, No.5, p.821-826 (Russ.).
  13. Baskin, I.I.; Burstein, K.Ya.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. Molecular Simulation of the Complexation Effects on Conformations and Electronic Absorption Spectra of Crown Ether Styryl Dyes. J. Molec. Struct. 1992, v.274, p.93-104.
  14. Skvortsova, M.I.; Baskin, I.I.; Slovokhotova, O.L.; Palyulin, V.A.; Zefirov, N.S. Inverse Problem in QSAR/QSPR Studies for the Case of Topological Indices Characterizing Molecular Shape (Kier Indices). J. Chem. Inf. Comput. Sci. 1993, v.33, No.4, p.630-634.
  15. Baskin, I.I.; Lyubimova, I.K.; Abilev, S.K.; Palyulin, V.A.; Zefirov, N.S. Quantitative Structure-Activity Relationship Study of Mutagenic Activity of Chemical Compounds. Substituted Biphenyls. Dokl. Akad. Nauk 1993, v.332, No.5, p.587-589 (Russ.).
  16. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Computational Neural Networks as an Alternative to the Linear Regression Analysis in the Studies of Quantitative Relationships 'Structure-Property' for the Case of Physicochemical Properties of Hydrocarbons. Dokl. Akad. Nauk 1993, v.332, No.6, p.713-716 (Russ.).
  17. Zefirov, N.S.; Baskin, I.I. Problems of Molecular Design and the Computer. XV. Description of Reaction Mechanisms in Term of the Formal-Logical Approach. Russ. J. Org. Chem. 1993, v.29, No.3, p.375-384.
  18. Baskin, I.I.; Burstein, K.Ya.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. Molecular Simulation of the Complexation Effects on Conformations and Electronic Absorption Spectra of Crown Ether Styryl Dyes. Zh. Strukt. Khim. 1993, v.34, No.2, p.39-45 (Russ.).
  19. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. A Methodology for Searching Direct Correlations between Structures and Properties of Organic Compounds by Using Computational Neural Networks. Dokl. Akad. Nauk 1993, v.333, No.2, p.176-179 (Russ.).
  20. Kavun, S.M.; Petelin, D.E.; Palyulin, V.A.; Baskin, I.I.; Genkina, Yu.M.; Tsybko, I.G.; Zefirov, N.S. New Descriptors of Molecular Structure for the Description of Reactivity of Mercaptobenzothiazol-2-sulphenamide Derivatives. Dokl. Akad. Nauk 1993, v.333, No.2, p.189-192 (Russ.).
  21. Zefirov, N.S.; Baskin, I.I.; Palyulin, V.A. SYMBEQ Program and its Application in Computer-Assisted Reaction Design. J. Chem. Inf. Comput. Sci. 1993, v.34, No.4, p.994-999.
  22. Baskin, I.I.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. The Use of Molecular Mechanics for Studying Regio- and Stereoselectivity of the Cation-Dependent [2+2]Auto- photocycloaddition of Crown Ether Styryl Dyes. Doklady Physical Chemistry 1994, v.335, No.1-3, p.55-57.
  23. Skvortsova, M.I.; Baskin, I.I.; Slovokhotova, O.L.; Zefirov, N.S. Methodology of Constructing a General Model for the Structure-Property Relationship at the Topological Level. Doklady Chemistry 1994, v.336, No.4-6, pp.109-112.
  24. Stankevich, I.V.; Gal'pern, E.G.; Chistyakov, A.L.; Baskin, I.I.; Skvortsova, M.I.; Zefirov, N.S.; Tomilin, O.B. Spectral Theory of Graphs in Chemistry. 1. Projection Operators and Canonical Numeration of Graph Vertices. J. Chem. Inf. Comput. Sci. 1994, v.34, No.5, p.1105-1108.
  25. Baskin, I.I.; Lyubimova, I.K.; Abilev, S.K.; Palyulin, V.A.; Zefirov, N.S. Quantitative Relationship between Mutagenicity and Structure of Heterocyclic Analogs of Pyrene and Phenanthrene. DokladyBiochemistry 1994, v.339, No.1-6, p.129.
  26. Baskin, I.I.; Skvortsova, M.I.; Stankevich, I.V.; Zefirov, N.S. Basis of Invariants of Labeled Molecular Graphs. Doklady Chemistry 1994, v.339, No.3, pp. 231-234.
  27. Baskin, I.I.; Skvortsova, M.I.; Stankevich, I.V.; Zefirov, N.S. On Basis of Invariants of Labeled Molecular Graphs. J. Chem. Inf. Comput. Sci. 1995, Vol. 35, No.3 , pp. 527-531.
  28. Zotov, A.Yu.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Quantitative Characteristics of Nine-membered Conformations. Journal of Chemical Research 1995, p.130-131(S), 951-976(M).
  29. Abilev, S.K.; Lyubimova, I.K.; Baskin, I.I.; Halberstam, N.M.; Palyulin, V.A. Structure-Genotoxic Activity Relationships of Aromatic Hydrocarbons: Comparison of Results from Experimental Assay and Computerized Analysis. Karadeniz Journal of Medical Sciences 1995, v.8, No. 4, p.227 (Russ.).
  30. Skvortsova, M.I.; Baskin, I.I.; Slovokhotova, O.L.; Palyulin, V.A.; Zefirov, N.S. The Inverse Problem of the Structure-Property Relationship Problem in the Case of the Correlation Equation with Arbitrary Topological Descriptors. Doklady Chemistry 1996, v.346, No.4/6, p.37.
  31. Sidorova, A.B.; Baskin, I.I.; Petelin, D.E.; Palyulin, V.A.; Zefirov, N.S. Structure Octane Numbers of Hydrocarbons Relationships Studies. Dokl. Akad. Nauk 1996, v.350, No.5, p.642-646 (Russ.).
  32. Skvortsova, M.I.; Stankevich, I.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Analytical Description of the Set of Similarity Measures of Molecular Graphs. Dokl. Akad. Nauk 1996, v.350, No.6, p.786-788 (Russ.).
  33. Barachevskii, V.A.; Ait, A.O.; Baskin, I.I.; Alfimov, M.V. Development of Data Base on the Structure and Properties of Organic Photochromic Compounds. Zhurnal Nauchnoy i Prikladnoy Photographii 1996, v.41, No.4, p.44-51 (Russ.).
  34. Baskin, I.I.; Skvortsova, M.I.; Palyulin, V.A.; Zefirov, N.S. Quantitative Chemical Structure-Property/Activity Studies Using Artificial Neural Networks. Foundations of Computing and Decision Sciences. 1997, v.22, No.2, p.107-116.
  35. Zefirov, N.S.; Baskin, I.I.; Palyulin, V.A. Structural Design. Foundations of Computing and Decision Sciences. 1997, v.22, No.2, p.117-123.
  36. Skvortsova, M.I.; Baskin, I.I.; Zefirov, N.S.; Stankevich, I.V. On a Method for the Construction of Linear Equations for the Structure-Property Relationship. Doklady Chemistry 1996, v.351, No.1/3, p.287.
  37. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. A Neural Device for Searching Direct Correlations between Structures and Properties of Organic Compounds. J. Chem. Inf. Comput. Sci. 1997, v.37, No.4, p.715-721.
  38. Baskin, I.I.; Buznikov, G.A.; Kabankin, A.S.; Landau, M.A.; Leksina, L.A.; Ordukhanian, A.A.; Palyulin, V.A.; Zefirov, N.S. Computer Study of Relationships between Embriotoxicity and the Structure of Synthetic Analogues of Biogenic Amines. Russ. Biol. Bull. 1997, No.4, p.407-413.
  39. Gromov, S.P.; Fedorova, O.A.; Ushakov, E.N.; Baskin, I.I.; Lindeman, A.V.; Malysheva, E.V.; Balashova, T.A.; Arseniev, A.S.; Alfimov, M.V. Crown Ether Styryl Dyes. 24. Synthesis of Multiphotochromic 15-Crown-5 Ethers with Rigid Spacers, Their Anion-Capped Complexes and Stereospecific [2+2]Autophotocycloaddition. Russ. Chem. Bull. 1998, v.47, No.1, p.97-106.
  40. Baskin, I.I.; Halbertstam, N.M.; Palyulin, V.A.; Zefirov, N.S. Computer implementation of artificial neural networks for studying "structure-property" relationships. Informational Technologies 1997, No.9, p.27-30 (Russ.).
  41. Baskin, I.I.; Freidzon, A.Ya.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. Application of Molecular Mechanics to the Study of Regio- and Stereoselectivity of Cation-dependent [2+2]-Photocycloaddition in Crown Ether Styryl Dyes. Internet Journal of Chemistry 1998, 1, 19.
  42. Baskin, I.I.; Ait, A.O.; Halberstam, N.M.; Palyulin, V.A.; Alfimov, M.V.; Zefirov, N.S. The Use of Artificial Neural Networks for Predicting Properties of Complex Molecular Systems. Prognosis of the Position of Long-Wave Absorption Band of Symmetrical Cyane Dyes. Doklady Physical Chemistry, 1997, Vol. 357, Nos. 1–3, pp. 353-355.
  43. Skvortsova, M.I.; Baskin, I.I.; Stankevich, I.V.; Palyulin, V.A.; Zefirov, N.S. Molecular Similarity. 1. Analytical Description of the Set of Graph Similarity Measures. J. Chem. Inf. Comput. Sci. 1998, v.38, No.5, p.785-790.
  44. Skvortsova, M.I.; Slovokhotova, O.L.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Inverse Problem in the Structure-Property Study for the Case of Informational Topological Indexes. Doklady Chemistry 1997, v.357, No.1, p.72-74.
  45. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Neuromathematics is the Future of Computational Chemistry. Neurocomputers: Design and Applications 2000, Vol.1, No. 2, pp. 53-62.
  46. Freidzon, A.Ya.;Baskin, I.I.; Bagatur'yants, A.A.; Gromov, S.P.; Alfimov, M.V. Crown Ether Styryl Dyes. 25. Application of Molecular Mechanics to the Study of Self-Organization into Dimeric Complexes, Regio-, and Stereoselectivity of Cation-dependent [2+2]-Photocycloaddition in Photochromic Crown Ethers. Russ. Chem. Bull. 1998, No.11, p.2185-2191.
  47. Palyulin, V.A.; Baskin, I.I.; Radchenko, E.V.; Zefirov, N.S. Computer Molecular Design of Novel Drug Preparation. Bashkirsky Khimichesky Zhurnal, 1997, v.4, No.4, p.46-48 (Russ.).
  48. Baskin, I.I.; Halberstam, N.M.; Mukhina, T.V.; Palyulin, V.A.; Zefirov, N.S. The Learned Symmetry Concept in Revealing Quantitative Structure-Activity Relationships with Artificial Neural Networks. SAR and QSAR in Environmental Research 2001, Vol.12, pp.401-416.
  49. Ushakov, E.N.; Gromov, S.P.; Buevich, A.V.; Baskin, I.I.; Fedorova, O.A.; Vedernikov, A.I.; Alfimov, M.V.; Eliasson, B.; Edlung, U.G. Crown-containing styryl dyes: cation-induced self-assembly of multiphotochromic 15 -crown-5 ethers into photoswitchable molecular devices J. Chem. Soc., Perkin Trans. 2., 1999, N 3, 601-607.
  50. Skvortsova, M.I.; Baskin, I.I.; Skvortsov, L.A.; Palyulin, V.A.; Zefirov, N.S.; Stankevich, I.V. Chemical graphs and their basis invariants. Journal of Molecular Structure (Theochem) 1999, vol.466, pp.211-217.
  51. Ait, A.; Baskin, I.; Barachevsky, V.; Alfimov, M. Data Base on Photochromic Compounds. Mol. Cryst. Liq. Cryst. 1997, vol.298, pp. 271-275.
  52. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Application of Artificial Neural Networks in Chemical and Biochemical Studies. Vestnik Moskovskogo Universiteta, Ser. 2. Khim. 1999, vol.40(5), pp.323-326 (Russ.).
  53. Baskin, I.I.; Belenikin, M.S.; Ekimova, E.V.; Costantino, G.; Palyulin, V.A.; Pellicciari, R.; Zefirov, N.S. Molecular Modeling of the Amino-Terminal Domain of the Metabotropic Glutamate Receptor mGluR1. Doklady Chemistry 2000, v.374, No.1-3, pp.191-194.
  54. Kostanyan, I.A.; Zhokhov, S.S.; Astapova, M.V.; Dranitsyna, S.M.; Bogachuk, A.P.; Baidakova, L.K.; Rodionov, I.L.; Baskin, I.I.; Golubeva, O.N.; Tombran-Tink, J.; Lipkin, V.M. The Biological Function of a Fragment of the Neurotrophic Factor from Pigment Epithelium: Structural and Functional Homology with the Differentiation Factor of the HL-60 Cell Line. Russian Journal of Bioorganic Chemistry 2000, vol.26, No.8, pp.505-511.
  55. Bachurin, S.; Tkachenko, S.; Baskin, I.; Lermontova, N.; Petrova, L.; Ustinov, A.; Proshin, A.; Grigoriev, V.; Lukoyanov, N.; Palyulin, V.; Zefirov, N. Neuroprotective and Cognition Enhancing Properties of MK-801 Flexible Analogs. Structure-Activity Relationships. The Annals of the New York Academy of Sciencies 2001, v.931, pp.219-236
  56. Baskin, I.I.; Ait, A.O.; Halberstam, N.M.; Palyulin, V.A.; Zefirov, N.S. An Approach to the Interpretation of Backpropagation Neural Network Models in QSAR studies. SAR and QSAR in Environmental Research, 2002, No. 1, pp. 35-41.
  57. Lubimova, I.K.; Abilev, S.K.; Halberstam, N.M.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Computer-Assisted Prediction of Mutagenic Activity of Substituted Polycyclic Compounds. Russ. Biol. Bull. 2001, No.2, pp.164-170.
  58. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Prognosis of the Formation Enthalpies of Aliphatic Nitrocompoounds. Vestnik Moskovskogo Universiteta, Ser. 2. Khim. 2001, vol.42, No.6, pp.387-389 (Russ.).
  59. Tikhonova, I.G.; Baskin, I.I; Palyulin, V.A.; Zefirov, N.S.; Bachurin, S.O. Structural Basis for Understanding Structure-Activity Relationships for the Glutamate-Binding Site of NMDA Receptor. J. Med. Chem. 2002, vol.45, pp.3836-3843.
  60. Tikhonova, I.G.; Baskin, I.I; Palyulin, V.A.; Zefirov, N.S. Computer Simulation of the Three-Dimensional Structure of the Glutamate Site of the NR2B Subunit of the NMDA Receptor. Doklady Biochemistry and Biophysics, 2002, vol.382, pp.38-41.
  61. Tikhonova, I.G.; Baskin, I.I; Palyulin, V.A.; Zefirov, N.S. A Spatial Model of the Glycine Site of the NR1 Subunit of NMDA-Receptor and Ligand Docking. Doklady Biochemistry and Biophysics 2002, vol.382, pp.67-70.
  62. Artemenko, N.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Prediction of Physical Properties of Organic Compounds Using Artificial Neural Networks within the Substructure Approach. Doklady Chemistry, 2001, vol.381, No.1-3, pp.317-320.
  63. Skvortsova, M.I.; Fedyaev, K.S.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. A New Technique for Coding Chemical Structures Based on Basis Fragments. Doklady Chemistry, 2002 vol.382, Nos.4-6, pp.33-36.
  64. Belenikin, M.S.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular Modeling of the Amino-Terminal Domain of the mGluR1 Glutamate Metabotropic Receptor by the Threading Method. Doklady Chemistry, 2002, Vol.383, Nos.4-6, pp.97-101.
  65. Belenikin, M.S.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. A New Binding Mode of Competitive Antagonists to Metabotropic Glutamate Receptors Exemplified by the mGluR1-Receptor Antagonist AIDA (RS-Aminoindan-1,5-Dicarboxylic Acid). Doklady Biochemistry and Biophysics, 2002, pp.131-135.
  66. Halberstam, N.M.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Construction of Neural-Network Structure-Condition-Property Relationships: Modeling of the Physicochemical Properties of Hydrocarbons. Doklady Chemistry, 2002, Vol.384, Nos.1-3, pp.140-143.
  67. Artemenko, N.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Artificial Neural Networks and Fragmental Approach in Predicting Physico-Chemical Properties of Organic Compounds. Russ. Chem. Bull, 2003, Vol.52, No.1 pp.20-29.
  68. Belenikin, M.S.; Baskin, I.I.; Costantino, G; Palyulin, V.A.; Pellicciari, R.; Zefirov, N.S. Comparative Analysis of the Ligand-Binding Sites of the Metabotropic Glutamate Receptors mGluR1-mGluR8. Doklady Biochemistry and Biophysics, 2002, Vol.386, Nos.1-6, pp.251-256.
  69. Halberstam, N.M.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Neural Networks as a Method of Revealing Structure-Property Relationships for Organic Compounds. Russ. Chem. Reviews, 2003, Vol.72, No.7, pp.706-727.
  70. Halberstam, N.M.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Quantitative Structure -Conditions - Property Relationships Studies. Neural Network Modelling of Acid Hydrolysis of Esters. Mendeleev Communications, 2002, Vol.12, No.6, pp.185-186.
  71. Ivanov, A.A.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular Modeling of the Human A1 Adenosine Receptor and Study of the Mechanisms of Its Selective Ligand Binding. Doklady Biochemistry and Biophysics, 2002, Vol. 386, Nos. 1-6, pp.271-274.
  72. Belenikin, M.S.; Baskin, I.I.; Costantino, G.; Palyulin, V.A.; Pellicciari, R.; Zefirov, N.S. Molecular Modeling of the Closed Forms of the Kainate-Binding Domains of Kainate Receptors and Qualitative Analysis of the Structure-Activity Relationships for Some Agonists. Doklady Biochemistry and Biophysics, 2002, Vol. 386, Nos. 1-6, pp.239-244.
  73. Ivanov, A.A; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular Modeling of Adenosine Receptors. Moscow University Chemistry Bulletin, 2002, Vol. 43, No.4, pp.231-236.
  74. Tikhonova, I.G.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. CoMFA and Homology-based Models of the Glycine Binding Site of NMDA Receptor. J. Med. Chem., 2003, Vol.46, pp.1609-1616.
  75. Ivanov, A.A.; Baskin, I.I.; Palyulin, V.A.; Baraldi, P.G.; Zefirov, N.S. Molecular Modeling of the Human A2b Adenosine Receptor and an Analysis of the Binding Modes of its Selective Ligands. Mendeleev Communications, 2002, pp.211-212.
  76. Baskin, I.I.; Tikhonova, I.G.; Palyulin, V.A.; Zefirov, N.S. Selectivity Fields. Comparative Molecular Field Analysis (CoMFA) of the Glycine/NMDA and AMPA Receptors. J. Med. Chem., 2003, Vol. 46, No. 19, pp. 4063-4069.
  77. Gromov, S.P.; Ushakov, E.N.; Fedorova, O.A.; Baskin, I.I.; Buevich, A.V.; Andryukhina, E.N; Alfimov, M.V.; Johnels, D.; Edlund, U.G.; Whitesell, J.K.; Fox, M.A. Novel Photoswitchable Receptors: Synthesis and Cation-Induced Self-Assembly into Dimeric Complexes Leading to Stereospecific [2+2]-Photocycloaddition of Styryl Dyes Containing a 15-Crown-5 Ether Unit. J. Org. Chem., 2003, Vol. 68, No. 16, pp.6115-6125.
  78. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. FragmentalDescriptorsinQSPR: ApplicationtoMolecularPolarizabilityCalculations. Russian Chemical Bulletin, 2003, Vol. 52, No. 5, pp. 1061-1065.
  79. Tikhonova, I.G.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. A Quantitative Model of Ligand Binding to the Glutamate Site of the GluR2 Subunit of AMPA Receptor. Doklady Biochemistry and Biophysics, 2003, Vol. 389, Nos. 1-6, pp. 75-78.
  80. Ivanov, A.A.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular Modeling of the Human A2a Adenosine Receptor. Doklady Biochemistry and Biophysics, 2003, Vol. 389, Nos. 1–6, pp. 94-97.
  81. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Calculation of the Enthalpy of Sublimation by the QSPR Method with the Use of a Fragment Approach. Russian Journal of Applied Chemistry, 2003, Vol. 76, No. 12, pp. 1914-1919.
  82. Ivanov, A.A.; Voronkov, A.E.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. The study of the mechanism of binding  of human ML1A melatonin receptor ligands using molecular modeling. Dokl. Biochem. Biophys., 2004, Vol.394, pp. 49-52.
  83. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Fragmental descriptors in QSPR: flash point calculations. Russian Chemical Bulletin, 2003, Vol. 53, No. 9, pp. 1885-1892.
  84. Voronov, S.V.; Binevski, P.V.; Zueva, N.A.; Palyulin, V.A.; Baskin, I.I.; Orlova, M.A.; Kost, O.A. Structural and Functional Peculiarities of Homologous Domains of Angiotensin-Converting Enzyme. Russian Journal of Bioorganic Chemistry, 2003, Vol. 29, No. 5, pp. 426-433.
  85. Tikhonova, I.G.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. 3D-Model of the Ion Channel of NMDA Receptor:Qualitative and Quantitative Modeling of the Blocker Binding. Dokl. Biochem. Biophys., 2004, Vol.396, Nos.1-6, pp. 181-186.
  86. Tikhonova, I.G.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular Modeling of N-Terminal Domains of NMDA-Receptor. Study of Ligand Binding to N-Terminal Domains.Dokl. Biochem. Biophys., 2004, Vol.397, Nos.1-6, pp. 242-250.
  87. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Fragmental Descriptors in QSPR: Application to Magnetic Susceptibility Calculations. Journal of Structural Chemistry, 2004, Vol. 45, No. 4, pp. 626-635.
  88. Tikhonova, I.G.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Virtual screening of organic molecule databases. Design of focused libraries of potential ligands of NMDA and AMPA receptors. Russian Chemical Bulletin, 2004, Vol. 53, No. 6, pp. 1335-1344.
  89. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Application of artificial neural networks for predicting properties of chemical compounds. Neurocomputer, 2005, No. 1-2, pp. 98-101.
  90. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Astudyoftheaffinityofdyesforcellulosefiberwithintheframework of a fragment approach in QSPR. Russian Journal of Applied Chemistry, 2005, Vol. 78, No.6, pp. 1013-1017.
  91. Voronkov, A.E.; Ivanov, A.A.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular modeling study of the mechanism of ligand binding to human melatonin receptors. DokladyBiochemistry and Biophysics, 2005, Vol. 403, No. 1-6, pp. 284-288.
  92. Ivanov, A.A.; Baskin, I.I.; Palyulin, V.A.; Piccagli, L.; Baraldi, P.G.; Zefirov, N.S. Molecular modeling and molecular dynamics simulation of the human A 2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists. Journal of Medicinal Chemistry, 2005, Vol. 48, No. 22, pp. 6813-6820.
  93. Moiseeva, N.A.; Binevski, P.V.; Baskin, I.I.; Palyulin, V.A.; Kost, O.A. Role of two chloride-binding sites in functioning of testicular angiotensin-converting enzyme. Biochemistry (Mosc.), 2005, v. 70, No. 10, pp. 1167-1172.
  94. Skirgello, O.E.; Balyasnikova, I.V.; Binevski, P.V.; Sun, Z.L.; Baskin, I.I.; Palyulin, V.A.; Nesterovitch, A.B.; Albrecht, R.F. 2nd; Kost, O.A.; Danilov, S.M. Inhibitory antibodies to human Angiotensin-converting enzyme: fine epitope mapping and mechanism of action. Biochemistry, 2006, v. 45, No. 15, pp. 4831-4947.
  95. Baskin, I.I.; Palyulin, V.A. Zefirov, N.S. Multilayered perceptrons in QSPR studies of organic compounds. Russian Chemical Journal, 2006, V. 50, p. 86-96.
  96. Kazachinskaya, E.P.; Baskin, I.I.; Mamonov, P.A.; Matveenko, V.N. Molecular Modeling of Complexation between Molecules of beta-Cyclodextrine and Vitamin K3 Vestnik Moskovskogo Universiteta, Ser. 2. Khim., 2006, V. 43, No. 4, pp. 278-283.
  97. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Fragmental descriptors in QSPR: application for computing evaporation enthalpy of organic compounds. Russ. J. Phys. Chem. A, 2007, V. 81, No. 1, pp. 9-12
  98. Ivanova, A.A.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Estimation of Ionization Constants for Different Classes of Organic Compounds with the Use of the Fragmental Approach to the Search of Structure–Property Relationships. Doklady Chemistry, 2007, Vol. 413, Part 2, pp. 90-94.
  99. Varnek, A.; Kireeva, N.; Tetko, I.V.; Baskin, I.I.; Solov’ev, V.P. Exhaustive QSPR Studies of Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points? J. Chem. Inf. Model., 2007, Vol. 47, No. 3, P. 1111-1122.
  100. Kravtsov, A.A. ; Karpov, P.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. "Bimolecular" QSPR: Estimation of the Solvation Free Energy of Organic Molecules in Different Solvents. Doklady Chemistry, 2007, Vol. 414, Part 1, pp. 128-131.
  101. Bugrin, V.S.; Kozlov, M.Yu.; Baskin, I.I.; Melik-Nubarov, N.S. Intermolecular Interactions Governing Solubilization in Micelles of Poly(alkylene oxide) Surfactants. Polymer Science, Ser. A, 2007, Vol. 49, No. 4, pp. 463–472.
  102. Zhokhova, N.I.; Bobkov, E.V.; Baskin, I.I.; Zefirov, A.N.; Zefirov, N.S. Calculation of the Stability of β-Cyclodextrin Complexes of Organic Compounds Using the QSPR Approach. Moscow University Chemistry Bulletin, 2007, Vol. 62, No. 5, pp. 269-272.
  103. Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Fragmental Descriptors with Labeled Atoms and Their Application in QSAR/QSPR Studies. Doklady Chemistry, 2007, Vol. 417, Part 2, pp. 282-284.
  104. Voronkov, A.E.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular modeling of the complex between the xWnt8 protein and the CRD domain of the mFZD8 receptor. Dokl. Biochem. Biophys., 2007, Vol. 412, pp. 8-11.
  105. Voronkov, A.E.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular modeling of modified peptides, potent inhibitors of the xWNT8 and hWNT8 proteins. J. Mol. Graph. Model, 2008, Vol. 26, No. 7, pp. 1179-1187.
  106. Baskin, I.; Varnek A. Building a chemical space based on fragment descriptors. Comb. Chem. High Throughput Screening, 2008, Vol. 11, No. 8, pp. 661-668.
  107. Voronkov, A.E.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular model of the Wnt protein binding site on the surface of dimeric CRD domain of the hFzd8 receptor. Dokl. Biochem. Biophys., 2008, Vol. 419, pp. 75-78.
  108. Varnek, A.; Gaudin, C.; Marcou, G.; Baskin, I.. Pandey, A.K.; Tetko I.V. Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients. J. Chem. Inf. Model., 2009, Vol. 49, No. 1, pp. 133-144.
  109. Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry. Russian Chemical Reviews, 2009, Vol. 78, No. 6, pp. 495-511.
  110. Baskin, I.I.; Zhokhova, N.I.; Palyulin, V.A.; Zefirov, A.N.; Zefirov, N.S. Multilevel Approach to the Prediction of Properties of Organic Compounds in the Framework of the QSAR/QSPR Methodology. Doklady Chemistry, 2009, Vol. 427, Part 1, pp. 172-175.
  111. Kondratovich, E.P.; Zhokhova, N.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Fragmental descriptors in (Q)SAR: prediction of the assignment of organic compounds to pharmacological groups using the support vector machine approach. Russian Chemical Bulletin, International Edition, 2009, Vol. 58, No. 4, pp. 657-662.
  112. Zhokhova, N.I.; Baskin, I.I.; Bakhronov, D.K.; Palyulin, V.A.; Zefirov, N.S. Method of Continuous Molecular Fields in the Search for Quantitative Structure-Activity Relationships. Doklady Chemistry, 2009, Vol. 429, Part 1, pp. 273-276.
  113. Lanin, S.N.; Palyulin, V.A.; Baskin, I.I. Calculation of Adiabatic Burning Temperatures of Alkanes C2-C11 – the Components of Mineral Oils by the Method of Artificial Neural Networks. Pozhari inchrezvichaunie situatsii: predotvraschenie, likvidatsia, 2009, No. 3, pp. 20-27 (Russ.).
  114. Zhokhova, N.I.; Baskin, I.I.; Zefirov, A.N.; Palyulin, V.A.; Zefirov, N.S. Pseudofragmental Descriptors Based on Combinations of Atomic Properties for Prediction of Physical Properties of Polymers in Quantitative Structure–Property Relationship Studies. Doklady Chemistry, 2010, Vol. 430, Nos. 4-6, pp. 39-42.
  115. Kurilo, M.N.; Karpov, P.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov. N.S. Neural network modeling of substituent constants on the basis of fragmental descriptors. Doklady Chemistry, 2010, Vol. 431, Part 1, pp. 85-88.
  116. Makhaeva, G.F.; Aksinenko, A.Y.; Sokolov, V.B.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S.; Hein, N.D.; Kampf, J.W.; Wijeyesakere, S.J.; Richardson, R.J. Kinetics and mechanism of inhibition of serine esterases by fluorinated aminophosphonates. Chemico-Biological Interactions, 2010, Vol. 187, Iss. 1-3, pp. 177-184.
  117. Baskin, I.; Kireeva, N.; Varnek, A. The One-Class Classification Approach to Data Description and to Models Applicability Domain. Mol. Inf., 2010, Vol. 29, Iss. 8-9, pp. 581-587.
  118. Sushko, I.; Novotarskyi, S.; KЖrner, R.; Pandey, A. K.; Cherkasov, A.; Li, J.; Gramatica, P.; Hansen, K.; Schroeter, T.; MЭller, K. R.; Xi, L.; Liu, H.; Yao, X.; жberg, T.; Hormozdiari, F.; Dao, P.; Sahinalp, C.; Todeschini, R.; Polishchuk, P.; Artemenko, A.; Kuz'Min, V.; Martin, T. M.; Young, D. M.; Fourches, D.; Muratov, E.; Tropsha, A.; Baskin, I.; Horvath, D.; Marcou, G.; Muller, C.; Varnek, A.; Prokopenko, V. V.; Tetko, I. V., Applicability domains for classification problems: Benchmarking of distance to models for ames mutagenicity set. J. Chem. Inf. Model. 2010, Vol. 50, No.12, pp. 2094-2111.
  119. Nurieva, E.V.; Semenova, I.S.; Nuriev, V.N.; Shishov, D.V.; Baskin, I.I.; Zefirova, O.N.; Zefirov, N.S. Diels-Alder reaction as a synthetic approach to bicyclo[3.3.1]nonane colchicine analogs. Russian Journal of Organic Chemistry, 2010, Vol. 46, No. 12, pp. 1892-1895.
  120. Varnek, A.; Baskin, I. Chemoinformatics as a Theoretical Chemistry Discipline. Mol. Inf., 2011, Vol. 30, pp. 20-32.
  121. Karpov, P.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Virtual Screening Based on One-Class Classification. Doklady Chemistry, 2011, Vol. 437, Part 2, pp. 107-111.
  122. Zefirova, O.N.; Nurieva, E.V.; Shishov, D.V.; Baskin, I.I.; Fuchs, F.; Lemcke, H.; Schroeder, F.; Weiss, D.G.; Zefirov, N.S.; Kuznetsov, S.A. Synthesis and SAR requirements of adamantane-colchicine conjugates with both microtubule depolymerizing and tubulin clustering activities. Bioorganic & Medicinal Chemistry, 2011, Vol. 19, Iss. 18, pp. 5529-5538.
  123. Sushko, I.; Novotarskyi, S.; Körner, R.; Pandey, A. K.; Rupp, M.; Teetz, W.; Brandmaier, S.; Abdelaziz, A.; Prokopenko, V. V.; Tanchuk, V. Y.; Todeschini, R.; Varnek, A.; Marcou, G.; Ertl, P.; Potemkin, V.; Grishina, M.; Gasteiger, J.; Schwab, C.; Baskin, I. I.; Palyulin, V. A.; Radchenko, E. V.; Welsh, W. J.; Kholodovych, V.; Chekmarev, D.; Cherkasov, A.; Aires-De-Sousa, J.; Zhang, Q. Y.; Bender, A.; Nigsch, F.; Patiny, L.; Williams, A.; Tkachenko, V.; Tetko, I. V., Online chemical modeling environment (OCHEM): Web platform for data storage, model development and publishing of chemical information. J. Comput.-Aided Mol. Des. 2011, Vol. 25, No. 6, pp. 533-554.
  124. Karpov, P.V.; Baskin, I.I.; Zhokhova, N.I.; Zefirov, N.S. Method of Continuous Molecular Fields in the One-Class Classification Task. Doklady Chemistry, 2011, Vol. 440, Part 2, pp. 263-265.
  125. Karpov, P.V.; Osolodkin, D.I.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. One-class classification as a novel method of ligand-based virtual screening: the case of glycogen synthase kinase 3β inhibitors. Bioorganic & Medicinal Chemistry Letters, 2011, Vol. 21. pp. 6728-6731.
  126. Kravtsov, A.A.; Karpov, P.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Prediction of Rate Constants of SN2 Reactions by the Multicomponent QSPR Method. Doklady Chemistry, 2011, Vol. 440, Part 2, pp. 299-301.
  127. Kravtsov, A.A.; Karpov, P.V.; Baskin, I.I.; Palyulin, V.A.; Zefirov, N.S. Prediction of the Preferable Mechanism of Nucleophilic Substitution at Saturated Carbon Atom and Prognosis of SN1 Rate Constants by Means of QSPR. Doklady Chemistry, 2011, Vol. 441, Part 1, pp. 314-317.
  128. Karpov, P.V.;  Baskin, I.I.;  Zhokhova, N.I.; Nawrozkij, M.B.; Zefirov, A.N.; Yablokov, A.S.; Novakov, I.A.; Zefirov, N.S. Russian Chemical Bulletin, International Edition, 2011, Vol. 60, No. 11, pp. 2418-2424.
  129. Kireeva, N.; Baskin, I.I.; Gaspar, H.A.;  Horvath, D.; Marcou, G.; Varnek, A. Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure-Activity Modeling and Dataset Comparison. Mol. Inf., 2012,  Vol. 31, pp. 301-312.
  130. Makhaeva, G.F.; Radchenko, E.V.; Baskin, I.I.; Richardson, R.J.; Zefirov, N.S.Combined QSAR studies of inhibitor properties of O-phosphorylated oximes toward serine esterases involved in neurotoxicity, drug metabolism and Alzheimer’s disease. SAR and QSAR in Environmental Research, 2012, Vol. 23, Nos. 7-8, pp. 627-647.
  131. Varnek, A.; Baskin, I. Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis? . J. Chem. Inf. Model. 2012, Vol. 52, No. 6, pp. 1413-1437.
  132. Kondratovich, E.; Baskin, I.I.; Varnek, A. Transductive Support Vector Machines: Promising Approach to Model Small and Unbalanced Datasets. Mol. Inf., 2013, Vol. 32, No. 3, pp. 261-266.
  133. Chupakhin, V.; Marcou, G.; Baskin, I.; Varnek, A.; Rognan, D. Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints. J. Chem. Inf. Model., 2013, Vol. 53, No. 4, pp. 763-772.
  134. Baskin, I.I.; Zhokhova, N.I. The continuous molecular fields approach to building 3D-QSAR models. J. Comput. Aided Mol. Des., 2013, Vol. 27, No. 5, pp. 427-442.