Dr. Igor I. Baskin
Complete list of publications
(book chapters and peer-reviewed journals)
Book
Chapters
- 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.
- 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.
- 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.).
- 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.
- 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
- 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.).
- 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.).
- 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.).
- 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.).
- 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.
- 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.
- 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.
- 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.
- Zefirov, N.S.; Baskin, I.I. Moby. Version
1.41. J. Chem. Inf. Comput. Sci. 1992, v.32, No.3,
p.260-261.
- 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.
- 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.
- 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.).
- 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.
- 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.
- 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.).
- 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.).
- 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.
- 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.).
- 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.).
- 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.).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.).
- 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.
- 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.).
- 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.).
- 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.).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.).
- 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.
- 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.
- 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.
- Ait,
A.; Baskin, I.; Barachevsky, V.; Alfimov,
M. Data Base on Photochromic Compounds. Mol. Cryst. Liq. Cryst. 1997,
vol.298, pp. 271-275.
- 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.).
- 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.
- 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.
- 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
- 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.
- 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.
- 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.).
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.).
- 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.
- 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.
- 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.
- 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.
- Sushko, I.;
Novotarskyi, S.; Körner, R.; Pandey, A. K.; Cherkasov, A.; Li, J.;
Gramatica, P.; Hansen, K.; Schroeter, T.; Müller, K. R.; Xi, L.; Liu, H.;
Yao, X.; Öberg, 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.
- 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.
- Varnek,
A.; Baskin, I. Chemoinformatics as a
Theoretical Chemistry Discipline. Mol.
Inf., 2011, Vol. 30, pp. 20-32.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.