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1

Tutorials in Chemoinformatics || Benchmarking Machine-Learning Methods

Varnek, Alexandre

Year:

2017

Language:

english

File:

PDF, 829 KB

english, 2017

2

Chemoinformatics as a Theoretical Chemistry Discipline

Alexandre Varnek, Igor I. Baskin

Journal:

Molecular Informatics

Year:

2011

Language:

english

File:

PDF, 405 KB

english, 2011

3

QSAR Modeling: Where Have You Been? Where Are You Going To?

Cherkasov, Artem, Muratov, Eugene N., Fourches, Denis, Varnek, Alexandre, Baskin, Igor I., Cronin, Mark, Dearden, John, Gramatica, Paola, Martin, Yvonne C., Todeschini, Roberto, Consonni, Viviana, Kuz

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 1.54 MB

english, 2014

4

Tutorials in Chemoinformatics || Compound Classification Using the scikit-learn Library

Varnek, Alexandre

Year:

2017

Language:

english

File:

PDF, 225 KB

english, 2017

5

Rescoring of docking poses under Occam’s Razor: are there simpler solutions?

Zhenin, Michael, Bahia, Malkeet Singh, Marcou, Gilles, Varnek, Alexandre, Senderowitz, Hanoch, Horvath, Dragos

Journal:

Journal of Computer-Aided Molecular Design

Year:

2018

Language:

english

File:

PDF, 1.24 MB

english, 2018

6

CGRtools: Python Library for Molecule, Reaction and Condensed Graph of Reaction Processing

Nugmanov, Ramil I., Mukhametgaleev, Ravil, Akhmetshin, Tagir, Gimadiev, Timur, Afonina, Valentina, Madzhidov, Timur I., Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 1.11 MB

2019

7

The One-Class Classification Approach to Data Description and to Models Applicability Domain

Igor I. Baskin, Natalia Kireeva, Alexandre Varnek

Journal:

Molecular Informatics

Year:

2010

Language:

english

File:

PDF, 240 KB

english, 2010

8

Recovery of uranium (VI) from concentrated phosphoric acid by mixtures of new bis(1,3- dialkyloxypropan-2-yl) phosphoric acids and tri-n-octylphosphine oxide

Beltrami, Denis, Chagnes, Alexandre, Haddad, Mansour, Varnek, Alexandre, Mokhtari, Hamid, Courtaud, Bruno, Cote, Gérard

Journal:

Hydrometallurgy

Year:

2013

Language:

english

File:

PDF, 447 KB

english, 2013

9

QSPR Modeling of the Am III /Eu III Separation Factor: How Far Can we Predict ?

Varnek, Alexandre, Fourches, D., Sieffert, N., Solov'ev, V. P., Hill, C., Lecomte, M.

Journal:

Solvent Extraction and Ion Exchange

Year:

2007

Language:

english

File:

PDF, 282 KB

english, 2007

10

Electrochemical Properties of Substituted 2-Methyl-1,4-Naphthoquinones: Redox Behavior Predictions

Elhabiri, Mourad, Sidorov, Pavel, Cesar-Rodo, Elena, Marcou, Gilles, Lanfranchi, Don Antoine, Davioud-Charvet, Elisabeth, Horvath, Dragos, Varnek, Alexandre

Journal:

Chemistry - A European Journal

Year:

2015

Language:

english

File:

PDF, 662 KB

english, 2015

11

An Evolutionary Optimizer of libsvm Models

Horvath, Dragos, Brown, J., Marcou, Gilles, Varnek, Alexandre

Journal:

Year:

2014

Language:

english

File:

PDF, 452 KB

english, 2014

12

MOLECULAR MODELLING IN SOLVENT EXTRACTION: IONOPHORES IN PURE SOLUTIONS AND AT THE LIQUID/LIQUID INTERFACE

Varnek, Alexandre, Wipff, Georges

Journal:

Solvent Extraction and Ion Exchange

Year:

1999

Language:

english

File:

PDF, 526 KB

english, 1999

13

Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis

Polishchuk, Pavel, Tinkov, Oleg, Khristova, Tatiana, Ognichenko, Ludmila, Kosinskaya, Anna, Varnek, Alexandre, Kuz’min, Victor

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 2.92 MB

english, 2016

14

Automatized assessment of protective group reactivity: a step toward big reaction data analysis

Lin, Arkadii I., Madzhidov, Timur Ismailovich, Klimchuk, Olga, Nugmanov, Ramil I., Antipin, Igor S., Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 1.64 MB

english, 2016

15

Trustworthiness, the Key to Grid-Based Map-Driven Predictive Model Enhancement and Applicability Domain Control

Horvath, Dragos, Marcou, Gilles, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 2.62 MB

2020

16

van der Waals host-guest complexes: Can one predict complexation selectivity of neutral guests by a cryptophane? MD-FEP studies in gas phase and chloroform solution

Varnek, Alexandre, Helissen, Severine, Wipff, Georges, Collet, Andr�

Journal:

Journal of Computational Chemistry

Year:

1998

Language:

english

File:

PDF, 336 KB

english, 1998

17

Quantitative Structure—Property Relationship Modeling of β-Cyclodextrin Complexation Free Energies.

Alan R. Katritzky, Dan C. Fara, Hongfang Yang, Mati Karelson, Takahiro Suzuki, Vitaly P. Solov'ev, Alexandre Varnek

Journal:

Year:

2004

File:

PDF, 55 KB

2004

18

ChemInform Abstract: Quantitative Structure—Property Relationships in Solvent Extraction and Complexation of Metals

Alexandre Varnek, Vitaly Solov'ev

Journal:

Year:

2010

File:

PDF, 11 KB

2010

19

ISIDA Property-Labelled Fragment Descriptors

Fiorella Ruggiu, Gilles Marcou, Alexandre Varnek, Dragos Horvath

Journal:

Molecular Informatics

Year:

2010

Language:

english

File:

PDF, 804 KB

english, 2010

20

QSAR modeling of blood:air and tissue:air partition coefficients using theoretical descriptors

Alan R. Katritzky, Minati Kuanar, Dan C. Fara, Mati Karelson, William E. Acree Jr., Vitaly P. Solov’ev, Alexandre Varnek

Journal:

Bioorganic & Medicinal Chemistry

Year:

2005

Language:

english

File:

PDF, 403 KB

english, 2005

21

Correlation of blood–brain penetration using structural descriptors

Alan R. Katritzky, Minati Kuanar, Svetoslav Slavov, Dimitar A. Dobchev, Dan C. Fara, Mati Karelson, William E. Acree Jr., Vitaly P. Solov’ev, Alexandre Varnek

Journal:

Bioorganic & Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 648 KB

english, 2006

22

A unified approach to the applicability domain problem of QSAR models

Dragos Horvath, Gilles Marcou, Alexandre Varnek

Journal:

Journal of Cheminformatics

Year:

2010

Language:

english

File:

PDF, 146 KB

english, 2010

23

Local neighborhood behavior in a combinatorial library context

Dragos Horvath, Christian Koch, Gisbert Schneider, Gilles Marcou, Alexandre Varnek

Journal:

Journal of Computer-Aided Molecular Design

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

24

Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis ?

Varnek, Alexandre, Baskin, Igor

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 2.91 MB

english, 2012

25

Stability constants of complexes of Zn2+, Cd2+, and Hg2+with organic ligands: QSPR consensus modeling and design of new metal binders

Vitaly Solov’ev, Igor Sukhno, Vladimir Buzko, Aleksey Polushin, Gilles Marcou, Aslan Tsivadze, Alexandre Varnek

Journal:

Journal of Inclusion Phenomena and Macrocyclic Chemistry

Year:

2012

Language:

english

File:

PDF, 1.58 MB

english, 2012

26

Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches

de Luca, Aurélie, Horvath, Dragos, Marcou, Gilles, Solov’ev, Vitaly, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.84 MB

english, 2012

27

Complexation of Mn 2+ , Fe 2+ , Y 3+ , La 3+ , Pb 2+ , and UO 22+ with Organic Ligands: QSPR Ensemble Modeling of Stability Constants

Solov’ev, Vitaly, Marcou, Gilles, Tsivadze, Aslan, Varnek, Alexandre

Journal:

Industrial & Engineering Chemistry Research

Year:

2012

Language:

english

File:

PDF, 461 KB

english, 2012

28

Supramolecular Chemistry: Computer-Assisted Instruction in Undergraduate and Graduate Chemistry Courses

Varnek, Alexandre A., Dietrich, Bernard, Wipff, Georges, Lehn, Jean-Marie, Boldyreva, Elena V.

Journal:

Journal of Chemical Education

Year:

2000

Language:

english

File:

PDF, 251 KB

english, 2000

29

Quantitative Structure–Property Relationship (QSPR) Modeling of Normal Boiling Point Temperature and Composition of Binary Azeotropes

Solov’ev, Vitaly P., Oprisiu, Ioana, Marcou, Gilles, Varnek, Alexandre

Journal:

Industrial & Engineering Chemistry Research

Year:

2011

Language:

english

File:

PDF, 853 KB

english, 2011

30

Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?

Varnek, Alexandre, Kireeva, Natalia, Tetko, Igor V., Baskin, Igor I., Solov'ev, Vitaly P.

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 330 KB

english, 2007

31

Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms

Muller, Christophe, Marcou, Gilles, Horvath, Dragos, Aires-de-Sousa, João, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 814 KB

english, 2012

32

Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection

Tetko, Igor V., Sushko, Iurii, Pandey, Anil Kumar, Zhu, Hao, Tropsha, Alexander, Papa, Ester, Öberg, Tomas, Todeschini, Roberto, Fourches, Denis, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 304 KB

english, 2008

33

Using self-organizing maps to accelerate similarity search

Fanny Bonachera, Gilles Marcou, Natalia Kireeva, Alexandre Varnek, Dragos Horvath

Journal:

Bioorganic & Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

34

Transductive Support Vector Machines: Promising Approach to Model Small and Unbalanced Datasets

Kondratovich, Evgeny, Baskin, Igor I., Varnek, Alexandre

Journal:

Molecular Informatics

Year:

2013

Language:

english

File:

PDF, 864 KB

english, 2013

35

Publicly available models to predict normal boiling point of organic compounds

Oprisiu, Ioana, Marcou, Gilles, Horvath, Dragos, Brunel, Damien Bernard, Rivollet, Fabien, Varnek, Alexandre

Journal:

Thermochimica Acta

Year:

2013

Language:

english

File:

PDF, 983 KB

english, 2013

36

Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints

Chupakhin, Vladimir, Marcou, Gilles, Baskin, Igor, Varnek, Alexandre, Rognan, Didier

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 653 KB

english, 2013

37

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

Zhu, Hao, Tropsha, Alexander, Fourches, Denis, Varnek, Alexandre, Papa, Ester, Gramatica, Paola, Öberg, Tomas, Dao, Phuong, Cherkasov, Artem, Tetko, Igor V.

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 529 KB

english, 2008

38

Electronic, Spectroscopic, and Ion-Sensing Properties of a Dehydro[ m ]pyrido[14]- and [15]annulene Isomer Library

Baxter, Paul N. W., Al Ouahabi, Abdelaziz, Gisselbrecht, Jean-Paul, Brelot, Lydia, Varnek, Alexandre

Journal:

Journal of Organic Chemistry

Year:

2012

Language:

english

File:

PDF, 4.83 MB

english, 2012

39

Do Not Hesitate to Use Tversky—and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors

Horvath, Dragos, Marcou, Gilles, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.49 MB

english, 2013

40

Synthesis of a Strained Acetylenic Macrocycle Incorporating a para -Oligo[2]cruciform Bridge Bent over Nanoscopic Dimensions: Structural, Electronic, Spectroscopic, and Ion-Sensing Properties

Baxter, Paul N. W., Gisselbrecht, Jean-Paul, Karmazin-Brelot, Lydia, Varnek, Alexandre, Allouche, Lionel

Journal:

Chemistry - A European Journal

Year:

2013

Language:

english

File:

PDF, 2.08 MB

english, 2013

41

Complexation of phosphoryl-containing mono-, bi- and tri-podands with alkali cations in acetonitrile. Structure of the complexes and binding selectivity

Solov’ev, Vitaly P., Baulin, Vladimir E., Strakhova, Nadezhda N., Kazachenko, Vladimir P., Belsky, Vitaly K., Varnek, Alexandre A., Volkova, Tatiana A., Wipff, Georges

Journal:

Journal of the Chemical Society Perkin Transactions 2

Year:

1998

Language:

english

File:

PDF, 244 KB

english, 1998

42

Generative Topographic Mapping-Based Classification Models and Their Applicability Domain: Application to the Biopharmaceutics Drug Disposition Classification System (BDDCS)

Gaspar, Héléna A., Marcou, Gilles, Horvath, Dragos, Arault, Alban, Lozano, Sylvain, Vayer, Philippe, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 967 KB

english, 2013

43

Computational chemogenomics: Is it more than inductive transfer?

Brown, J. B., Okuno, Yasushi, Marcou, Gilles, Varnek, Alexandre, Horvath, Dragos

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 1.52 MB

english, 2014

44

Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models

Dragos, Horvath, Gilles, Marcou, Alexandre, Varnek

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 3.58 MB

english, 2009

45

QSPR ensemble modelling of the 1:1 and 1:2 complexation of Co2+, Ni2+, and Cu2+with organic ligands: relationships between stability constants

Solov’ev, Vitaly, Varnek, Alexandre, Tsivadze, Aslan

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 3.00 MB

english, 2014

46

Skin Permeation Rate as a Function of Chemical Structure

Katritzky, Alan R., Dobchev, Dimitar A., Fara, Dan C., Hür, Evrim, Tämm, Kaido, Kurunczi, Ludovic, Karelson, Mati, Varnek, Alexandre, Solov'ev, Vitaly P.

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 136 KB

english, 2006

47

Quantitative Structure–Property Relationship Modeling: A Valuable Support in High-Throughput Screening Quality Control

Ruggiu, Fiorella, Gizzi, Patrick, Galzi, Jean-Luc, Hibert, Marcel, Haiech, Jacques, Baskin, Igor, Horvath, Dragos, Marcou, Gilles, Varnek, Alexandre

Journal:

Analytical Chemistry

Year:

2014

Language:

english

File:

PDF, 2.87 MB

english, 2014

48

Simple Ligand–Receptor Interaction Descriptor (SILIRID) for alignment-free binding site comparison

Chupakhin, Vladimir, Marcou, Gilles, Gaspar, Helena, Varnek, Alexandre

Journal:

Computational and Structural Biotechnology Journal

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

49

Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients

Varnek, Alexandre, Gaudin, Cédric, Marcou, Gilles, Baskin, Igor, Pandey, Anil Kumar, Tetko, Igor V.

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 2.57 MB

english, 2009

50

Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure−Property Relationship Studies of Metal Complexation with Ionophores

Tetko, Igor V., Solov'ev, Vitaly P., Antonov, Alexey V., Yao, Xiaojun, Doucet, Jean Pierre, Fan, Botao, Hoonakker, Frank, Fourches, Denis, Jost, Piere, Lachiche, Nicolas, Varnek, Alexandre

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 274 KB

english, 2006

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