List of works - Vladimir Palyulin

3D-model of the ion channel of NMDA receptor: qualitative and quantitative modeling of the blocker binding.

scientific article published in May 2004

A molecular model and Monte Carlo simulation of flavivirus envelope building block.

scientific article published on 23 July 2012

A new scheme for electronegativity equalization as a source of electronic descriptors: application to chemical reactivity

scientific article published on 01 March 2002

A spatial model of the glycine site of the NR1 subunit of NMDA-receptor and ligand docking.

scientific article

An approach to the interpretation of backpropagation neural network models in QSAR studies

scientific article published in March 2002

Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features

scientific article published in 2022

Bioinformatic analysis of glycogen synthase kinase 3: human versus parasite kinases.

scientific article

Bivalent AMPA receptor positive allosteric modulators of the bis(pyrimidine) series

scientific article published on 12 July 2019

CoMFA and homology-based models of the glycine binding site of N-methyl-d-aspartate receptor

scientific article published in April 2003

Complex formation of albumin with tricarbocyanine dyes containing phosphonate groups

scientific article published in November 2016

Computer aided comparative analysis of the binding modes of the adenosine receptor agonists for all known subtypes of adenosine receptors

scientific article published on 27 June 2006

Computer-aided design of negative allosteric modulators of NMDA receptor ⬇️

scientific article published on January 1, 2013

Computer-aided modeling of activity and selectivity of quinazolinones as noncompetitive NMDA receptor antagonists

scientific article published on 01 March 2012

Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach.

scientific article

Design of topological indices: computer-oriented approach.

scientific article published on January 2009

Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies

scientific article published on 11 July 2020

Fast tools for calculation of atomic charges well suited for drug design

scientific article published on 01 January 2008

Fragmental approach in QSPR

scientific article published on 01 September 2002

General Purpose Electronegativity Relaxation Charge Models Applied to CoMFA and CoMSIA Study of GSK-3 Inhibitors.

scientific article

Generation of molecular graphs for QSAR studies: an approach based on supergraphs

scientific article published on 24 October 2007

Inhibitors of tick-borne flavivirus reproduction from structure-based virtual screening

scientific article

Inhibitory antibodies to human angiotensin-converting enzyme: fine epitope mapping and mechanism of action

scientific article published in April 2006

Interaction of Flaviviruses with Reproduction Inhibitors Binding in β-OG Pocket: Insights from Molecular Dynamics Simulations

scientific article published on 26 September 2014

Iterative Solvers for Empirical Partial Atomic Charges: Breaking the Curse of Cubic Numerical Complexity

scientific article published on 03 April 2019

Kirchhoff atomic charges fitted to multipole moments: implementation for a virtual screening system.

scientific article published in June 2008

MM-GBSA and MM-PBSA performance in activity evaluation of AMPA receptor positive allosteric modulators.

scientific article published on 27 July 2017

Modeling and analysis of ligand-receptor interactions in the GABAc receptor

scientific article published on 01 January 2007

Modeling of the relationships between the structure of O-phosphorylated oximes and their anticholinesterase activity and selectivity using molecular field topology analysis (MFTA)

scientific article published on 01 January 2008

Molecular Field Topology Analysis Method in QSAR Studies of Organic Compounds

article

Molecular design of O-phosphorylated oximes—Selective inhibitors of butyrylcholinesterase

scientific article published on 01 March 2012

Molecular design of selective ligands of chemokine receptors

scientific article published on 05 May 2015

Molecular dynamic simulation of the ligand-receptor complexes of the aminoterminal domain of the metabotropic glutamate receptor mGluR1

scientific article published on 01 March 2003

Molecular model of the Wnt protein binding site on the surface of dimeric CRD domain of the hFzd8 receptor.

scientific article

Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists

scientific article

Molecular modeling of modified peptides, potent inhibitors of the xWNT8 and hWNT8 proteins

scientific article published on 9 November 2007

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.

scientific article published in September 2002

Molecular modeling of the complex between the XWNT8 protein and the CRD domain of the MFZD8 receptor

scientific article published on 01 January 2007

Molecular modeling of the ligand-binding domains of the NR3A and NR3B subunits of the NMDA receptor.

scientific article

Molecular modeling of the mGluR1 metabotropic glutamate receptor transmembrane domain and construction of the model of its dimer.

scientific article published in November 2003

Molecular modeling of the transmembrane domain of mGluR2 metabotropic glutamate receptor and the binding site of its positive allosteric modulators

scientific article published on 01 January 2014

Molecular modeling the human A1 adenosine receptor and study of the mechanisms of its selective ligand binding.

scientific article published in September 2002

Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

Multipole models of sulphur for accurate anisotropic electrostatic interactions within force fields

scientific article published on 19 December 2017

New Hybrids of 4-Amino-2,3-polymethylene-quinoline and p-Tolylsulfonamide as Dual Inhibitors of Acetyl- and Butyrylcholinesterase and Potential Multifunctional Agents for Alzheimer's Disease Treatment

scientific article published on 27 August 2020

New Multifunctional Agents Based on Conjugates of 4-Amino-2,3-polymethylenequinoline and Butylated Hydroxytoluene for Alzheimer's Disease Treatment

scientific article published on 12 December 2020

New developments in hydrogen bonding acidity and basicity of small organic molecules for the prediction of physical and ADMET properties. Part 2. The universal solvation equation

scientific article published in March 2009

Novel Positive Allosteric Modulators of AMPA Receptors Based on 3,7-Diazabicyclo[3.3.1]nonane Scaffold

scientific article published on 12 September 2019

Novel bivalent positive allosteric modulators of AMPA receptor.

scientific article published in September 2015

On mechanism of allosteric modulation of NMDA receptor via amino-terminal domains

scientific article published on 10 July 2012

One-class classification as a novel method of ligand-based virtual screening: the case of glycogen synthase kinase 3β inhibitors

scientific article published on 21 September 2011

Organophosphorus compound esterase profiles as predictors of therapeutic and toxic effects ⬇️

scientific article published on November 2, 2012

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

scientific article published on 18 June 2015

Progress in visual representations of chemical space.

scientific article published on 22 June 2015

Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding

scientific article published on 07 January 2019

Role of two chloride-binding sites in functioning of testicular angiotensin-converting enzyme.

scientific article published in October 2005

Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors

scientific article published in September 2003

Signatures of the ATP-binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram-positive bacteria

scientific article published on 13 February 2012

Structural basis for understanding structure-activity relationships for the glutamate binding site of the NMDA receptor

scientific article published in August 2002

Structure-based virtual screening of glycogen synthase kinase 3β inhibitors: analysis of scoring functions applied to large true actives and decoy sets.

scientific article

Study of the structural determinants of acute and delayed neurotoxicity of O-phosphorylated oximes by molecular field topology analysis (MFTA)

scientific article published on 01 November 2009

Synthesis and assessment of 4-aminotetrahydroquinazoline derivatives as tick-borne encephalitis virus reproduction inhibitors.

scientific article published on March 2015

The "hockey sticks" effect revisited: the conformational and electronic properties of 3,7-dithia-1,5-diazabicyclo[3.3.1]nonane from the QTAIM perspective

scientific article published on 01 September 2011

The binding site for allosteric modulators of AMPA receptor.

scientific article published in November 2004

The choice of atomic charges calculation scheme in 3D-QSAR modelling of GSK-3β inhibition by paullones.

scientific article

The learned symmetry concept in revealing quantitative structure-activity relationships with artificial neural networks.

scientific article published in January 2001

Theoretical scales of hydrogen bond acidity and basicity for application in QSAR/QSPR studies and drug design. Partitioning of aliphatic compounds

scientific article

Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors

scientific article published on 19 July 2019

Towards Deep Neural Network Models for the Prediction of the Blood-Brain Barrier Permeability for Diverse Organic Compounds

scientific article published on 13 December 2020

List of works by Vladimir Palyulin

3D-model of the ion channel of NMDA receptor: qualitative and quantitative modeling of the blocker binding.

A molecular model and Monte Carlo simulation of flavivirus envelope building block.

A new scheme for electronegativity equalization as a source of electronic descriptors: application to chemical reactivity

A spatial model of the glycine site of the NR1 subunit of NMDA-receptor and ligand docking.

An approach to the interpretation of backpropagation neural network models in QSAR studies

Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features

Bioinformatic analysis of glycogen synthase kinase 3: human versus parasite kinases.

Bivalent AMPA receptor positive allosteric modulators of the bis(pyrimidine) series

CoMFA and homology-based models of the glycine binding site of N-methyl-d-aspartate receptor

Complex formation of albumin with tricarbocyanine dyes containing phosphonate groups

Computer aided comparative analysis of the binding modes of the adenosine receptor agonists for all known subtypes of adenosine receptors

Computer-aided design of negative allosteric modulators of NMDA receptor ⬇️

Computer-aided modeling of activity and selectivity of quinazolinones as noncompetitive NMDA receptor antagonists

Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach.

Design of topological indices: computer-oriented approach.

Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies

Fast tools for calculation of atomic charges well suited for drug design

Fragmental approach in QSPR

General Purpose Electronegativity Relaxation Charge Models Applied to CoMFA and CoMSIA Study of GSK-3 Inhibitors.

Generation of molecular graphs for QSAR studies: an approach based on supergraphs

Inhibitors of tick-borne flavivirus reproduction from structure-based virtual screening

Inhibitory antibodies to human angiotensin-converting enzyme: fine epitope mapping and mechanism of action

Interaction of Flaviviruses with Reproduction Inhibitors Binding in β-OG Pocket: Insights from Molecular Dynamics Simulations

Iterative Solvers for Empirical Partial Atomic Charges: Breaking the Curse of Cubic Numerical Complexity

Kirchhoff atomic charges fitted to multipole moments: implementation for a virtual screening system.

MM-GBSA and MM-PBSA performance in activity evaluation of AMPA receptor positive allosteric modulators.

Modeling and analysis of ligand-receptor interactions in the GABAc receptor

Modeling of the relationships between the structure of O-phosphorylated oximes and their anticholinesterase activity and selectivity using molecular field topology analysis (MFTA)

Molecular Field Topology Analysis Method in QSAR Studies of Organic Compounds

Molecular design of O-phosphorylated oximes—Selective inhibitors of butyrylcholinesterase

Molecular design of selective ligands of chemokine receptors

Molecular dynamic simulation of the ligand-receptor complexes of the aminoterminal domain of the metabotropic glutamate receptor mGluR1

Molecular model of the Wnt protein binding site on the surface of dimeric CRD domain of the hFzd8 receptor.

Molecular modeling and molecular dynamics simulation of the human A2B adenosine receptor. The study of the possible binding modes of the A2B receptor antagonists

Molecular modeling of modified peptides, potent inhibitors of the xWNT8 and hWNT8 proteins

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.

Molecular modeling of the complex between the XWNT8 protein and the CRD domain of the MFZD8 receptor

Molecular modeling of the ligand-binding domains of the NR3A and NR3B subunits of the NMDA receptor.

Molecular modeling of the mGluR1 metabotropic glutamate receptor transmembrane domain and construction of the model of its dimer.

Molecular modeling of the transmembrane domain of mGluR2 metabotropic glutamate receptor and the binding site of its positive allosteric modulators

Molecular modeling the human A1 adenosine receptor and study of the mechanisms of its selective ligand binding.

Molecular simulation of receptors of physiologically active compounds for purposes of medical chemistry

Multipole models of sulphur for accurate anisotropic electrostatic interactions within force fields

New Hybrids of 4-Amino-2,3-polymethylene-quinoline and p-Tolylsulfonamide as Dual Inhibitors of Acetyl- and Butyrylcholinesterase and Potential Multifunctional Agents for Alzheimer's Disease Treatment

New Multifunctional Agents Based on Conjugates of 4-Amino-2,3-polymethylenequinoline and Butylated Hydroxytoluene for Alzheimer's Disease Treatment

New developments in hydrogen bonding acidity and basicity of small organic molecules for the prediction of physical and ADMET properties. Part 2. The universal solvation equation

Novel Positive Allosteric Modulators of AMPA Receptors Based on 3,7-Diazabicyclo[3.3.1]nonane Scaffold

Novel bivalent positive allosteric modulators of AMPA receptor.

On mechanism of allosteric modulation of NMDA receptor via amino-terminal domains

One-class classification as a novel method of ligand-based virtual screening: the case of glycogen synthase kinase 3β inhibitors

Organophosphorus compound esterase profiles as predictors of therapeutic and toxic effects ⬇️

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

Progress in visual representations of chemical space.

Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding

Role of two chloride-binding sites in functioning of testicular angiotensin-converting enzyme.

Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors

Signatures of the ATP-binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram-positive bacteria

Structural basis for understanding structure-activity relationships for the glutamate binding site of the NMDA receptor

Structure-based virtual screening of glycogen synthase kinase 3β inhibitors: analysis of scoring functions applied to large true actives and decoy sets.

Study of the structural determinants of acute and delayed neurotoxicity of O-phosphorylated oximes by molecular field topology analysis (MFTA)

Synthesis and assessment of 4-aminotetrahydroquinazoline derivatives as tick-borne encephalitis virus reproduction inhibitors.

The "hockey sticks" effect revisited: the conformational and electronic properties of 3,7-dithia-1,5-diazabicyclo[3.3.1]nonane from the QTAIM perspective

The binding site for allosteric modulators of AMPA receptor.

The choice of atomic charges calculation scheme in 3D-QSAR modelling of GSK-3β inhibition by paullones.

The learned symmetry concept in revealing quantitative structure-activity relationships with artificial neural networks.

Theoretical scales of hydrogen bond acidity and basicity for application in QSAR/QSPR studies and drug design. Partitioning of aliphatic compounds

Time-Domain Analysis of Molecular Dynamics Trajectories Using Deep Neural Networks: Application to Activity Ranking of Tankyrase Inhibitors

Towards Deep Neural Network Models for the Prediction of the Blood-Brain Barrier Permeability for Diverse Organic Compounds