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Ramil Nugmanov

Principal Scientist at Johnson & Johnson

Publications

ReacLLaMA: Merging chemical and textual information in chemical reactivity AI models

arXiv preprint arXiv:2401.17267, 2024

PaCh (Packed Chemicals): Computationally Effective Binary Format for Chemical Structure Encoding

Journal of Chemical Information and Modeling, 2024

Analysis of Atom-level pretraining with QM data for Graph Neural Networks Molecular property models

arXiv preprint arXiv:2405.14837, 2024

Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modeling

arXiv preprint arXiv:2410.08024, 2024

Global reactivity models are impactful in industrial synthesis applications

Journal of cheminformatics, 2023

Stereoelectronic Effect in the Reaction of $\alpha$-Methylene Lactones with Tertiary Phosphines and Its Application in Organocatalysis

The Journal of Organic Chemistry, 2023

Atom-to-atom mapping: a benchmarking study of popular mapping algorithms and consensus strategies

Molecular Informatics, 2022

Bidirectional graphormer for reactivity understanding: neural network trained to reaction atom-to-atom mapping task

Journal of Chemical Information and Modeling, 2022

Hydrazine-mediated CO bond reductive cleavage in some bis-and mono-O-substituted derivatives of 4-tert-butylcalix [4] arene

Russian Chemical Bulletin, 2022

Oxyethylated Fluoresceine—(thia) calix [4] arene Conjugates: Synthesis and Visible-Light Photoredox Catalysis in Water--Organic Media

Molecules, 2022

Discovery of novel chemical reactions by deep generative recurrent neural network

Scientific reports, 2021

Combined graph/relational database management system for calculated chemical reaction pathway data

Journal of Chemical Information and Modeling, 2021

QSAR modeling based on conformation ensembles using a multi-instance learning approach

Journal of chemical information and modeling, 2021

Cross-validation strategies in QSPR modelling of chemical reactions

SAR and QSAR in Environmental Research, 2021

Switching ion binding selectivity of thiacalix [4] arene monocrowns at liquid--liquid and 2D-confined interfaces

International Journal of Molecular Sciences, 2021

Functional supramolecular systems: Design and applications

Russian Chemical Reviews, 2021

Reaction data curation I: chemical structures and transformations standardization

Molecular Informatics, 2021

Azocalix [4] arene-rhodamine supramolecular hypoxia-sensitive systems: a search for the best calixarene hosts and rhodamine guests

Molecules, 2021

CGRdb2. 0: a python database management system for molecules, reactions, and chemical data

Journal of Chemical Information and Modeling, 2021

Machine learning modelling of chemical reaction characteristics: yesterday, today, tomorrow

Mendeleev Communications, 2021

Prediction of optimal conditions of hydrogenation reaction using the likelihood ranking approach

International Journal of Molecular Sciences, 2021

Alkyl-malonate-substituted thiacalix [4] arenes as ligands for bottom-up design of paramagnetic Gd (III)-containing colloids with low cytotoxicity

Arabian Journal of Chemistry, 2020

Comprehensive analysis of applicability domains of QSPR models for chemical reactions

International Journal of Molecular Sciences, 2020

Predictive models for kinetic parameters of cycloaddition reactions

Molecular Informatics, 2019

Bimolecular nucleophilic substitution reactions: Predictive models for rate constants and molecular reaction pairs analysis

Molecular informatics, 2019

CGRtools: Python library for molecule, reaction, and condensed graph of reaction processing

Journal of chemical information and modeling, 2019

Sydnone-alkyne cycloaddition: Which factors are responsible for reaction rate?

Journal of Molecular Structure, 2019

Conjugated quantitative structure--property relationship models: application to simultaneous prediction of tautomeric equilibrium constants and acidity of molecules

Journal of Chemical Information and Modeling, 2019

Prediction of aromatic hydroxylation sites for human cyp1a2 substrates using condensed graph of reactions

BioNanoScience, 2018

Assessment of tautomer distribution using the condensed reaction graph approach

Journal of Computer-Aided Molecular Design, 2018

Visualization and analysis of complex reaction data: The case of tautomeric equilibria

Molecular Informatics, 2018

Synthesis of new p-tert-butylcalix [4] arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

Beilstein journal of organic chemistry, 2018

An Approach for Automated Detection of Missing Reagents and Products in Chemical Reaction Equations

UCHENYE ZAPISKI KAZANSKOGO UNIVERSITETA-SERIYA ESTESTVENNYE NAUKI, 2018

A New Approach to Atom-to-Atom Mapping Using the Naive Bayesian Classifier

UCHENYE ZAPISKI KAZANSKOGO UNIVERSITETA-SERIYA ESTESTVENNYE NAUKI, 2018

Automatic detection of missed reagents and products in chemical reaction equations

Uchenye Zapiski Kazanskogo Universiteta, 2018

An approach for creating atom-to-atomic mapping using a naive Bayesian classifier

Uchenye Zapiski Kazanskogo Universiteta, 2018

Detection of sulfate surface-active substances via fluorescent response using new amphiphilic thiacalix [4] arenes bearing cationic headgroups with Eosin Y dye

Colloids and Surfaces A: Physicochemical and Engineering Aspects, 2017

Handling of Markush Structures

Tutorials in Chemoinformatics, 2017

Structure--reactivity modeling using mixture-based representation of chemical reactions

Journal of computer-aided molecular design, 2017

Unusual reactivity of aliphatic and aromatic amines with bromoalkyl derivatives of thiacalix [4] arene in 1, 3-alternate stereoisomeric form

methods, 2017

Structure--reactivity relationship in Diels--Alder reactions obtained using the condensed reaction graph approach

Journal of Structural Chemistry, 2017

Using semantic analysis of texts for the identification of drugs with similar therapeutic effects

Russian Chemical Bulletin, 2017

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

Journal of Chemical Information and Modeling, 2016

‘Click chemistry’in the synthesis of new amphiphilic 1, 3-alternate thiacalixarenes

Mendeleev Communications, 2015

Synthesis and structure of lower rim-substituted alkynyl derivatives of thiacalix [4] arene

Russian Journal of Organic Chemistry, 2015

Structure--reactivity relationship in bimolecular elimination reactions based on the condensed graph of a reaction

Journal of Structural Chemistry, 2015

Effect of copper (I) on the conformation of the thiacalixarene platform in azide-alkyne cycloaddition

Russian Chemical Bulletin, 2015

Consensus approach to atom-to-atom mapping in chemical reactions

Butlerov Commun, 2015

Structure-reactivity relationships in terms of the condensed graphs of reactions

Russian Journal of Organic Chemistry, 2014

Development of “structure-property” models in nucleophilic substitution reactions involving azides

Journal of Structural Chemistry, 2014

Bifunctional derivatives of (Thia) calix [4] arenes with terminal double and triple bonds: Synthesis and azide-alkyne click reactions

Макрогетероциклы, 2014

Microwave-assisted alkylation of p-tert-butylcalix [4] arene lower rim: The effect of alkyl halides

Mendeleev Communications, 2013