Artificial intelligence and cheminformatics tools: a contribution to the drug development and chemical science

I Saifi, BA Bhat, SS Hamdani, UY Bhat… - Journal of …, 2024 - Taylor & Francis
In the ever-evolving field of drug discovery, the integration of Artificial Intelligence (AI) and
Machine Learning (ML) with cheminformatics has proven to be a powerful combination …

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

R Nugmanov, N Dyubankova, A Gedich… - Journal of Chemical …, 2022 - ACS Publications
This work introduces GraphormerMapper, a new algorithm for reaction atom-to-atom
mapping (AAM) based on a transformer neural network adopted for the direct processing of …

Autonomous reaction network exploration in homogeneous and heterogeneous catalysis

M Steiner, M Reiher - Topics in Catalysis, 2022 - Springer
Autonomous computations that rely on automated reaction network elucidation algorithms
may pave the way to make computational catalysis on a par with experimental research in …

China Sponge City database development and urban runoff source control facility configuration comparison between China and the US

C Xu, X Shi, M Jia, Y Han, R Zhang, S Ahmad… - Journal of Environmental …, 2022 - Elsevier
Urban runoff source control facilities (URSCFs) are important parts of Sponge City (SC) by
controlling urban flooding, restoring eco-balance, and enhancing city resilience. To evaluate …

LinChemIn: SynGraph—a data model and a toolkit to analyze and compare synthetic routes

M Pasquini, M Stenta - Journal of Cheminformatics, 2023 - Springer
Background The increasing amount of chemical reaction data makes traditional ways to
navigate its corpus less effective, while the demand for novel approaches and instruments is …

Chemistry in a graph: modern insights into commercial organic synthesis planning

C Avila, A West, AC Vicini, W Waddington… - Digital …, 2024 - pubs.rsc.org
Across the chemical sciences, synthesis planning is a key aspect for defining synthesis
routes, starting from idea generation, combining literature searches and laboratory …

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

T Gimadiev, R Nugmanov, A Khakimova… - Journal of Chemical …, 2021 - ACS Publications
This work introduces CGRdb2. 0─ an open-source database management system for
molecules, reactions, and chemical data. CGRdb2. 0 is a Python package connecting to a …

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

R Nugmanov - Journal of Chemical Information and Modeling, 2024 - ACS Publications
In this work, we propose a versatile molecule and reaction encoding binary data format that
aims to bridge the gap between the advantages of SMILES, like local stereo-and implicit …

Python tools for structural tasks in chemistry

FV Ryzhkov, YE Ryzhkova, MN Elinson - Molecular Diversity, 2024 - Springer
In recent decades, the use of computational approaches and artificial intelligence in the
scientific environment has become more widespread. In this regard, the popular and …

Vector Embeddings by Sequence Similarity and Context for Improved Compression, Similarity Search, Clustering, Organization, and Manipulation of cDNA Libraries

DH Um, DA Knowles, GE Kaiser - arXiv preprint arXiv:2308.05118, 2023 - arxiv.org
This paper demonstrates the utility of organized numerical representations of genes in
research involving flat string gene formats (ie, FASTA/FASTQ5). FASTA/FASTQ files have …