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 …
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 …
mapping (AAM) based on a transformer neural network adopted for the direct processing of …
Autonomous reaction network exploration in homogeneous and heterogeneous catalysis
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 …
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
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 …
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 …
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 …
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 …
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 …
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 …
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 …
research involving flat string gene formats (ie, FASTA/FASTQ5). FASTA/FASTQ files have …