Molecular representations in AI-driven drug discovery: a review and practical guide

L David, A Thakkar, R Mercado, O Engkvist - Journal of Cheminformatics, 2020 - Springer
The technological advances of the past century, marked by the computer revolution and the
advent of high-throughput screening technologies in drug discovery, opened the path to the …

Glycoinformatics in the artificial intelligence era

D Bojar, F Lisacek - Chemical Reviews, 2022 - ACS Publications
Artificial intelligence (AI) methods have been and are now being increasingly integrated in
prediction software implemented in bioinformatics and its glycoscience branch known as …

Deep-learning resources for studying glycan-mediated host-microbe interactions

D Bojar, RK Powers, DM Camacho, JJ Collins - Cell Host & Microbe, 2021 - cell.com
Glycans, the most diverse biopolymer, are shaped by evolutionary pressures stemming from
host-microbe interactions. Here, we present machine learning and bioinformatics methods to …

GlycoDraw: a python implementation for generating high-quality glycan figures

J Lundstrøm, J Urban, L Thomès, D Bojar - Glycobiology, 2023 - academic.oup.com
Glycans are essential to all scales of biology, with their intricate structures being crucial for
their biological functions. The structural complexity of glycans is communicated through …

Towards a standardized bioinformatics infrastructure for N- and O-glycomics

MA Rojas-Macias, J Mariethoz, P Andersson… - Nature …, 2019 - nature.com
The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released
from proteins, lipids and proteoglycans increasingly relies on databases and software. Here …

GlyTouCan 1.0–The international glycan structure repository

K Aoki-Kinoshita, S Agravat, NP Aoki… - Nucleic acids …, 2016 - academic.oup.com
Glycans are known as the third major class of biopolymers, next to DNA and proteins. They
cover the surfaces of many cells, serving as the 'face'of cells, whereby other biomolecules …

[HTML][HTML] Molecular similarity: Theory, applications, and perspectives

K López-Pérez, JF Avellaneda-Tamayo, L Chen… - Artificial Intelligence …, 2024 - Elsevier
Molecular similarity pervades much of our understanding and rationalization of chemistry.
This has become particularly evident in the current data-intensive era of chemical research …

Glycowork: A Python package for glycan data science and machine learning

L Thomès, R Burkholz, D Bojar - Glycobiology, 2021 - academic.oup.com
While glycans are crucial for biological processes, existing analysis modalities make it
difficult for researchers with limited computational background to include these diverse …

Property graph vs RDF triple store: A comparison on glycan substructure search

D Alocci, J Mariethoz, O Horlacher, JT Bolleman… - PloS one, 2015 - journals.plos.org
Resource description framework (RDF) and Property Graph databases are emerging
technologies that are used for storing graph-structured data. We compare these …

Glycoscience data content in the NCBI Glycans and PubChem

S Kim, J Zhang, T Cheng, Q Li, EE Bolton - Analytical and Bioanalytical …, 2024 - Springer
Studying glycans and their functions in the body aids in the understanding of disease
mechanisms and developing new treatments. This necessitates resources that provide …