Multifaceted computational modeling in glycoscience

S Perez, O Makshakova - Chemical Reviews, 2022 - ACS Publications
Glycoscience assembles all the scientific disciplines involved in studying various molecules
and macromolecules containing carbohydrates and complex glycans. Such an ensemble …

Three-dimensional structures of carbohydrates and where to find them

SI Scherbinina, PV Toukach - International journal of molecular sciences, 2020 - mdpi.com
Analysis and systematization of accumulated data on carbohydrate structural diversity is a
subject of great interest for structural glycobiology. Despite being a challenging task …

DIONYSUS: a database of protein–carbohydrate interfaces

A Gheeraert, T Bailly, Y Ren, A Hamraoui… - Nucleic Acids …, 2024 - academic.oup.com
Protein-carbohydrate interactions govern a wide variety of biological processes and play an
essential role in the development of different diseases. Here, we present DIONYSUS, the …

LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification

F Bonnardel, J Mariethoz, S Pérez… - Nucleic Acids …, 2021 - academic.oup.com
Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their
annotation in newly sequenced organisms is lacking. The limited size of functional domains …

AI-Driven Enhancements in Drug Screening and Optimization

A Serghini, S Portelli, DB Ascher - Computational Drug Discovery and …, 2023 - Springer
The greatest challenge in drug discovery remains the high rate of attrition across the
different phases of the process, which cost the industry billions of dollars every year. While …

Exploring the impact of carbohydrate chain length on binding affinity with lectin-a protein from common edible mushroom (Agaricus bisporus)

M He, L Condict, SJ Richardson, CS Brennan… - Food …, 2025 - Elsevier
The present work investigates the impact of dietary-carbohydrate chain length on the
binding affinity with Agaricus bisporus lectin (ABL) using sugars of varying chain length …

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite

X He, L Zhao, Y Tian, R Li, Q Chu, Z Gu… - Nature …, 2024 - nature.com
As the most abundant organic substances in nature, carbohydrates are essential for life.
Understanding how carbohydrates regulate proteins in the physiological and pathological …

Modernized uniform representation of carbohydrate molecules in the Protein Data Bank

C Shao, Z Feng, JD Westbrook, E Peisach… - …, 2021 - academic.oup.com
Abstract Since 1971, the Protein Data Bank (PDB) has served as the single global archive
for experimentally determined 3D structures of biological macromolecules made freely …

Development and Evaluation of GlycanDock: a protein–glycoligand docking refinement algorithm in Rosetta

ML Nance, JW Labonte, J Adolf-Bryfogle… - The Journal of Physical …, 2021 - ACS Publications
Carbohydrate chains are ubiquitous in the complex molecular processes of life. These
highly diverse chains are recognized by a variety of protein receptors, enabling glycans to …

Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems

S Kassem, SA McPhee, N Berisha… - Journal of the American …, 2023 - ACS Publications
Minimalistic peptide-based systems that bind sugars in water are challenging to design due
to the weakness of interactions and required cooperative contributions from specific amino …