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 …

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins

M Ertelt, VK Mulligan, JB Maguire… - PLOS Computational …, 2024‏ - journals.plos.org
Post-translational modifications (PTMs) of proteins play a vital role in their function and
stability. These modifications influence protein folding, signaling, protein-protein …

Computational toolbox for the analysis of protein–glycan interactions

F Nieto-Fabregat, MP Lenza… - Beilstein Journal of …, 2024‏ - beilstein-journals.org
Protein–glycan interactions play pivotal roles in numerous biological processes, ranging
from cellular recognition to immune response modulation. Understanding the intricate …

Structure-based neural network protein–carbohydrate interaction predictions at the residue level

SW Canner, S Shanker, JJ Gray - Frontiers in Bioinformatics, 2023‏ - frontiersin.org
Carbohydrates dynamically and transiently interact with proteins for cell–cell recognition,
cellular differentiation, immune response, and many other cellular processes. Despite the …

Adeno‐associated virus serotype 2 capsid variants for improved liver‐directed gene therapy

N Meumann, M Cabanes‐Creus, M Ertelt… - Hepatology, 2023‏ - journals.lww.com
Conclusions: In conclusion, MLIV. K and MLIV. A are AAV peptide display variants selected
in immunocompetent mice with improved hepatocyte tropism and transduction efficiency …

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design

J Adolf-Bryfogle, JW Labonte, JC Kraft… - PLoS computational …, 2024‏ - journals.plos.org
Carbohydrates and glycoproteins modulate key biological functions. However, experimental
structure determination of sugar polymers is notoriously difficult. Computational approaches …

Iterative Knowledge-Based Scoring Function for Protein–Ligand Interactions by Considering Binding Affinity Information

X Zhao, H Li, K Zhang, SY Huang - The Journal of Physical …, 2023‏ - ACS Publications
Scoring functions for protein–ligand interactions play a critical role in structure-based drug
design. Owing to the good balance between general applicability and computational …

Modeling Protein–Glycan Interactions with HADDOCK

A Ranaudo, M Giulini, A Pelissou Ayuso… - Journal of Chemical …, 2024‏ - ACS Publications
The term glycan refers to a broad category of molecules composed of monosaccharide units
linked to each other in a variety of ways, whose structural diversity is related to different …

In vitro and in silico study of new biscoumarin glycosides from Paramignya trimera against Angiotensin-converting enzyme 2 (ACE-2) for preventing SARS-CoV-2 …

NX Ha, TT Huong, PN Khanh, NP Hung… - Chemical and …, 2024‏ - jstage.jst.go.jp
In Vietnam, the stems and roots of the Rutaceous plant Paramignya trimera (Oliv.) Burkill
(known locally as “Xáo tam phân”) are widely used to treat liver diseases such as viral …

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

J Koehler Leman, S Lyskov, SM Lewis… - Nature …, 2021‏ - nature.com
Each year vast international resources are wasted on irreproducible research. The scientific
community has been slow to adopt standard software engineering practices, despite the …