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 …

Structural evolution of Delta lineage of SARS-CoV-2

MM Gomari, P Tarighi, E Choupani, S Abkhiz… - International journal of …, 2023 - Elsevier
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of
the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of …

FBXO5-mediated RNF183 degradation prevents endoplasmic reticulum stress-induced apoptosis and promotes colon cancer progression

J Ji, A **g, Y Ding, X Ma, Q Qian, T Geng… - Cell Death & …, 2024 - nature.com
Endoplasmic reticulum (ER) stress induces the unfolded protein response (UPR), and
prolonged ER stress leads to cell apoptosis. Despite increasing research in this area, the …

Rational Prediction of PROTAC-Compatible Protein–Protein Interfaces by Molecular Docking

GP Pereira, B Jiménez-García, R Pellarin… - Journal of Chemical …, 2023 - ACS Publications
Proteolysis targeting chimeras (PROTACs) are heterobifunctional ligands that mediate the
interaction between a protein target and an E3 ligase, resulting in a ternary complex, whose …

Robustification of rosettaantibody and rosetta snugdock

JR Jeliazkov, R Frick, J Zhou, JJ Gray - PloS one, 2021 - journals.plos.org
In recent years, the observed antibody sequence space has grown exponentially due to
advances in high-throughput sequencing of immune receptors. The rise in sequences has …

[HTML][HTML] Coarse-grained (hybrid) integrative modeling of biomolecular interactions

J Roel-Touris, AMJJ Bonvin - Computational and structural biotechnology …, 2020 - Elsevier
The computational modeling field has vastly evolved over the past decades. The early
developments of simplified protein systems represented a step** stone towards …

Protein docking and steered molecular dynamics suggest alternative phospholamban-binding sites on the SERCA calcium transporter

RF Alford, N Smolin, HS Young, JJ Gray… - Journal of Biological …, 2020 - ASBMB
The transport activity of the sarco (endo) plasmic reticulum calcium ATPase (SERCA) in
cardiac myocytes is modulated by an inhibitory interaction with a transmembrane peptide …

PyRosetta Jupyter notebooks teach biomolecular structure prediction and design

KH Le, J Adolf-Bryfogle, JC Klima, S Lyskov… - The …, 2021 - meridian.allenpress.com
Biomolecular structure drives function, and computational capabilities have progressed such
that the prediction and computational design of biomolecular structures is increasingly …

Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations

M Kurcinski, S Kmiecik, M Zalewski… - International journal of …, 2021 - mdpi.com
Most of the protein–protein docking methods treat proteins as almost rigid objects. Only the
side-chains flexibility is usually taken into account. The few approaches enabling docking …