Investigating protein–peptide interactions using the Schrödinger computational suite

J Bhachoo, T Beuming - Modeling peptide-protein interactions: methods …, 2017 - Springer
The Schrödinger software suite contains a broad array of computational chemistry and
molecular modeling tools that can be used to study the interaction of peptides with proteins …

Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

C Geng, LC Xue, J Roel‐Touris… - Wiley Interdisciplinary …, 2019 - Wiley Online Library
Predicting the structure and thermodynamics of protein–protein interactions (PPIs) are key to
a proper understanding and modulation of their function. Since experimental methods might …

[HTML][HTML] Controlling the SARS-CoV-2 spike glycoprotein conformation

R Henderson, RJ Edwards, K Mansouri… - Nature structural & …, 2020 - nature.com
The coronavirus (CoV) spike (S) protein, involved in viral–host cell fusion, is the primary
immunogenic target for virus neutralization and the current focus of many vaccine design …

[HTML][HTML] Common activation mechanism of class A GPCRs

Q Zhou, D Yang, M Wu, Y Guo, W Guo, L Zhong, X Cai… - Elife, 2019 - elifesciences.org
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human
physiology. Understanding receptor activation mechanism is critical for discovering novel …

Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants

J Pitts, J Li, JK Perry, V Du Pont, N Riola… - Antimicrobial agents …, 2022 - Am Soc Microbiol
Genetic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has
resulted in the emergence and rapid spread of multiple variants throughout the pandemic, of …

[HTML][HTML] Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies

X Zhu, D Mannar, SS Srivastava, AM Berezuk… - PLoS …, 2021 - journals.plos.org
The recently reported “UK variant”(B. 1.1. 7) of SARS-CoV-2 is thought to be more infectious
than previously circulating strains as a result of several changes, including the N501Y …

[HTML][HTML] Structure–function analysis of the SHOC2–MRAS–PP1C holophosphatase complex

JJ Kwon, B Hajian, Y Bian, LC Young, AJ Amor… - Nature, 2022 - nature.com
Receptor tyrosine kinase (RTK)–RAS signalling through the downstream mitogen-activated
protein kinase (MAPK) cascade regulates cell proliferation and survival. The SHOC2–MRAS …

[HTML][HTML] Crystal structure of antagonist bound human lysophosphatidic acid receptor 1

JE Chrencik, CB Roth, M Terakado, H Kurata, R Omi… - Cell, 2015 - cell.com
Lipid biology continues to emerge as an area of significant therapeutic interest, particularly
as the result of an enhanced understanding of the wealth of signaling molecules with …

AB‐bind: antibody binding mutational database for computational affinity predictions

S Sirin, JR Apgar, EM Bennett, AE Keating - Protein Science, 2016 - Wiley Online Library
Antibodies (Abs) are a crucial component of the immune system and are often used as
diagnostic and therapeutic agents. The need for high‐affinity and high‐specificity antibodies …

[HTML][HTML] Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2

J Dong, B Huang, B Wang, A Titong… - Scientific reports, 2020 - nature.com
SARS-CoV-2 is a newly emergent coronavirus, which has adversely impacted human health
and has led to the COVID-19 pandemic. There is an unmet need to develop therapies …