[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …
molecules. Thus, one may obtain biological insights into protein functions, disease …
Machine learning solutions for predicting protein–protein interactions
R Casadio, PL Martelli… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Proteins are “social molecules.” Recent experimental evidence supports the notion that
large protein aggregates, known as biomolecular condensates, affect structurally and …
large protein aggregates, known as biomolecular condensates, affect structurally and …
The SARS-CoV-2 Spike variant D614G favors an open conformational state
RA Mansbach, S Chakraborty, K Nguyen… - Biophysical …, 2021 - cell.com
The COVID-19 global pandemic is an international health emergency. It is caused by the
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
SARS-CoV-2 virus, which binds with its trimeric Spike protein to the ACE2 receptor in the …
The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA
Abstract The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the
viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step …
viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step …
An effective MM/GBSA protocol for absolute binding free energy calculations: A case study on SARS-CoV-2 spike protein and the human ACE2 receptor
N Forouzesh, N Mishra - Molecules, 2021 - mdpi.com
The binding free energy calculation of protein–ligand complexes is necessary for research
into virus–host interactions and the relevant applications in drug discovery. However, many …
into virus–host interactions and the relevant applications in drug discovery. However, many …
BFEE2: automated, streamlined, and accurate absolute binding free-energy calculations
Accurate absolute binding free-energy estimation in silico, following either an alchemical or
a geometrical route, involves several subprocesses and requires the introduction of …
a geometrical route, involves several subprocesses and requires the introduction of …
Standard Binding Free-Energy Calculations: How Far Are We from Automation?
Recent success stories suggest that in silico protein–ligand binding free-energy calculations
are approaching chemical accuracy. However, their widespread application remains limited …
are approaching chemical accuracy. However, their widespread application remains limited …
Predicting the mutation effects of protein–ligand interactions via end-point binding free energy calculations: strategies and analyses
Protein mutations occur frequently in biological systems, which may impact, for example, the
binding of drugs to their targets through impairing the critical H-bonds, changing the …
binding of drugs to their targets through impairing the critical H-bonds, changing the …
In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2
F Jafary, S Jafari, MR Ganjalikhany - Scientific reports, 2021 - nature.com
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered
coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS …
coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS …
A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand binding potencies
J Wang, A Ishchenko, W Zhang, A Razavi… - Scientific Reports, 2022 - nature.com
Although seeking to develop a general and accurate binding free energy calculation method
for protein–protein and protein–ligand interactions has been a continuous effort for decades …
for protein–protein and protein–ligand interactions has been a continuous effort for decades …