Large scale relative protein ligand binding affinities using non-equilibrium alchemy
Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …
Advances in the calculation of binding free energies
A de Ruiter, C Oostenbrink - Current opinion in structural biology, 2020 - Elsevier
Highlights•Binding free energy calculations are increasing used in drug design and
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …
biotechnology.•We distinguish end-state methods, alchemical methods and pathway …
Computational studies of protein–drug binding affinity changes upon mutations in the drug target
R Friedman - Wiley Interdisciplinary Reviews: Computational …, 2022 - Wiley Online Library
Mutations that lead to drug resistance limit the efficacy of antibiotics, antiviral drugs, targeted
cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity …
cancer therapies, and other treatments. Accurately calculating protein–drug binding affinity …
Evolution of alchemical free energy methods in drug discovery
The goal of the present manuscript is to succinctly trace the key technological steps in the
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a …
Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e
CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address
human genetic diseases caused by point mutations. ABEs were developed by combining …
human genetic diseases caused by point mutations. ABEs were developed by combining …
SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations
The SAMPL challenges focus on testing and driving progress of computational methods to
help guide pharmaceutical drug discovery. However, assessment of methods for predicting …
help guide pharmaceutical drug discovery. However, assessment of methods for predicting …
Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
Exascale computing has been a dream for ages and is close to becoming a reality that will
impact how molecular simulations are being performed, as well as the quantity and quality of …
impact how molecular simulations are being performed, as well as the quantity and quality of …
Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets
Accurate prediction of protein stability upon a point mutation has important applications in
drug discovery and personalized medicine. It remains a challenging issue in computational …
drug discovery and personalized medicine. It remains a challenging issue in computational …
Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics
P Procacci - Current Opinion in Structural Biology, 2021 - Elsevier
Highlights•Computational approaches are becoming an essential tool in modern drug
design.•Development of automated workflows from docking to MD techniques for drug …
design.•Development of automated workflows from docking to MD techniques for drug …
QresFEP: an automated protocol for free energy calculations of protein mutations in Q
Predicting the effect of single-point mutations on protein stability or protein–ligand binding is
a major challenge in computational biology. Free energy calculations constitute the most …
a major challenge in computational biology. Free energy calculations constitute the most …