[HTML][HTML] A guide to in silico drug design
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …
few candidates progress from hit compound to a commercially available product, often due …
Alchemical transformations and beyond: Recent advances and real-world applications of free energy calculations in drug discovery
Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …
drug molecules. A critical factor in this process is the binding affinity between candidate …
Accurate prediction of GPCR ligand binding affinity with free energy perturbation
The computational prediction of relative binding free energies is a crucial goal for drug
discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug …
discovery, and G protein-coupled receptors (GPCRs) are arguably the most important drug …
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 …
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 …
Improving the accuracy of protein thermostability predictions for single point mutations
Accurately predicting the protein thermostability changes upon single point mutations in
silico is a challenge that has implications for understanding diseases as well as industrial …
silico is a challenge that has implications for understanding diseases as well as industrial …
Large-scale application of free energy perturbation calculations for antibody design
Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate
the free energy difference between distinct chemical systems. Here we report our …
the free energy difference between distinct chemical systems. Here we report our …
Selection pressures on evolution of ribonuclease H explored with rigorous free–energy–based design
Understanding natural protein evolution and designing novel proteins are motivating interest
in development of high-throughput methods to explore large sequence spaces. In this work …
in development of high-throughput methods to explore large sequence spaces. In this work …
[PDF][PDF] Principles of cold adaptation of fish lactate dehydrogenases revealed by computer simulations of the catalytic reaction
Cold-adapted enzymes from psychrophilic and psychrotolerant species are characterized by
a higher catalytic activity at low temperature than their mesophilic orthologs and are also …
a higher catalytic activity at low temperature than their mesophilic orthologs and are also …
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs
Mutations in human proteins lead to diseases. The structure of these proteins can help
understand the mechanism of such diseases and develop therapeutics against them. With …
understand the mechanism of such diseases and develop therapeutics against them. With …