Calculation of absolute protein-ligand binding free energy from computer simulations.

By H. Woo, Benoît Roux. Proceedings of the National Academy of Sciences of the United States of America, 2005

611 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6028582733d89bbaf0be2ea28dd954fd0f64ebc8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Philip E. Bourne
2. Lei Xie
3. Li Xie
4. David L. Mobley
5. Michael K. Gilson
6. Peng Sang
7. Benoît Roux
8. Xing Du

Citations in the corpus

• Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery (2020, neutral): “20 − 27 1.2.”
• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “On the contrary, a PMF-based path method performs the binding free energy calculations through initially restraining the ligand into the bound state in the bulk solvent, followed by translating the ligand into the binding site and then releasing restraints completely [208].”
• Standard binding free energies from computer simulations: What is the best strategy? (2012, background): “…covering the slowly evolving degree of freedom and calculate a two-dimensional PMF, from which the unidimensional separation PMF can be recovered; 5 however, this solution can become computationally expensive and is particularly challenging if the degrees of freedom to target are not obvious.”
• Predicting binding free energies: Frontiers and benchmarks (2016, background): “Although, by definition, the pathway used must be a physical one that could occur in nature, it need not be probable, and improbable pathways, governed by an order parameter specifying how far the ligand is from the binding site, are often used [11, 73, 78, 179, 192, 200].”
• Structure-based Systems Biology for Analyzing Off-target Binding (2011, methodology): “Following MD simulation, MM-PBSA/GBSA [96] and absolute free energy calculations [93,97–99] can be applied to accurately estimate the binding affinity of the ligand to the putative off-targets.”