Converging free energy estimates: MM‐PB(GB)SA studies on the protein–protein complex Ras–Raf

By Holger Gohlke, David A. Case. Journal of Computational Chemistry, 2004

828 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9d01e231a8445b2c4351551be1959cd6b7b501a4

How researchers see this paper

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

In Atomic and Molecular Physics, and Optics

1. Samuel Genheden
2. Ulf Ryde
3. Gaoqi Weng
4. Ray Luo
5. Tingjun Hou
6. Feng Zhu
7. Zhe Wang
8. Hui Liu

In Materials Chemistry

1. Ray Luo
2. Tingjun Hou
3. Pedro Alexandrino Fernandes
4. Maria João Ramos
5. Samuel Genheden
6. Sérgio Filipe Sousa
7. Hui Liu
8. Ulf Ryde

In Molecular Biology

1. Samuel Genheden
2. Ulf Ryde
3. Gaoqi Weng
4. Ray Luo
5. Tingjun Hou
6. António J. M. Ribeiro
7. Rui P. P. Neves
8. Pedro Alexandrino Fernandes

Citations in the corpus

• Recent Developments and Applications of the MMPBSA Method (2018, methodology): “…simulation methods, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach (Srinivasan et al., 1998; Kollman et al., 2000; Gohlke and Case, 2004; Yang et al., 2011; Miller et al., 2012; Wang C. H. et al., 2016) has emerged as an efficient and reliable method to model…”
• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, neutral): “, normal mode [222] or quasi-harmonic analysis [223] for ∆Sconf, and Sackur-Tetrode equation [224] or alternative models [22] for ∆Sr/t.”
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, background): “In fact, the calculation of the entropic contribution is computationally very expensive as it requires extremely well minimized structures for a Normal Mode analysis, or large numbers of conformations for a Quasi-harmonic analysis [126-128].”
• HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, methodology): “…methodologies, Molecular Mechanics / Poisson Boltzmann Surface Area (MM / PBSA) and Molecular Mechanics / Generalized Born Surface Area (MM / GBSA) (21), which are more theoretically rigorous than scoring functions, have been widely used to predict binding free energies and identify correct…”
• The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities (2015, methodology): “Gohlke and Case have made a detailed study on how the results depend on the polar solvation energy [11].”