Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.

By Peter A. Kollman, I. Massova, Carolina Reyes, Bernd Kuhn, Shuanghong Huo, Lillian T. Chong, Matthew Lee, Tai-Sung Lee, Y. Duan, Wei Wang and 5 more. Accounts of Chemical Research, 2000

4,533 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/aa7d03d8364a1e6ed8299934a718baa2e511dbdb

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In Molecular Biology

1. David A. Case
2. Carlos H. M. Rodrigues
3. Douglas E. V. Pires
4. Alexey V. Onufriev
5. David B. Ascher
6. Samuel Genheden
7. Ulf Ryde
8. Donald Bashford

Citations in the corpus

• Recent Developments and Applications of the MMPBSA Method (2018, methodology): “Among the classical 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 ”
• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, methodology): “Another two similar endpoint methods, which have often been applied to the protein-ligand binding free energy calculations, are molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized born surface area (MM-GBSA) [218,219].”
• 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.”
• mCSM-PPI2: predicting the effects of mutations on protein–protein interactions (2019, methodology): “Previous methods were limited either in terms of their throughput (21,22) or in terms of their performance (23).”
• Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. (2003, methodology): “Here, (absolute) free energies of protein–protein binding have been computed with the molecular mechanics (MM)-generalized Born surface area (GBSA) approach.(54,55) In this approach, gas-phase energies, solvation free energies, and entropic contributions are summed and averaged over snapshots from M”