Generalized born models of macromolecular solvation effects.
By Donald Bashford, David A. Case. Annual review of physical chemistry (Print), 2000
1,005 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/0af3b13d028eafa23e842d3388bb68f1e4957df8
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In Materials Chemistry
- David Baker
- Jeffrey J. Gray
- Tanja Kortemme
- Jens Meiler
- Michael Feig
- Frank DiMaio
- Hahnbeom Park
- Brian Kuhlman
In Molecular Biology
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- Jeffrey J. Gray
- Tanja Kortemme
- Jens Meiler
- Michael Feig
- Rhiju Das
- Frank DiMaio
- Hahnbeom Park
Citations in the corpus
- Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap (2013, neutral): “Solvation models, that is, theoretical treatments that describe the effect of solvent range from continuum (implicit) solvent models [20-27] to explicit solvent models [28-31] and in the most sophisticated cases a quantum mechanical treatment [15,32,33] (not discussed in this article).”
- Potential energy functions for protein design. (2007, methodology): “Alternatively, the generalized Born equation [29] provides a fast approximate solution to the PB equation, and it has been used for protein design [30].”
- Improvements to the APBS biomolecular solvation software suite (2017, methodology): “Numerical solution methods tend to be computationally intensive, which has led to the adoption of analytical approaches for solvation calculations such as generalized Born [65] and the approaches developed by Head-Gordon and implemented in APBS.”
- Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. (2011, methodology): “MD simulations of each replica are typically performed using 20ns Langevin dynamics [128] with an integration time step of 0.002ps in the presence of an implicit solvent model [129-132], such as Generalized Born Continuum Solvent Model (GBMV) [133,134].”
- MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. (2004, methodology): “Here, we are using a scoring function that includes implicit solvation based on a generalized Born formalism [27], in this case the GBMV method [39,40], as implemented in CHARMM as the default when GB is requested.”
- Force fields for protein simulations. (2003, background): “The basic ansatz of generalized Born theory (Still et al., 1990; Bashford and Case, 2000) is to extend these ideas to non-spherical molecules by casting the electrostatic contribution to solvation into the following form: Ges ¼ 1 2 X i X j qiqj fGB 1 1 eout ð24Þ A simple plausibility argument for…”