A smooth permittivity function for Poisson–Boltzmann solvation methods

By J. Grant, B. T. Pickup, Anthony Nicholls. Journal of Computational Chemistry, 2001

317 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/70f11857450c8ad412cc54d64677693d2827158c

How researchers see this paper

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In Biomedical Engineering

1. T. Head‐Gordon
2. G. Wei
3. Emil Alexov
4. David A. Case
5. Chuan Li
6. Lin Li
7. Ö. Civalek
8. Yang Xiang

In Molecular Biology

1. Shengyou Huang
2. Xiaoqin Zou
3. James Andrew McCammon
4. Nathan A. Baker
5. Elaine C. Meng
6. Eric F. Pettersen
7. Irwin D. Kuntz
8. Jens Erik Nielsen

Citations in the corpus

• On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi (2013, methodology): “Given a molecule in the water phase, we applied the Gaussian equation and implemented three steps as follows to calculate the dielectric distribution of a protein from its density distribution as originally described by Nicholls et al. 40 Given a macro-molecule with N atoms, the density of an atom i”
• Improvements to the APBS biomolecular solvation software suite (2017, background): “The most significant (based on user base and citations) of these include CHARMM [12], AMBER [13], DelPhi [14], Jaguar [15], Zap [16], MIBPB [17], and APBS [18].”
• DelPhi: a comprehensive suite for DelPhi software and associated resources (2012, methodology): “The Poisson-* Boltzmann Equation (PBE) is one of the most successful implicit solvation models and was implemented in many well-known programs, such as DelPhi [35,36], APBS [37,38], MEAD [39], ZAP [40], PBEQ [41], MIBPB [42], UHBD [43], ITPACT [44], and several others.”
• DOCK 6: combining techniques to model RNA-small molecule complexes. (2009, methodology): “SA) scoring function is an implementation of the ZAP library from OpenEye (Grant et al. 2001).”
• Advances and Challenges in Protein-Ligand Docking (2010, background): “The Poisson-Boltzmann/surface area (PB/SA) models [89–99] and the generalized-Born/surface area (GB/SA) models [100–111] are typical examples of such implicit solvent models.”