Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects

By W. Rocchia, S. Sridharan, Anthony Nicholls, Emil Alexov, A. Chiabrera, Barry Honig. Journal of Computational Chemistry, 2002

648 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Electrical and Electronic Engineering

View Paper: https://www.semanticscholar.org/paper/9c11f46c8f075c216ae857bbf080f328911b50b0

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In Atomic and Molecular Physics, and Optics

1. James Andrew McCammon
2. Nathan A. Baker

Citations in the corpus

• Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods (2016, background): “The solvent effect can be accounted for either by treating water molecules explicitly or using the implicit (or continuum) solvent models such as Poisson–Boltzmann surface area (PBSA) model [178,179] and the generalized-Born surface area (GBSA) model [180,181].”
• Improved prediction of protein-protein binding sites using a support vector machines approach. (2005, methodology): “Electrostatic potential Electrostatic potentials were computed for each individual protein using the Delphi v4 software package (Rocchia et al., 2001, 2002).”
• Origins of specificity in protein-DNA recognition (2010, neutral): “The electrostatic potentials were calculated as described in (66) by solving the PoissonBoltzmann equation with DelPhi (67, 222) at a salt concentration of 0.”
• 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.”
• PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations (2004, methodology): “Finally, there are a number of tools available (12,15) for converting from PQR format to other formats required by continuum electrostatics software such as Delphi (16) and UHBD (17).”
• DelPhi: a comprehensive suite for DelPhi software and associated resources (2012, methodology): “…energy is almost scale-independent and reaches steady value of − 28089 kT. Achieving such steady value at scale 1 – 2 points/Å demonstrates the robustness of the algorithm that calculates the electrostatic component of solvation energy, so termed the corrected reaction field energy method [35].”
• Functional specificity of a Hox protein mediated by the recognition of minor groove structure. (2007, neutral): “Electrostatic potentials were calculated using the DelPhi program (Rocchia et al., 2002).”
• TPR proteins: the versatile helix. (2003, methodology): “made using DELPHI (http://trantor.bioc.columbia.edu/delphi/) [ 39 ] and image generated using GRASP (http://trantor.bioc.columbia.edu/grasp/) [40].”