Exploring protein native states and large‐scale conformational changes with a modified generalized born model

By Alexey V. Onufriev, Donald Bashford, David A. Case. Proteins: Structure, Function, and Bioinformatics, 2004

2,370 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Cell Biology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1884b4451b900522f4186ba324560dea2818f329

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Citations in the corpus

DOCK 6: combining techniques to model RNA-small molecule complexes. (2009, methodology): “…Hawkins, Cramer, and Truhlar model with parameters described by Tsui and Case, (2) Onufriev, Bashford, and Case model, and (3) Onufriev, Bashford, and Case model with modified parameters (Hawkins et al. 1995, 1996; Onufriev et al. 2000; Tsui and Case 2000; Feig et al. 2004; Onufriev et al. 2004).”
Fast Identification of Possible Drug Treatment of Coronavirus Disease −19 (COVID-19) Through Computational Drug Repurposing Study (2020, methodology): “Besides the electrostatic and van der Waals interactions, the solvation effect was taken into account using a Generalized GB model developed by Onufriev et al. 40 The ligand-residue MM-GBSA interaction energies were calculated using the Sander program in AMBER18.”
Extended tight‐binding quantum chemistry methods (2020, methodology): “85 are the parameters for the OBC correction, which correspond to the GBII model.(87) The OBC correction increases the Born radii for atoms buried deep inside a molecular cavity, which would usually be underestimated.”
H++: a server for estimating pKas and adding missing hydrogens to macromolecules (2005, methodology): “The particular GB model we are using was found earlier (32) to work reasonably well in pK calculations on proteins; here its improved version ( 33 ) is used.”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, methodology): “In our previous study, the MM/GBSA calculation based on the ff02 force field (39) and the GBOBC1 model (40) yielded the best predictions for protein–protein binding free energies.”
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE (2006, background): “…the orientation-dependent hydrogen bonding potential (Kortemme et al., 2003), and the Generalized Born electrostatics and solvation model (Onufriev et al., 2004): DGdirect ¼ wLJrepELJrep þ wLJattrELJattr þ whbEhb þ welGel‚ ð15Þ where each term is a sum over all protein-DNA and…”