Constant pH molecular dynamics in generalized Born implicit solvent
By John T Mongan, David A. Case, J. A. McCammon. Journal of Computational Chemistry, 2004
490 citations recorded by the source corpus.
Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9fd1e2294832648b22d31c20fb69e4c13ac75c7a
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In Atomic and Molecular Physics, and Optics
In Materials Chemistry
In Molecular Biology
Citations in the corpus
- H++: a server for estimating pKas and adding missing hydrogens to macromolecules (2005, background): “Some approaches go beyond this and explicitly take into account the solvent’s degrees of freedom (19,21,27), albeit at a significantly larger computational expense.”
- A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO. (2017, methodology): “…DNA pDEST15 N/A Software and Algorithms Phenix Adams et al., 2010 https://www.phenix-online.org/ Coot Emsley et al., 2010 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ CpHMD Mongan et al., 2004 N/A MOLProbity Chen et al., 2010 http://molprobity.biochem.duke.edu/ Other Structure.”
- H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations (2012, background): “Many theoretical methods have been developed for predicting protonation states of titratable groups (9–23).”
- Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm (2005, unknown): “In a separate development the use of a genetic algorithm (GA) for the analysis of NMR spectra in integrated form of solutes in liquid crystals was reported in a short Letter that gave little detail [12].”
- An overview of the Amber biomolecular simulation package (2013, unknown): “Constant pH was first implemented in sander 61 as of version 9 and has been expanded in later versions as well as being added to pmemd as of v12.”