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Improved side-chain torsion potentials for the Amber ff99SB protein force field.
(2010) Proteins 78
PubMed: 20408171 | PubMedCentral: PMC2970904 | DOI: 10.1002/prot.22711
Simulations of HEWL, BPTI, Ubq, and GB3 were initiated from PDB 22 entries 6LYT, 5PTI, 1UBQ, and 1P7E solvated in cubic water boxes containing 10,594, 4215, 6080, and 5156 water molecules, respectivel... .
Publication Year: 2010
Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning.
(2013) J Chem Theory Comput 9
PubMed: 23894231 | PubMedCentral: PMC3719162 | DOI: 10.1021/ct400279d
We now put this into practice by performing molecular dynamics (MD) simulations of the three proteins described previously (PDB: 1UBQ, 1MHN, 6LYT) using force fields based on our calculated DDEC charg... s.
We have utilized the linear-scaling nature of our DDEC implementation to calculate DDEC charges of three proteins: ubiquitin, the SMN Tudor Domain, and hen egg lysozyme (PDB: 1UBQ, 1MHN, 6LYT).
Figure 10 Backbone C α root-mean-square deviation (RMSd) with respect to the initial experimental PDB structure for 1UBQ, 1MHN, and 6LYT, with running averages taken over 50 ps windows.
Publication Year: 2013
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