Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 121, Issue 15, Pages 3597-3606Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.6b09388
Keywords
-
Categories
Funding
- National Science Foundation Graduate Research Fellowship Program [DGE-1144086]
- NIH Molecular Biophysics Training Program [T32-GM008326]
- NIH Directors New Innovator Award [DP2 OD007237]
- National Biomedical Computation Resource (NBCR) [NIH P41 GM103426]
- XSEDE [NSF TG-CHE060073]
Ask authors/readers for more resources
We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package;a suite of open-source scripts anti tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the k(on), k(off) and Delta G(bind) for the protein trypsin with its noncovalent binder, benzamidine, and examine the kinetics and other results generated in the context of the new software, and compare our findings to previous studies performed on the same system. We compute a k(on) estimate of (2.1 +/- 0.3) x 10(7) M-1 s(-1) a k(off) estimate of 83 +/- 14 s(-1), and a Delta G(bind) of -7.4 +/- 0.1 kcal.mol(-1), all of which compare closely to the experimentally measured values of 2.9 X 10(7) M-1 S-1, 600 +/- 300 s(-1), and -6.71 +/- 0.05 kcal.mo(-1), respectively.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available