Open AccessSEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine
Author(s) -
Lane Votapka,
Andrew Stokely,
Anupam Anand Ojha,
Rommie E. Amaro
Publication year - 2022
Publication title -
journal of chemical information and modeling
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 160
eISSN - 1549-960X
pISSN - 1549-9596
DOI - 10.1021/acs.jcim.2c00501
Subject(s) - molecular dynamics , brownian dynamics , usability , computer science , extensibility , kinetics , statistical physics , computational science , brownian motion , chemistry , computational chemistry , physics , programming language , quantum mechanics , human–computer interaction
We present SEEKR2 (simulation-enabled estimation of kinetic rates version 2)─the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability and with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2. Furthermore, this version of SEEKR supports hydrogen mass repartitioning, which significantly reduces computational cost, while showing little, if any, loss of accuracy in the predicted kinetics.