Brownian Dynamics Simulations of Biological Molecules
نویسندگان
چکیده
منابع مشابه
Profile of RNA Helices: Brownian Dynamics Simulations
Bends in nucleic acid helices can be quantified in a transient electric birefringence (TEB) experiment from the ratio of the terminal decay times of the bent molecule and its fully duplex counterpart (T-ratio method). The apparent bend angles can be extracted from the experimental T-ratios through the application of static (equilibrium-ensemble) hydrodynamic models; however, such models do not ...
متن کاملPredicting Protein Interactions by Brownian Dynamics Simulations
We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation ef...
متن کاملOn Algorithms for Brownian Dynamics Computer Simulations
Several Brownian Dynamics numerical schemes for treating stochastic differential equations at the position Langevin level are analyzed from the point of view of their algorithmic efficiency. The algorithms are tested using model colloidal fluid of particles interacting via the Yukawa potential. Limitations in the conventional Brownian Dynamics algorithm are shown and it is demonstrated that muc...
متن کاملTwo-Dimensional Reaction of Biological Molecules Studied by Weighted-Ensemble Brownian Dynamics
Computer simulations offer critical insights into the reaction of biological macromolecules, especially when the molecular shapes are too complex to be amenable to analytical solution. In this work, the Weighted-Ensemble Brownian (WEB) Dynamics simulation algorithm is adapted to a reaction of two unlike biological molecules, with the interaction modeled by a two-parameter system: a spherical mo...
متن کاملMolecular Dynamics Simulations of RNA Molecules
a Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc, Tr. 17. Listopadu 12, 771 46 Olomouc, Czech Republic; Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 N...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Trends in Chemistry
سال: 2019
ISSN: 2589-5974
DOI: 10.1016/j.trechm.2019.07.008