Flexible Docking in PDZ domains using Elastic Network Model and Replica Exchange Molecular Dynamics
نویسندگان
چکیده
منابع مشابه
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.
Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of...
متن کاملConvergence of replica exchange molecular dynamics.
Replica exchange molecular dynamics (REMD) method is one of the generalized-ensemble algorithms which performs random walk in energy space and helps a system to escape from local energy traps. In this work, we studied the accuracy and efficiency of REMD by examining its ability to reproduce the results of multiple extended conventional molecular dynamics (MD) simulations and to enhance conforma...
متن کاملOptimizing replica exchange moves for molecular dynamics.
We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.
متن کاملReplica-Exchange Molecular Dynamics on Hadoop Report
In most implementations, swaps are only considered for simulations with the nearest temperature. If the higher temperature simulation has lower energy than the lower temperature simulation, the exchange is automatically accepted. However, there is also a chance for the exchange even if this is not the case (the exponential term). These concept are similar to Monte-Carlo based optimization techn...
متن کاملHamiltonian replica exchange molecular dynamics using soft-core interactions.
To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively s...
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: Biophysical Journal
سال: 2009
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2008.12.3132