Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation
Authors
Keywords
-
Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 144, Issue 3, Pages 034107
Publisher
AIP Publishing
Online
2016-01-21
DOI
10.1063/1.4939768
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Optimally Adjusted Mixture Sampling and Locally Weighted Histogram Analysis
- (2017) Zhiqiang Tan JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
- Asynchronous replica exchange software for grid and heterogeneous computing
- (2015) Emilio Gallicchio et al. COMPUTER PHYSICS COMMUNICATIONS
- Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression
- (2015) Yilin Meng et al. Journal of Chemical Theory and Computation
- Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
- (2015) Junchao Xia et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A Stochastic Solution to the Unbinned WHAM Equations
- (2015) Bin W. Zhang et al. Journal of Physical Chemistry Letters
- Weak Convergence Rates of Population Versus Single-Chain Stochastic Approximation MCMC Algorithms
- (2014) Qifan Song et al. ADVANCES IN APPLIED PROBABILITY
- Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
- (2014) Hao Wu et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model
- (2014) Edina Rosta et al. Journal of Chemical Theory and Computation
- Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge
- (2014) Emilio Gallicchio et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States
- (2014) Antonia S. J. S. Mey et al. Physical Review X
- Communication: Simulated tempering with fast on-the-fly weight determination
- (2013) Phuong H. Nguyen et al. JOURNAL OF CHEMICAL PHYSICS
- Computation of transit times using the milestoning method with applications to polymer translocation
- (2013) Alexander T. Hawk et al. JOURNAL OF CHEMICAL PHYSICS
- Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process
- (2013) Lauren Wickstrom et al. Journal of Chemical Theory and Computation
- Two-dimensional replica-exchange method for predicting protein-ligand binding structures
- (2013) Hironori Kokubo et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods
- (2012) Daniel B. Smith et al. CHEMICAL PHYSICS LETTERS
- Theory of binless multi-state free energy estimation with applications to protein-ligand binding
- (2012) Zhiqiang Tan et al. JOURNAL OF CHEMICAL PHYSICS
- Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
- (2012) Wei Jiang et al. Journal of Chemical Theory and Computation
- w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
- (2012) Mehrnoosh Arrar et al. Journal of Chemical Theory and Computation
- Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)
- (2012) Emilio Gallicchio et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
- (2011) John D. Chodera et al. JOURNAL OF CHEMICAL PHYSICS
- Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations
- (2011) Mauro Lapelosa et al. Journal of Chemical Theory and Computation
- Convergence and error estimation in free energy calculations using the weighted histogram analysis method
- (2011) Fangqiang Zhu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Error and efficiency of simulated tempering simulations
- (2010) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Optimal Weights in Serial Generalized-Ensemble Simulations
- (2010) Riccardo Chelli Journal of Chemical Theory and Computation
- Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities
- (2010) Emilio Gallicchio et al. Journal of Chemical Theory and Computation
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- Simulated-tempering replica-exchange method for the multidimensional version
- (2009) Ayori Mitsutake JOURNAL OF CHEMICAL PHYSICS
- Error and efficiency of replica exchange molecular dynamics simulations
- (2009) Edina Rosta et al. JOURNAL OF CHEMICAL PHYSICS
- Multidimensional generalized-ensemble algorithms for complex systems
- (2009) Ayori Mitsutake et al. JOURNAL OF CHEMICAL PHYSICS
- Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling
- (2009) Sarah Rauscher et al. Journal of Chemical Theory and Computation
- The AGBNP2 Implicit Solvation Model
- (2009) Emilio Gallicchio et al. Journal of Chemical Theory and Computation
- Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
- (2008) Xuhui Huang et al. JOURNAL OF CHEMICAL PHYSICS
- Comparison of sampling efficiency between simulated tempering and replica exchange
- (2008) Cheng Zhang et al. JOURNAL OF CHEMICAL PHYSICS
- Statistically optimal analysis of samples from multiple equilibrium states
- (2008) Michael R. Shirts et al. JOURNAL OF CHEMICAL PHYSICS
- Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding†
- (2008) Weihua Zheng et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Finding Transition Pathways Using the String Method with Swarms of Trajectories
- (2008) Albert C. Pan et al. JOURNAL OF PHYSICAL CHEMISTRY B
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started