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Journal of chemical theory and computation, ISSN 1549-9618, 01/2007, Volume 3, Issue 1, pp. 26 - 41
The growing adoption of generalized-ensemble algorithms for biomolecular simulation has resulted in a resurgence in the use of the weighted histogram analysis... 
MONTE-CARLO | ENSEMBLE | MULTICANONICAL ALGORITHM | TEMPERATURE | PHASE-TRANSITIONS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | SYSTEMS | ERROR | MOLECULAR-DYNAMICS SIMULATIONS | FREE-ENERGY
Journal Article
Journal of chemical theory and computation, ISSN 1549-9618, 01/2013, Volume 9, Issue 1, pp. 153 - 164
A novel variational method for construction of free energy profiles from molecular simulation data is presented. The variational free energy profile (VFEP)... 
MONTE-CARLO | ELECTROSTATIC INTERACTIONS | INTERPOLATION | THERMODYNAMIC INTEGRATION | BIOMOLECULAR SYSTEMS | DYNAMICS SIMULATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | MULTICANONICAL ENSEMBLE | EFFICIENT | HISTOGRAM ANALYSIS METHOD
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 08/2011, Volume 135, Issue 6, pp. 061103 - 061103-4
We present an iteration-free weighted histogram method in terms of intensive variables that directly determines the inverse statistical temperature, β S = ∂ S... 
FREE-ENERGY CALCULATIONS | MOLECULAR-DYNAMICS | STATISTICS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MULTICANONICAL ENSEMBLE | SIMULATIONS | Models, Molecular | Temperature | Entropy | Models, Statistical | Methods | Communications
Journal Article
Protein engineering, design and selection, ISSN 1741-0134, 2016, Volume 29, Issue 11, pp. 477 - 484
Abstract The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular,... 
crystal packing | multicanonical molecular dynamics simulation | antibody | free energy landscape | CDR-H3 loop | PROTEIN | SINGLE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | CONFORMATIONS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | STRUCTURAL CLASSIFICATION | MOLECULAR-DYNAMICS SIMULATIONS | FREE-ENERGY | BINDING | Original
Journal Article
International journal of molecular sciences, ISSN 1422-0067, 2018, Volume 19, Issue 4, p. 937
We present a new approach for automated exploration of free energy landscapes on the basis of the umbrella integration (UI) method. The method to search points... 
Potential of mean force | Automated search | Umbrella integration | MOLECULAR-DYNAMICS | FORCE | FLUID | potential of mean force | BIOCHEMISTRY & MOLECULAR BIOLOGY | MULTICANONICAL ENSEMBLE | PARTICLE MESH EWALD | SIMULATIONS | automated search | umbrella integration | CHEMISTRY, MULTIDISCIPLINARY | Models, Theoretical | Thermodynamics | Alanine | Automation | Algorithms
Journal Article
Physical chemistry chemical physics : PCCP, ISSN 1463-9076, 2017, Volume 19, Issue 7, pp. 5454 - 5464
Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to... 
SPIN-GLASS SIMULATIONS | POLARIZED VISIBLE RAMAN | BIOMOLECULAR SYSTEMS | PHASE-TRANSITIONS | BIOLOGICAL MOLECULES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MULTICANONICAL ENSEMBLE | 2-DIMENSIONAL VIBRATIONAL SPECTROSCOPY | MOLECULAR-DYNAMICS SIMULATIONS | MONTE-CARLO SIMULATIONS | AQUEOUS-SOLUTION
Journal Article
Journal of computational physics, ISSN 0021-9991, 03/2017, Volume 333, pp. 128 - 141
We study the effect of helical structure on the aggregation of proteins using a simplified lattice protein model with an implicit membrane environment. A... 
Protein aggregation | Multicanonical sampling | Lattice Monte Carlo | Twin-arginine translocation | Parallel tempering | TRANSPORT-SYSTEM | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | EXPORT PATHWAY | MODEL | TATA COMPONENT | PHYSICS, MATHEMATICAL | Proteins | Monte Carlo method | Analysis
Journal Article
The Journal of chemical physics, ISSN 0021-9606, 10/2015, Volume 143, Issue 13, p. 134114
Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied... 
LENNARD-JONES CLUSTERS | POLYMERS | ALGORITHM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | 1ST-ORDER PHASE-TRANSITIONS | CHEMISTRY, PHYSICAL | MULTICANONICAL ENSEMBLE | AGGREGATION | Histograms | Simulation | Computer simulation | Conservation | Angular momentum | Molecular dynamics | Phase transitions
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 08/2016, Volume 37, Issue 21, pp. 2017 - 2028
Simulated tempering (ST) is a generalized‐ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy... 
mass scaling | Nosé–Hoover thermostat | molecular dynamics | simulated tempering | generalized‐ensemble algorithm | generalized-ensemble algorithm | TIME-STEP | MULTICANONICAL ENSEMBLE | ALGORITHMS | FREE-ENERGY | CHEMISTRY, MULTIDISCIPLINARY | Nose-Hoover thermostat | Molecular dynamics | Usage
Journal Article