| scholarly article | Q13442814 |
| P50 | author | J. Andrew McCammon | Q6104601 |
| P2093 | author name string | Donald Hamelberg | |
| Mikolai Fajer | |||
| P2860 | cites work | Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials | Q35051978 |
| A Hamiltonian Replica Exchange Approach and Its Application to the Study of Side-Chain Type and Neighbor Effects on Peptide Backbone Conformations | Q35859610 | ||
| Direct calculation of the binding free energies of FKBP ligands | Q39131231 | ||
| Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. | Q45962822 | ||
| Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules | Q46058456 | ||
| Sampling of slow diffusive conformational transitions with accelerated molecular dynamics | Q46685715 | ||
| Simulated scaling method for localized enhanced sampling and simultaneous "alchemical" free energy simulations: a general method for molecular mechanical, quantum mechanical, and quantum mechanical/molecular mechanical simulations. | Q51925086 | ||
| A statistical analysis of the precision of reweighting-based simulations | Q59600411 | ||
| Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy | Q80001758 | ||
| Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations | Q86855911 | ||
| P433 | issue | 10 | |
| P304 | page(s) | 1565-1569 | |
| P577 | publication date | 2008-09-03 | |
| P1433 | published in | Journal of Chemical Theory and Computation | Q1768377 |
| P1476 | title | Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration | |
| P478 | volume | 4 |
| Q30578414 | Accelerated adaptive integration method |
| Q36520871 | Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design |
| Q35987280 | Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation |
| Q38302840 | Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations. |
| Q35169470 | Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD). |
| Q34385618 | Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange |
| Q48057535 | Constructing a multidimensional free energy surface like a spider weaving a web. |
| Q36927467 | Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC) |
| Q27318807 | Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2 |
| Q57943282 | Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration |
| Q36972272 | Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model |
| Q47567806 | Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator. |
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| Q42161091 | Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach. |
| Q35169555 | Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations |
| Q37651766 | Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics |
| Q27334941 | Full Atom Simulations of Spin Label Conformations |
| Q28652087 | Functional loop dynamics of the streptavidin-biotin complex |
| Q48050759 | Gaussian Accelerated Molecular Dynamics in NAMD. |
| Q55481649 | Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. |
| Q27301372 | Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation |
| Q33763745 | Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. |
| Q57943288 | Hamiltonian replica exchange in GROMACS: a flexible implementation |
| Q35047293 | Implementation of Accelerated Molecular Dynamics in NAMD |
| Q35435838 | Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange |
| Q33893633 | Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation |
| Q89174818 | Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials |
| Q26773062 | Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods |
| Q27334394 | Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis |
| Q64111973 | Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network |
| Q60913129 | Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study |
| Q51608927 | Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules. |
| Q30554344 | Population based reweighting of scaled molecular dynamics |
| Q57038883 | Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis |
| Q36157014 | Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling |
| Q34300133 | Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics |
| Q36960616 | Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions |
| Q35794917 | Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition |
| Q34225993 | Studying functional dynamics in bio-molecules using accelerated molecular dynamics |
| Q30381463 | Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding. |
| Q37114199 | Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review |
| Q34291803 | Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations |
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