| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/jcamd/KlimovichSM15 |
| P356 | DOI | 10.1007/S10822-015-9840-9 |
| P932 | PMC publication ID | 4420631 |
| P698 | PubMed publication ID | 25808134 |
| P5875 | ResearchGate publication ID | 274091269 |
| P50 | author | David L. Mobley | Q55143475 |
| P2093 | author name string | Pavel V Klimovich | |
| Michael R Shirts | |||
| P2860 | cites work | Matplotlib: A 2D Graphics Environment | Q17278583 |
| Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site | Q27657572 | ||
| Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics | Q27678383 | ||
| GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit | Q29615867 | ||
| Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions | Q30278077 | ||
| Statistically optimal analysis of samples from multiple equilibrium states | Q30438437 | ||
| Identifying low variance pathways for free energy calculations of molecular transformations in solution phase | Q30453963 | ||
| Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations | Q30457582 | ||
| A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods | Q30459884 | ||
| Mechanical unfolding intermediates in titin modules. | Q31431985 | ||
| Computations of standard binding free energies with molecular dynamics simulations | Q37335295 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations | Q39901298 | ||
| Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies | Q43493450 | ||
| Variance minimization of free energy estimates from optimized expanded ensembles | Q45169023 | ||
| Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. | Q46037009 | ||
| Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations | Q46477254 | ||
| Good practices in free-energy calculations | Q46484190 | ||
| THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method | Q56157177 | ||
| High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases | Q56745022 | ||
| Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins | Q56776034 | ||
| Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules | Q57875442 | ||
| Multistate Gaussian Model for Electrostatic Solvation Free Energies | Q57875496 | ||
| Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation | Q59346182 | ||
| Steered molecular dynamics simulations of force-induced protein domain unfolding | Q77924666 | ||
| Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence | Q80369348 | ||
| In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats | Q81661544 | ||
| Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations | Q84014403 | ||
| Linear-scaling soft-core scheme for alchemical free energy calculations | Q85002750 | ||
| New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations | Q86751568 | ||
| Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field | Q86825224 | ||
| P433 | issue | 5 | |
| P304 | page(s) | 397-411 | |
| P577 | publication date | 2015-03-26 | |
| P1433 | published in | Journal of Computer - Aided Molecular Design | Q15766522 |
| P1476 | title | Guidelines for the analysis of free energy calculations | |
| P478 | volume | 29 |
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