| review article | Q7318358 |
| scholarly article | Q13442814 |
| P2093 | author name string | Ronald P White | |
| Hagai Meirovitch | |||
| Srinath Cheluvaraja | |||
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| beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain | Q30164941 | ||
| Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data | Q30579093 | ||
| On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data | Q31032500 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
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| Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent | Q34190144 | ||
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| The GROMOS software for biomolecular simulation: GROMOS05. | Q34457783 | ||
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| Simulation method for calculating the entropy and free energy of peptides and proteins | Q35316252 | ||
| Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration | Q36104911 | ||
| Comparison of free energy methods for molecular systems | Q36658081 | ||
| Calculation of protein-ligand binding affinities. | Q36698596 | ||
| Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation | Q36774840 | ||
| New theoretical methodology for elucidating the solution structure of peptides from NMR data. II. Free energy of dominant microstates of Leu-enkephalin and population-weighted average nuclear Overhauser effects intensities | Q36804812 | ||
| Potentials of mean force for acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain | Q36897559 | ||
| Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
| Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method | Q40306265 | ||
| Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides | Q40441735 | ||
| Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water. | Q40456761 | ||
| Computer simulation of the free energy of peptides with the local states method: analogues of gonadotropin releasing hormone in the random coil and stable states | Q40685170 | ||
| Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids | Q41497542 | ||
| Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo method | Q41868273 | ||
| Calculation of absolute protein-ligand binding affinity using path and endpoint approaches | Q42132116 | ||
| Entropy and free energy of a mobile protein loop in explicit water | Q42140475 | ||
| Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force | Q42587806 | ||
| Tork: Conformational analysis method for molecules and complexes | Q44609341 | ||
| Structural evidence for induced fit as a mechanism for antibody-antigen recognition | Q45203554 | ||
| Evaluating the Accuracy of the Quasiharmonic Approximation | Q46144156 | ||
| Evaluating the conformational entropy of macromolecules using an energy decomposition approach | Q46219850 | ||
| Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions | Q46358954 | ||
| Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches | Q46798591 | ||
| Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions | Q47935276 | ||
| Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins | Q48020079 | ||
| Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems. | Q50867856 | ||
| Order-parameter-based Monte Carlo simulation of crystallization. | Q51226765 | ||
| A general framework for non-Boltzmann Monte Carlo sampling. | Q51274130 | ||
| Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation. | Q51439297 | ||
| Multicanonical schemes for mapping out free-energy landscapes of single-component and multicomponent systems. | Q51439336 | ||
| Direct calculation of solid-liquid equilibria from density-of-states Monte Carlo simulations. | Q51499283 | ||
| Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others. | Q51626047 | ||
| An efficient, path-independent method for free-energy calculations. | Q51629370 | ||
| On the use of Bennett's acceptance ratio method in multi-canonical-type simulations. | Q51642626 | ||
| Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods? | Q51937283 | ||
| Collective Langevin dynamics of conformational motions in proteins. | Q51939837 | ||
| Concepts in receptor optimization: targeting the RGD peptide. | Q51944653 | ||
| Simple estimation of absolute free energies for biomolecules. | Q51945700 | ||
| Equilibrium free energies from fast-switching trajectories with large time steps. | Q51952426 | ||
| Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. | Q51989869 | ||
| Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior. | Q52068717 | ||
| Cooperative folding mechanism of a β-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation | Q57905970 | ||
| Estimating entropies from molecular dynamics simulations | Q58005574 | ||
| Free energy landscape and folding mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study | Q58429825 | ||
| Adaptive integration method for Monte Carlo simulations | Q59732522 | ||
| Optimized Monte Carlo data analysis | Q59732808 | ||
| Rare events and the convergence of exponentially averaged work values | Q62126189 | ||
| Stability of polypeptide conformational states. II. Folding of a polypeptide chain by the scanning simulation method, and calculation of the free energy of the statistical coil | Q68020418 | ||
| Stability of polypeptide conformational states as determined by computer simulation of the free energy | Q69052607 | ||
| Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin | Q69706390 | ||
| Mechanisms of antibody binding to a protein | Q69766097 | ||
| Exploring the energy landscape of a beta hairpin in explicit solvent | Q73379963 | ||
| Ab initio prediction of the solution structures and populations of a cyclic pentapeptide in DMSO based on an implicit solvation model | Q73595085 | ||
| Backbone entropy of loops as a measure of their flexibility: application to a ras protein simulated by molecular dynamics | Q73784255 | ||
| Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions | Q77819303 | ||
| Evaluation of configurational entropy methods from peptide folding-unfolding simulation | Q79895609 | ||
| Absolute and relative entropies from computer simulation with applications to ligand binding | Q79937033 | ||
| Peptide conformational equilibria computed via a single-stage shifting protocol | Q79938504 | ||
| Single-ensemble nonequilibrium path-sampling estimates of free energy differences | Q80368833 | ||
| Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes | Q80990533 | ||
| Absolute free energy calculations by thermodynamic integration in four spatial dimensions | Q81006447 | ||
| Packing structures and transitions in liquids and solids | Q81031838 | ||
| A skewed-momenta method to efficiently generate conformational-transition trajectories | Q81360917 | ||
| Free energy surfaces from nonequilibrium processes without work measurement | Q83179266 | ||
| Stability of the Free and Bound Microstates of a Mobile Loop of α-Amylase Obtained from the Absolute Entropy and Free Energy | Q86831965 | ||
| 2D Entropy of Discrete Molecular Ensembles | Q86839373 | ||
| P433 | issue | 3 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | ligand binding | Q61659151 |
| P1104 | number of pages | 15 | |
| P304 | page(s) | 229-243 | |
| P577 | publication date | 2009-06-01 | |
| P1433 | published in | Current Protein and Peptide Science | Q15745198 |
| P1476 | title | Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding | |
| P478 | volume | 10 |
| Q90643615 | A protein interaction free energy model based on amino acid residue contributions: Assessment of point mutation stability of T4 lysozyme |
| Q36601750 | A simplified confinement method for calculating absolute free energies and free energy and entropy differences |
| Q28392482 | Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties |
| Q42153838 | Calculating free energies of organic molecules on insulating substrates |
| Q57903229 | Computational Analysis for the Rational Design of Anti-Amyloid Beta (Aβ) Antibodies |
| Q28397659 | Conformational Entropy of Intrinsically Disordered Proteins from Amino Acid Triads |
| Q89049133 | Determinants of human glucokinase activation and implications for small molecule allosteric control |
| Q51612612 | Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors. |
| Q38253726 | Exploring the free-energy landscapes of biological systems with steered molecular dynamics. |
| Q28386158 | Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space |
| Q34562935 | Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping |
| Q34130507 | T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles |
| Q39597361 | Thermal nanostructure: an order parameter multiscale ensemble approach |
| Q38675847 | Thermodynamic integration network study of electron transfer: from proteins to aggregates. |
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