| scholarly article | Q13442814 |
| P2093 | author name string | Michael K Gilson | |
| David L Mobley | |||
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| Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations | Q30457582 | ||
| Standard binding free energies from computer simulations: What is the best strategy? | Q30540733 | ||
| Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics | Q30670127 | ||
| Cucurbit[7]uril⋅guest pair with an attomolar dissociation constant. | Q30725024 | ||
| On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. | Q36523088 | ||
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| Using MD Simulations To Calculate How Solvents Modulate Solubility | Q37095169 | ||
| Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects | Q37337108 | ||
| Host-guest complexes with protein-ligand-like affinities: computational analysis and design | Q37343448 | ||
| Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics. | Q37588671 | ||
| Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds | Q37614213 | ||
| Basic ingredients of free energy calculations: a review | Q37662435 | ||
| Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations | Q37761334 | ||
| Cucurbiturils: from synthesis to high-affinity binding and catalysis | Q38260429 | ||
| Synthesis and separation of cucurbit[n]urils and their derivatives | Q38780166 | ||
| Overview of the SAMPL5 host-guest challenge: Are we doing better? | Q38818618 | ||
| Accuracy assessment and automation of free energy calculations for drug design | Q39311409 | ||
| D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions | Q39328873 | ||
| The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method | Q39379522 | ||
| Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge | Q39509919 | ||
| Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations | Q40296720 | ||
| Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context | Q40297155 | ||
| Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method | Q40579705 | ||
| Sensitivity in Binding Free Energies Due to Protein Reorganization | Q41081254 | ||
| Binding Hydrated Anions with Hydrophobic Pockets | Q41521132 | ||
| Binding of carboxylate and trimethylammonium salts to octa-acid and TEMOA deep-cavity cavitands | Q41521138 | ||
| Overcoming dissipation in the calculation of standard binding free energies by ligand extraction | Q41972661 | ||
| Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease | Q41989179 | ||
| On the use of orientational restraints and symmetry corrections in alchemical free energy calculations | Q42106721 | ||
| Calculation of absolute protein-ligand binding affinity using path and endpoint approaches | Q42132116 | ||
| A contribution to the drug resistance mechanism of darunavir, amprenavir, indinavir, and saquinavir complexes with HIV-1 protease due to flap mutation I50V: a systematic MM-PBSA and thermodynamic integration study | Q42285420 | ||
| Absolute FKBP binding affinities obtained via nonequilibrium unbinding simulations | Q42729386 | ||
| Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation | Q43013072 | ||
| Is pressure-induced signal loss in NMR spectra for the Leu99Ala cavity mutant of T4 lysozyme due to unfolding? | Q43131107 | ||
| Reply to Kitahara and Mulder: An ensemble view of protein stability best explains pressure effects in a T4 lysozyme cavity mutant | Q43179714 | ||
| Cucurbituril homologues and derivatives: new opportunities in supramolecular chemistry | Q44553289 | ||
| Hit identification and binding mode predictions by rigorous free energy simulations | Q46333106 | ||
| Cucurbit[7]uril host-guest complexes with small polar organic guests in aqueous solution | Q46615465 | ||
| Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. | Q47567527 | ||
| Role of cavities and hydration in the pressure unfolding of T4 lysozyme | Q30848822 | ||
| Cavity as a source of conformational fluctuation and high-energy state: high-pressure NMR study of a cavity-enlarged mutant of T4 lysozyme | Q30883065 | ||
| Deciphering the specific high-affinity binding of cucurbit[7]uril to amino acids in water | Q30908074 | ||
| Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. | Q30986053 | ||
| ITC and NMR Analysis of the Encapsulation of Fatty Acids within a Water-Soluble Cavitand and its Dimeric Capsule | Q31061176 | ||
| Binding of cyclic carboxylates to octa-acid deep-cavity cavitand | Q33599960 | ||
| Guests of Differing Polarities Provide Insight into Structural Requirements for Templates of Water-Soluble Nano-Capsules | Q33626394 | ||
| The SAMPL4 host-guest blind prediction challenge: an overview. | Q33740864 | ||
| Calculation of absolute protein-ligand binding free energy from computer simulations | Q33784404 | ||
| Anion binding to hydrophobic concavity is central to the salting-in effects of Hofmeister chaotropes | Q33882768 | ||
| The statistical-thermodynamic basis for computation of binding affinities: a critical review | Q33915676 | ||
| Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies | Q34155663 | ||
| Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields | Q34249481 | ||
| Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. | Q34257034 | ||
| Testing a flexible-receptor docking algorithm in a model binding site | Q34309041 | ||
| The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities | Q34352706 | ||
| Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field | Q34459931 | ||
| The cucurbit[n]uril family: prime components for self-sorting systems. | Q34466152 | ||
| Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge | Q34541312 | ||
| New ultrahigh affinity host-guest complexes of cucurbit[7]uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations | Q34731466 | ||
| Molecular dynamics simulations of biomolecules | Q34799927 | ||
| Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design | Q35117666 | ||
| Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations | Q35169555 | ||
| CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. | Q35232599 | ||
| A large-scale test of free-energy simulation estimates of protein-ligand binding affinities. | Q35284129 | ||
| Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange | Q35435838 | ||
| Homologous ligands accommodated by discrete conformations of a buried cavity | Q35549133 | ||
| Structure-relaxation mechanism for the response of T4 lysozyme cavity mutants to hydrostatic pressure | Q35616068 | ||
| Conformational sampling for the impatient | Q35669059 | ||
| On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities | Q35751099 | ||
| Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems | Q36060291 | ||
| Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics | Q36331553 | ||
| Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. | Q36344868 | ||
| Accurate calculation of the absolute free energy of binding for drug molecules | Q36427764 | ||
| P433 | issue | 1 | |
| P407 | language of work or name | English | Q1860 |
| P304 | page(s) | 531-558 | |
| P577 | publication date | 2017-04-07 | |
| P1433 | published in | Annual Review of Biophysics | Q4034062 |
| P1476 | title | Predicting Binding Free Energies: Frontiers and Benchmarks | |
| P478 | volume | 46 |
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| Q92904692 | Inclusion Complexation of Organic Micropollutants with β-Cyclodextrin |
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| Q108127363 | Nonadditivity in public and inhouse data: implications for drug design |
| Q58556734 | Overview of the SAMPL6 host-guest binding affinity prediction challenge |
| Q60044836 | Phytochemical analysis and antidiabetic potential of Elaeagnus umbellata (Thunb.) in streptozotocin-induced diabetic rats: pharmacological and computational approach |
| Q52646070 | Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation. |
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