Works matching DE "FREE energy (Thermodynamics)"
Results: 1210
Minerals, Magic, and Science: IMA Designates 2022 as the Year of Mineralogy.
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- Rocks & Minerals, 2022, v. 97, n. 2, p. 130, doi. 10.1080/00357529.2022.2004511
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A problem of scope for the free energy principle as a theory of cognition.
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- Philosophical Psychology, 2016, v. 29, n. 7, p. 967, doi. 10.1080/09515089.2016.1200024
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Influence of Graphene Oxide on Crystallization Behavior and Chain Folding Surface Free Energy of Poly(vinylidenefluoride- co-hexafluoropropylene).
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- Macromolecular Chemistry & Physics, 2017, v. 218, n. 19, p. n/a, doi. 10.1002/macp.201700103
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Investigation of an Abnormal α Polymorph Formation in Miscible PVDF Nanocomposite Blend Using Kinetics of Crystallization.
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- Macromolecular Chemistry & Physics, 2016, v. 217, n. 4, p. 543, doi. 10.1002/macp.201500344
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Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.
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- Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 5, p. 487, doi. 10.1007/s10822-019-00201-3
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Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3.
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- Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 61, doi. 10.1007/s10822-018-0143-9
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Force field development phase II: Relaxation of physics-based criteria... or inclusion of more rigorous physics into the representation of molecular energetics.
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- Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 2, p. 205, doi. 10.1007/s10822-018-0134-x
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Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations.
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- Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 93, doi. 10.1007/s10822-018-0161-7
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Mathematical deep learning for pose and binding affinity prediction and ranking in D3R Grand Challenges.
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- Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 71, doi. 10.1007/s10822-018-0146-6
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Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1087, doi. 10.1007/s10822-018-0147-5
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SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 965, doi. 10.1007/s10822-018-0151-9
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An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1191, doi. 10.1007/s10822-018-0167-1
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Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1075, doi. 10.1007/s10822-018-0166-2
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Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 983, doi. 10.1007/s10822-018-0165-3
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SAMPL6 host-guest challenge: binding free energies via a multistep approach.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1097, doi. 10.1007/s10822-018-0159-1
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Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1027, doi. 10.1007/s10822-018-0158-2
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Blinded predictions of standard binding free energies: lessons learned from the SAMPL6 challenge.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1047, doi. 10.1007/s10822-018-0154-6
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Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1013, doi. 10.1007/s10822-018-0153-7
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High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1139, doi. 10.1007/s10822-018-0145-7
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SAMPL6: calculation of macroscopic pK<sub>a</sub> values from ab initio quantum mechanical free energies.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 10, p. 1203, doi. 10.1007/s10822-018-0138-6
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Role of protein structure and the role of individual fingers in zinc finger protein-DNA recognition: a molecular dynamics simulation study and free energy calculations.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 6, p. 657, doi. 10.1007/s10822-018-0119-9
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Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 2, p. 331, doi. 10.1007/s10822-018-0097-y
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Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 273, doi. 10.1007/s10822-017-0054-1
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Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 239, doi. 10.1007/s10822-017-0055-0
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Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 211, doi. 10.1007/s10822-017-0056-z
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Predicting the affinity of Farnesoid X Receptor ligands through a hierarchical ranking protocol: a D3R Grand Challenge 2 case study.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 231, doi. 10.1007/s10822-017-0063-0
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Relative binding affinity prediction of farnesoid X receptor in the D3R Grand Challenge 2 using FEP+.
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- Journal of Computer-Aided Molecular Design, 2018, v. 32, n. 1, p. 265, doi. 10.1007/s10822-017-0064-z
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Binding mode prediction and MD/MMPBSA-based free energy ranking for agonists of REV-ERBα/NCoR.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 8, p. 755, doi. 10.1007/s10822-017-0040-7
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Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 7, p. 643, doi. 10.1007/s10822-017-0029-2
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Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 2, p. 183, doi. 10.1007/s10822-016-0001-6
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Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 61, doi. 10.1007/s10822-016-9933-0
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Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 119, doi. 10.1007/s10822-016-9948-6
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A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 29, doi. 10.1007/s10822-016-9956-6
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Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 87, doi. 10.1007/s10822-016-9957-5
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Absolute binding free energies for octa-acids and guests in SAMPL5.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 107, doi. 10.1007/s10822-016-9965-5
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Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 71, doi. 10.1007/s10822-016-9968-2
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The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 133, doi. 10.1007/s10822-016-9970-8
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On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.
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- Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 1, p. 47, doi. 10.1007/s10822-016-9980-6
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Collaborating to improve the use of free-energy and other quantitative methods in drug discovery.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 12, p. 1139, doi. 10.1007/s10822-016-9996-y
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Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1019, doi. 10.1007/s10822-016-9928-x
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Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 989, doi. 10.1007/s10822-016-9936-x
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The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous p K , and cyclohexane-water log D.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1035, doi. 10.1007/s10822-016-9939-7
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Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 977, doi. 10.1007/s10822-016-9958-4
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Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1059, doi. 10.1007/s10822-016-9950-z
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Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1079, doi. 10.1007/s10822-016-9951-y
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Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 927, doi. 10.1007/s10822-016-9954-8
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Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p K corrections.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1087, doi. 10.1007/s10822-016-9955-7
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Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1045, doi. 10.1007/s10822-016-9949-5
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Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1067, doi. 10.1007/s10822-016-9961-9
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Partition coefficients for the SAMPL5 challenge using transfer free energies.
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- Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 11, p. 1129, doi. 10.1007/s10822-016-9964-6
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