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Journal articles on the topic 'Relative free energy calculations'

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

Song, Lin Frank, Tai-Sung Lee, Chun Zhu, Darrin M. York, and Kenneth M. Merz. "Using AMBER18 for Relative Free Energy Calculations." Journal of Chemical Information and Modeling 59, no. 7 (2019): 3128–35. http://dx.doi.org/10.1021/acs.jcim.9b00105.

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2

Liu, Shuai, Lingle Wang, and David L. Mobley. "Is Ring Breaking Feasible in Relative Binding Free Energy Calculations?" Journal of Chemical Information and Modeling 55, no. 4 (2015): 727–35. http://dx.doi.org/10.1021/acs.jcim.5b00057.

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3

Cappel, Daniel, Michelle Lynn Hall, Eelke B. Lenselink, et al. "Relative Binding Free Energy Calculations Applied to Protein Homology Models." Journal of Chemical Information and Modeling 56, no. 12 (2016): 2388–400. http://dx.doi.org/10.1021/acs.jcim.6b00362.

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4

Kim, Seonghoon, and Wonpil Im. "Charmm-Gui Ligand Binder for Relative Binding Free Energy Calculations." Biophysical Journal 116, no. 3 (2019): 291a. http://dx.doi.org/10.1016/j.bpj.2018.11.1572.

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5

Kaus, Joseph W., and J. Andrew McCammon. "Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations." Journal of Physical Chemistry B 119, no. 20 (2015): 6190–97. http://dx.doi.org/10.1021/acs.jpcb.5b02348.

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6

Ge, Yunhui, David F. Hahn, and David L. Mobley. "A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations." Journal of Chemical Information and Modeling 61, no. 3 (2021): 1048–52. http://dx.doi.org/10.1021/acs.jcim.0c01424.

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7

Dickson, Callum J., Viktor Hornak, and Jose S. Duca. "Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots." Journal of Chemical Information and Modeling 61, no. 12 (2021): 5923–30. http://dx.doi.org/10.1021/acs.jcim.1c01147.

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8

Nanda, Hirsh, Nandou Lu, and Thomas B. Woolf. "Using non-Gaussian density functional fits to improve relative free energy calculations." Journal of Chemical Physics 122, no. 13 (2005): 134110. http://dx.doi.org/10.1063/1.1877252.

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9

Klimovich, Pavel V., and David L. Mobley. "A Python tool to set up relative free energy calculations in GROMACS." Journal of Computer-Aided Molecular Design 29, no. 11 (2015): 1007–14. http://dx.doi.org/10.1007/s10822-015-9873-0.

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10

Saito, Minoru, and Akinori Sarai. "Free energy calculations for the relative binding affinity between DNA and ?-repressor." Proteins: Structure, Function, and Genetics 52, no. 2 (2003): 129–36. http://dx.doi.org/10.1002/prot.10333.

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11

Vilseck, Jonah Z., Julian Tirado-Rives, and William L. Jorgensen. "Determination of partial molar volumes from free energy perturbation theory." Physical Chemistry Chemical Physics 17, no. 13 (2015): 8407–15. http://dx.doi.org/10.1039/c4cp05304d.

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Free Energy Perturbation calculations are employed to determine free energies of solvation (ΔG<sub>solv</sub>) for benzene and benzene-derivatives at elevated pressures. Absolute and relative partial molar volumes are determined as the pressure derivative of ΔG<sub>solv</sub>.

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12

Mark, Alan E., Wilfred F. van Gunsteren, and Herman J. C. Berendsen. "Calculation of relative free energy via indirect pathways." Journal of Chemical Physics 94, no. 5 (1991): 3808–16. http://dx.doi.org/10.1063/1.459753.

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13

Cournia, Zoe, Bryce Allen, and Woody Sherman. "Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations." Journal of Chemical Information and Modeling 57, no. 12 (2017): 2911–37. http://dx.doi.org/10.1021/acs.jcim.7b00564.

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14

Rocklin, Gabriel J., David L. Mobley, and Ken A. Dill. "Separated topologies—A method for relative binding free energy calculations using orientational restraints." Journal of Chemical Physics 138, no. 8 (2013): 085104. http://dx.doi.org/10.1063/1.4792251.

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15

Wang, Cun Xin, Hai Yan Liu, Yun Yu Shi, and Fu Hua Huang. "Calculations of relative free energy surfaces in configuration space using an integration method." Chemical Physics Letters 179, no. 5-6 (1991): 475–78. http://dx.doi.org/10.1016/0009-2614(91)87089-t.

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16

Woolf, Thomas B. "Path corrected functionals of stochastic trajectories: towards relative free energy and reaction coordinate calculations." Chemical Physics Letters 289, no. 5-6 (1998): 433–41. http://dx.doi.org/10.1016/s0009-2614(98)00427-8.

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17

Raman, E. Prabhu, Thomas J. Paul, Ryan L. Hayes, and Charles L. Brooks. "Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics." Journal of Chemical Theory and Computation 16, no. 12 (2020): 7895–914. http://dx.doi.org/10.1021/acs.jctc.0c00830.

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18

Saito, Minoru, and Ryuji Tanimura. "Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations." Chemical Physics Letters 236, no. 1-2 (1995): 156–61. http://dx.doi.org/10.1016/0009-2614(95)00181-3.

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19

Zhang, Xia, and Yue Zeng. "Calculations of Henry's law constants for organic species using relative Gibbs free energy change." Fluid Phase Equilibria 376 (August 2014): 234–38. http://dx.doi.org/10.1016/j.fluid.2014.05.024.

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20

Yunyu, Shi, Zhao Huimin, and Wang Cunxin. "Relative binding free energy calculations of DNA to daunomycin and its 13-dihydro analogue." International Journal of Biological Macromolecules 15, no. 4 (1993): 247–51. http://dx.doi.org/10.1016/0141-8130(93)90045-n.

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21

Ries, Benjamin, Salomé Rieder, Clemens Rhiner, Philippe H. Hünenberger, and Sereina Riniker. "RestraintMaker: a graph-based approach to select distance restraints in free-energy calculations with dual topology." Journal of Computer-Aided Molecular Design 36, no. 3 (2022): 175–92. http://dx.doi.org/10.1007/s10822-022-00445-6.

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AbstractThe calculation of relative binding free energies (RBFE) involves the choice of the end-state/system representation, of a sampling approach, and of a free-energy estimator. System representations are usually termed “single topology” or “dual topology”. As the terminology is often used ambiguously in the literature, a systematic categorization of the system representations is proposed here. In the dual-topology approach, the molecules are simulated as separate molecules. Such an approach is relatively easy to automate for high-throughput RBFE calculations compared to the single-topology

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22

Azimi, Solmaz, Sheenam Khuttan, Joe Z. Wu, Rajat K. Pal, and Emilio Gallicchio. "Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method." Journal of Chemical Information and Modeling 62, no. 2 (2022): 309–23. http://dx.doi.org/10.1021/acs.jcim.1c01129.

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23

Zou, Junjie, Jian Yin, Lei Fang, et al. "Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations." Journal of Chemical Information and Modeling 60, no. 12 (2020): 5794–802. http://dx.doi.org/10.1021/acs.jcim.0c00679.

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24

Nuno Palma, P., Maria João Bonifácio, Ana Isabel Loureiro, and Patrício Soares-da-Silva. "Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations." Journal of Computational Chemistry 33, no. 9 (2012): 970–86. http://dx.doi.org/10.1002/jcc.22926.

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25

Ries, Benjamin, Karl Normak, R. Gregor Weiß, et al. "Relative free-energy calculations for scaffold hopping-type transformations with an automated RE-EDS sampling procedure." Journal of Computer-Aided Molecular Design 36, no. 2 (2022): 117–30. http://dx.doi.org/10.1007/s10822-021-00436-z.

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AbstractThe calculation of relative free-energy differences between different compounds plays an important role in drug design to identify potent binders for a given protein target. Most rigorous methods based on molecular dynamics simulations estimate the free-energy difference between pairs of ligands. Thus, the comparison of multiple ligands requires the construction of a “state graph”, in which the compounds are connected by alchemical transformations. The computational cost can be optimized by reducing the state graph to a minimal set of transformations. However, this may require individu

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26

Firaha, Dzmitry, Yifei Michelle Liu, Jacco van de Streek, et al. "Predicting crystal form stability under real-world conditions." Nature 623, no. 7986 (2023): 324–28. http://dx.doi.org/10.1038/s41586-023-06587-3.

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AbstractThe physicochemical properties of molecular crystals, such as solubility, stability, compactability, melting behaviour and bioavailability, depend on their crystal form1. In silico crystal form selection has recently come much closer to realization because of the development of accurate and affordable free-energy calculations2–4. Here we redefine the state of the art, primarily by improving the accuracy of free-energy calculations, constructing a reliable experimental benchmark for solid–solid free-energy differences, quantifying statistical errors for the computed free energies and pl

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27

Hirono, Shuichi, and Peter A. Kollman. "Relative binding free energy calculations of inhibitors to two mutants (Glu46— Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches." "Protein Engineering, Design and Selection" 4, no. 3 (1991): 233–43. http://dx.doi.org/10.1093/protein/4.3.233.

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28

Rustamov, Nassim, Asal Kasimova, Rashida Tursunkhodjaeva, and Mukaddas Tashmatova. "Calculation of the speed of movement of the car along the entire length of the path profile with different inclines of the sorting slide." E3S Web of Conferences 460 (2023): 06024. http://dx.doi.org/10.1051/e3sconf/202346006024.

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In the article, a formula derived on the basis of the kinetic energy change theorem for a non-free material point in a finite form is used to calculate the speed of movement of the car on various sections of the sorting slide. Examples of calculations show that in the intermediate section of the sorting slide to the dividing switch, the relative calculation error is 10.3%, in the section of the switching zone of the sorting slide of the second dividing switch – δv6s2 ≈ 9.0 %, in the section of the first sorting path – δv7 ≈ 16.1%.

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29

Fuller, Jonathan C., Richard M. Jackson та Michael R. Shirts. "Configurational Preferences of Arylamide α-Helix Mimetics via Alchemical Free Energy Calculations of Relative Binding Affinities". Journal of Physical Chemistry B 116, № 35 (2012): 10856–69. http://dx.doi.org/10.1021/jp209041x.

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30

Kaus, Joseph W., Edward Harder, Teng Lin, Robert Abel, J. Andrew McCammon, and Lingle Wang. "How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations." Journal of Chemical Theory and Computation 11, no. 6 (2015): 2670–79. http://dx.doi.org/10.1021/acs.jctc.5b00214.

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31

Al-Mazaideh, Ghassab. "A Study effect of Substituents X on Methylenecyclopentane and 1- Methylcyclopentene System." JORDANIAN JOURNAL OF ENGINEERING AND CHEMICAL INDUSTRIES (JJECI) 1, no. 1 (2018): 38–44. http://dx.doi.org/10.48103/jjeci142018.

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In this study, the geometry optimizations, orbital energies (HOMO-LUMO) and relative stabilities of methylene cyclopentane and 1-methylcyclopentene were investigated by DFT calculations. 1-methylcyclopentene was found to be more stable than methylene cyclopentane isomer with enthalpy value H=18.518 kJ/mol. Also, the effect of substituents X (F, OH, CH3, NH2, CN, NO2, CHO and CF3) also studied on the relative stabilities of these two tautomers. The results showed that the stability of both isomers is increased by all substitutes. Gibbs free energy calculations have been used to find the effect

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32

Fowler, Philip W., Shantenu Jha, and Peter V. Coveney. "Grid-based steered thermodynamic integration accelerates the calculation of binding free energies." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 363, no. 1833 (2005): 1999–2015. http://dx.doi.org/10.1098/rsta.2005.1625.

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The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differen

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33

Wan, Shunzhou, Peter V. Coveney, and Darren R. Flower. "Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson–Boltzmann and linear interaction energy approximations." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 363, no. 1833 (2005): 2037–53. http://dx.doi.org/10.1098/rsta.2005.1627.

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The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson–Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the

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34

Wan, Shunzhou, Andrew Potterton, Fouad S. Husseini, et al. "Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors." Interface Focus 10, no. 6 (2020): 20190128. http://dx.doi.org/10.1098/rsfs.2019.0128.

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We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A 1 and A 2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied. Relative binding free energies, calculated using TIES, accurately pr

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35

Miyamoto, Shuichi, and Peter A. Kollman. "Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches." Proteins: Structure, Function, and Genetics 16, no. 3 (1993): 226–45. http://dx.doi.org/10.1002/prot.340160303.

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36

Poon, H. C., S. Y. Tong, W. F. Chung, and M. S. Altman. "Low Energy Electron Diffraction Analysis of Ultrathin Ag Films on W(110)." Surface Review and Letters 05, no. 06 (1998): 1143–49. http://dx.doi.org/10.1142/s0218625x9800147x.

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We have measured low energy electron diffraction data for clean W(110), ultrathin and thick Ag films on W(110). The data are analyzed by full dynamical multiple scattering calculations to determine the structure of the Ag-film/W(110) system. The multiple scattering calculation takes into account the incommensurate scattering between the non-pseudomorphic Ag films and the W(110) substrate. We have examined the effect of dynamical inputs used in the calculation. We find that for normally incident electrons, the surface barrier at the vacuum-film interface and the inelastic damping modify mainly

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37

Bhati, Agastya P., and Peter V. Coveney. "Large Scale Study of Ligand–Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols." Journal of Chemical Theory and Computation 18, no. 4 (2022): 2687–702. http://dx.doi.org/10.1021/acs.jctc.1c01288.

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38

Pimenta, A. C., J. M. Martins, R. Fernandes, and I. S. Moreira. "Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations." Journal of Chemical Information and Modeling 53, no. 10 (2013): 2648–58. http://dx.doi.org/10.1021/ci400269d.

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39

Bubenchikov, Mikhail A., Dmitriy V. Mamontov, and Anna S. Chelnokova. "Relative dynamics of shells of a bifullerene complex." Vestnik Tomskogo gosudarstvennogo universiteta. Matematika i mekhanika, no. 77 (2022): 54–67. http://dx.doi.org/10.17223/19988621/77/5.

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In this work, mathematical modeling of relative dynamics of a bifullerene complex is carried out on the assumption that the inner shell does not form covalent bonds with an outer carbon skeleton. This fact enables free angular movements of the inner shell. In particular, the directed rotation of the inner fullerene can be provided. This, in turn, allows for accumulating of a significant fraction of kinetic energy at internal degrees of freedom of the complex under consideration. In this case, the direction of rotations is not related to temperature; the outer shell of the complex restrains the

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40

Reddy, M. Rami, and Mark D. Erion. "Calculation of relative solvation free energy differences by thermodynamic perturbation method: Dependence of free energy results on simulation length." Journal of Computational Chemistry 20, no. 10 (1999): 1018–27. http://dx.doi.org/10.1002/(sici)1096-987x(19990730)20:10<1018::aid-jcc4>3.0.co;2-b.

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41

M, Sailendra, Sibbala S, Tripuramallu S, Kasula S, and Raj S. "Design of new Rivastigmine analogs based on Molecular Docking and Binding Free Energy calculations." International Journal of Drug Design and Discovery 3, no. 3 (2025): 869–77. https://doi.org/10.37285/ijddd.3.3.6.

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Alzheimer’s disease (AD) is a relative lack of brain chemical neurotransmitter, Acetylcholine. Dementia is a progressive, degenerative brain disease affecting memory, thinking and behavior due to increase in the accumulation of specific protein, beta-amyloid protein in the brain that leads to nerve cell death. Acetyl cholinesterase (Ach E) is an essential enzyme for metabolism of acetylcholine. The cholinesterase inhibitors, like rivastigmine block the breakdown of acetylcholine. The present paper describes the molecular docking studies of novel drug rivastigmine which inhibits the activity of

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42

Reddy, M. Rami, U. C. Singh, and Mark D. Erion. "Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies." Journal of Computational Chemistry 28, no. 2 (2006): 491–94. http://dx.doi.org/10.1002/jcc.20510.

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43

Yuan, Chengwu, and Gary A. Pope. "A New Method To Model Relative Permeability in Compositional Simulators To Avoid Discontinuous Changes Caused by Phase-Identification Problems." SPE Journal 17, no. 04 (2012): 1221–30. http://dx.doi.org/10.2118/142093-pa.

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Summary Simple methods, such as the use of density during compositional simulations, often fail to identify the phases correctly, and this can cause discontinuities in the computed relative permeability values. The results are then physically incorrect. Furthermore, numerical simulators often slow down or even stop because of discontinuities. There are many important applications in which the phase behavior can be single phase, gas/liquid, liquid/liquid, gas/ liquid/liquid, or gas/liquid/solid at different times in different gridblocks. Assigning physically correct phase identities during a co

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44

Cappel, Daniel, Jean-Christophe Mozziconacci, Tatjana Braun, and Thomas Steinbrecher. "Performance of Relative Binding Free Energy Calculations on an Automatically Generated Dataset of Halogen–Deshalogen Matched Molecular Pairs." Journal of Chemical Information and Modeling 61, no. 7 (2021): 3421–30. http://dx.doi.org/10.1021/acs.jcim.1c00290.

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45

Clark, Anthony J., Tatyana Gindin, Baoshan Zhang, et al. "Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1." Journal of Molecular Biology 429, no. 7 (2017): 930–47. http://dx.doi.org/10.1016/j.jmb.2016.11.021.

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46

Kuyper, Lee F., Robert N. Hunter, and David Ashton. "Free energy calculations on the relative solvation free energies of benzene, anisole, and 1,2,3-trimethoxybenzene: theoretical and experimental analysis of aromatic methoxy solvation." Journal of Physical Chemistry 95, no. 17 (1991): 6661–66. http://dx.doi.org/10.1021/j100170a052.

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47

Meng, Qingxi, Peiying Su, Fen Wang, and Shuhua Zhu. "Substituent effect and ligand exchange control the reactivity in ruthenium(II)-catalyzed hydroacylation of isoprenes and aldehydes ‖ A DFT study." Journal of Theoretical and Computational Chemistry 15, no. 03 (2016): 1650019. http://dx.doi.org/10.1142/s021963361650019x.

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Density functional theory (DFT) was used to investigate the reaction mechanisms of ruthenium(II)-catalyzed hydroacylation of isoprene with benzaldehyde, and o-methoxyl, m-methoxyl and p-methoxyl benzaldehyde. All intermediates and transition states were entirely optimized at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Ru). The results demonstrated that the hydroacylation had two different catalytic cycles (path I and II), path II was more favorable than path I. Ru(II)-catalyzed hydroacylation began from the first catalytic cycle, and the nucleophilic reaction was the rate-determining step. The

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48

Hahn, David F., Gerhard König та Philippe H. Hünenberger. "Overcoming Orthogonal Barriers in Alchemical Free Energy Calculations: On the Relative Merits of λ-Variations, λ-Extrapolations, and Biasing". Journal of Chemical Theory and Computation 16, № 3 (2020): 1630–45. http://dx.doi.org/10.1021/acs.jctc.9b00853.

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49

Thomas, Bert E. IV, and Peter A. Kollman. "Free Energy Perturbation Calculations of the Relative Binding Affinities of an 8-Subunit Cavitand for Alkali Ions in Methanol." Journal of the American Chemical Society 116, no. 8 (1994): 3449–52. http://dx.doi.org/10.1021/ja00087a034.

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50

König, Gerhard, and Bernard R. Brooks. "Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations." Journal of Computer-Aided Molecular Design 26, no. 5 (2011): 543–50. http://dx.doi.org/10.1007/s10822-011-9525-y.

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