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61.
An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ~82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n=3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions. 相似文献
62.
R. Meurice J. Cartiaux W. H. Ross K. C. Beeson L. M. White A. R. Merz K. Scharrer H. Schorstein R. Brill M. Popp H. Westerhoff H. Terlet A. Briau F. Kaminski F. Erdheim K. D. Jacob L. F. Rader Jr. T. H. Tremearne J. Contzen W. Sauerlandt Commission technique permanente de la Répression des Fraudes 《Analytical and bioanalytical chemistry》1941,122(5-6):230-237
63.
F. Nydahl W. D. Troadwell W. H. Ross A. R. Merz K. D. Jacob und P. Krumholz 《Fresenius' Journal of Analytical Chemistry》1943,126(9):342-347
Ohne Zusammenfassung 相似文献
64.
K. Merz 《Commentarii Mathematici Helvetici》1940,13(1):49-53
Ohne Zusammenfassung 相似文献
65.
F. Selmi und Gustav Merz 《Fresenius' Journal of Analytical Chemistry》1876,15(1):461-462
Ohne Zusammenfassung 相似文献
66.
67.
G. Merz 《Fresenius' Journal of Analytical Chemistry》1868,7(1):275-276
Ohne Zusammenfassung 相似文献
68.
K. Merz 《Commentarii Mathematici Helvetici》1935,8(1):379-381
Ohne Zusammenfassung 相似文献
69.
Nupur Bansal Zheng Zheng David S. Cerutti Kenneth M. Merz 《Journal of computer-aided molecular design》2017,31(1):47-60
We review our performance in the SAMPL5 challenge for predicting host–guest binding affinities using the movable type (MT) method. The challenge included three hosts, acyclic Cucurbit[2]uril and two octa-acids with and without methylation at the entrance to their binding cavities. Each host was associated with 6–10 guest molecules. The MT method extrapolates local energy landscapes around particular molecular states and estimates the free energy by Monte Carlo integration over these landscapes. Two blind submissions pairing MT with variants of the KECSA potential function yielded mean unsigned errors of 1.26 and 1.53 kcal/mol for the non-methylated octa-acid, 2.83 and 3.06 kcal/mol for the methylated octa-acid, and 2.77 and 3.36 kcal/mol for Cucurbit[2]uril host. While our results are in reasonable agreement with experiment, we focused on particular cases in which our estimates gave incorrect results, particularly with regard to association between the octa-acids and an adamantane derivative. Working on the hypothesis that differential solvation effects play a role in effecting computed binding affinities for the parent octa-acid and the methylated octa-acid and that the ligands bind inside the pockets (rather than on the surface) we devised a new solvent accessible surface area term to better quantify solvation energy contributions in MT based studies. To further explore this issue a, molecular dynamics potential of mean force (PMF) study indicates that, as found by our docking calculations, the stable binding mode for this ligand is inside (rather than surface bound) the octa-acid cavity whether the entrance is methylated or not. The PMF studies also obtained the correct order for the methylation-induced change in binding affinities and associated the difference, to a large extent to differential solvation effects. Overall, the SAMPL5 challenge yielded in improvements our solvation modeling and also demonstrated the need for thorough validation of input data integrity prior to any computational analysis. 相似文献
70.