Amadei A - Search Results

1

Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis.

Nardi AN, Olivieri A, Amadei A, Salvio R, D'Abramo M. Nardi AN, et al. Among authors: amadei a. Molecules. 2023 Feb 24;28(5):2152. doi: 10.3390/molecules28052152. Molecules. 2023. PMID: 36903398 Free PMC article.

2

Essential dynamics of proteins.

Amadei A, Linssen AB, Berendsen HJ. Amadei A, et al. Proteins. 1993 Dec;17(4):412-25. doi: 10.1002/prot.340170408. Proteins. 1993. PMID: 8108382

3

Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.

de Groot BL, Hayward S, van Aalten DM, Amadei A, Berendsen HJ. de Groot BL, et al. Among authors: amadei a. Proteins. 1998 May 1;31(2):116-27. doi: 10.1002/(sici)1097-0134(19980501)31:2<116::aid-prot2>3.0.co;2-k. Proteins. 1998. PMID: 9593186

4

Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding.

Daidone I, Ulmschneider MB, Di Nola A, Amadei A, Smith JC. Daidone I, et al. Among authors: amadei a. Proc Natl Acad Sci U S A. 2007 Sep 25;104(39):15230-5. doi: 10.1073/pnas.0701401104. Epub 2007 Sep 19. Proc Natl Acad Sci U S A. 2007. PMID: 17881585 Free PMC article.

5

Essential dynamics of the cellular retinol-binding protein--evidence for ligand-induced conformational changes.

van Aalten DM, Findlay JB, Amadei A, Berendsen HJ. van Aalten DM, et al. Among authors: amadei a. Protein Eng. 1995 Nov;8(11):1129-35. doi: 10.1093/protein/8.11.1129. Protein Eng. 1995. PMID: 8819978

6

The consistency of large concerted motions in proteins in molecular dynamics simulations.

de Groot BL, van Aalten DM, Amadei A, Berendsen HJ. de Groot BL, et al. Among authors: amadei a. Biophys J. 1996 Oct;71(4):1707-13. doi: 10.1016/S0006-3495(96)79372-4. Biophys J. 1996. PMID: 8889148 Free PMC article.

7

Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin.

de Groot BL, Amadei A, van Aalten DM, Berendsen HJ. de Groot BL, et al. Among authors: amadei a. J Biomol Struct Dyn. 1996 Apr;13(5):741-51. doi: 10.1080/07391102.1996.10508888. J Biomol Struct Dyn. 1996. PMID: 8723770

8

A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy.

Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. Davis CM, et al. Among authors: amadei a. Chem Sci. 2018 Oct 3;9(48):9002-9011. doi: 10.1039/c8sc03786h. eCollection 2018 Dec 28. Chem Sci. 2018. PMID: 30647892 Free PMC article.

9

Regulation of the function of eukaryotic DNA topoisomerase I: analysis of the binding step and of the catalytic constants of topoisomerization as a function of DNA topology.

Caserta M, Amadei A, Camilloni G, Di Mauro E. Caserta M, et al. Among authors: amadei a. Biochemistry. 1990 Sep 4;29(35):8152-7. doi: 10.1021/bi00487a024. Biochemistry. 1990. PMID: 2175650

10

An extended sampling of the configurational space of HPr from E. coli.

de Groot BL, Amadei A, Scheek RM, van Nuland NA, Berendsen HJ. de Groot BL, et al. Among authors: amadei a. Proteins. 1996 Nov;26(3):314-22. doi: 10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D. Proteins. 1996. PMID: 8953652

Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. ...We find a cluster of conformations that is an order of magnitude larger than that found for a usual MD simulation of comparable length. ...

Recently, we developed a method (Amadei et al., J. Biomol. Str. Dyn. 13: 615-626; de Groot et al., J. ...We find a clus …

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