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Items: 35

1.

Evolutionary Switches Structural Transitions via Coarse-Grained Models.

Delfino F, Porozov Y, Stepanov E, Tamazian G, Tozzini V.

J Comput Biol. 2019 Nov 26. doi: 10.1089/cmb.2019.0338. [Epub ahead of print]

PMID:
31770035
2.

Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin.

Delfino F, Porozov Y, Stepanov E, Tamazian G, Tozzini V.

Front Mol Biosci. 2019 Oct 15;6:104. doi: 10.3389/fmolb.2019.00104. eCollection 2019.

3.

Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin.

Brancolini G, Lopez H, Corni S, Tozzini V.

Int J Mol Sci. 2019 Aug 8;20(16). pii: E3866. doi: 10.3390/ijms20163866.

4.

Building Minimalist Models for Functionalized Metal Nanoparticles.

Brancolini G, Tozzini V.

Front Mol Biosci. 2019 Jul 2;6:50. doi: 10.3389/fmolb.2019.00050. eCollection 2019. No abstract available.

5.

Intrinsic structural and electronic properties of the Buffer Layer on Silicon Carbide unraveled by Density Functional Theory.

Cavallucci T, Tozzini V.

Sci Rep. 2018 Aug 30;8(1):13097. doi: 10.1038/s41598-018-31490-7.

6.

Electronic properties of single-layer tungsten disulfide on epitaxial graphene on silicon carbide.

Forti S, Rossi A, Büch H, Cavallucci T, Bisio F, Sala A, Menteş TO, Locatelli A, Magnozzi M, Canepa M, Müller K, Link S, Starke U, Tozzini V, Coletti C.

Nanoscale. 2017 Nov 2;9(42):16412-16419. doi: 10.1039/c7nr05495e.

PMID:
29058741
7.

Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models.

Mereghetti P, Maccari G, Spampinato GL, Tozzini V.

J Phys Chem B. 2016 Aug 25;120(33):8571-9. doi: 10.1021/acs.jpcb.6b02555. Epub 2016 May 18.

PMID:
27150459
8.

2D materials. Graphene, related two-dimensional crystals, and hybrid systems for energy conversion and storage.

Bonaccorso F, Colombo L, Yu G, Stoller M, Tozzini V, Ferrari AC, Ruoff RS, Pellegrini V.

Science. 2015 Jan 2;347(6217):1246501. doi: 10.1126/science.1246501.

PMID:
25554791
9.

Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules.

Trovato F, Tozzini V.

Biophys J. 2014 Dec 2;107(11):2579-91. doi: 10.1016/j.bpj.2014.09.043. Epub 2014 Dec 2.

10.

A multi-scale-multi-stable model for the rhodopsin photocycle.

Tavanti F, Tozzini V.

Molecules. 2014 Sep 18;19(9):14961-78. doi: 10.3390/molecules190914961.

11.

Minimalist Model for the Dynamics of Helical Polypeptides: A Statistic-Based Parametrization.

Spampinato GL, Maccari G, Tozzini V.

J Chem Theory Comput. 2014 Sep 9;10(9):3885-95. doi: 10.1021/ct5004059. Epub 2014 Jul 31.

PMID:
26588532
12.

Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field.

Leonarski F, Trovato F, Tozzini V, Leś A, Trylska J.

J Chem Theory Comput. 2013 Nov 12;9(11):4874-89. doi: 10.1021/ct4005036. Epub 2013 Oct 21.

PMID:
26583407
13.

SecStAnT: secondary structure analysis tool for data selection, statistics and models building.

Maccari G, Spampinato GL, Tozzini V.

Bioinformatics. 2014 Mar 1;30(5):668-74. doi: 10.1093/bioinformatics/btt586. Epub 2013 Oct 15.

PMID:
24130306
14.

Prospects for hydrogen storage in graphene.

Tozzini V, Pellegrini V.

Phys Chem Chem Phys. 2013 Jan 7;15(1):80-9. doi: 10.1039/c2cp42538f. Epub 2012 Nov 19.

PMID:
23165421
15.

Minimalist models for proteins: a comparative analysis.

Tozzini V.

Q Rev Biophys. 2010 Aug;43(3):333-71. doi: 10.1017/S0033583510000132. Epub 2010 Aug 16. Review.

PMID:
20707940
16.

GCN5-dependent acetylation of HIV-1 integrase enhances viral integration.

Terreni M, Valentini P, Liverani V, Gutierrez MI, Di Primio C, Di Fenza A, Tozzini V, Allouch A, Albanese A, Giacca M, Cereseto A.

Retrovirology. 2010 Mar 12;7:18. doi: 10.1186/1742-4690-7-18.

17.

Multiscale modeling of proteins.

Tozzini V.

Acc Chem Res. 2010 Feb 16;43(2):220-30. doi: 10.1021/ar9001476.

PMID:
19785400
18.

Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition.

Di Fenza A, Rocchia W, Tozzini V.

Proteins. 2009 Sep;76(4):946-58. doi: 10.1002/prot.22399.

PMID:
19306343
19.

Raman study of chromophore states in photochromic fluorescent proteins.

Luin S, Voliani V, Lanza G, Bizzarri R, Amat P, Tozzini V, Serresi M, Beltram F.

J Am Chem Soc. 2009 Jan 14;131(1):96-103. doi: 10.1021/ja804504b.

PMID:
19061323
20.

Supercoiling and local denaturation of plasmids with a minimalist DNA model.

Trovato F, Tozzini V.

J Phys Chem B. 2008 Oct 23;112(42):13197-200. doi: 10.1021/jp807085d. Epub 2008 Sep 30.

PMID:
18826184
21.

Coarse-grained force field for the nucleosome from self-consistent multiscaling.

Voltz K, Trylska J, Tozzini V, Kurkal-Siebert V, Langowski J, Smith J.

J Comput Chem. 2008 Jul 15;29(9):1429-39. doi: 10.1002/jcc.20902.

PMID:
18270964
22.
23.

HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics.

Trylska J, Tozzini V, Chang CE, McCammon JA.

Biophys J. 2007 Jun 15;92(12):4179-87. Epub 2007 Mar 23.

24.

Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations.

Chang CE, Trylska J, Tozzini V, McCammon JA.

Chem Biol Drug Des. 2007 Jan;69(1):5-13.

PMID:
17313452
25.

Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.

Tozzini V, Trylska J, Chang CE, McCammon JA.

J Struct Biol. 2007 Mar;157(3):606-15. Epub 2006 Aug 23.

PMID:
17029846
26.

The chromophore of asFP595: a theoretical study.

Amat P, Granucci G, Buda F, Persico M, Tozzini V.

J Phys Chem B. 2006 May 11;110(18):9348-53.

PMID:
16671754
27.

The influence of macromolecular crowding on HIV-1 protease internal dynamics.

Minh DD, Chang CE, Trylska J, Tozzini V, McCammon JA.

J Am Chem Soc. 2006 May 10;128(18):6006-7.

28.

Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model.

Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA.

Biophys J. 2006 Jun 1;90(11):3880-5. Epub 2006 Mar 13.

29.
30.

Vibrational properties of DsRed model chromophores.

Tozzini V, Giannozzi P.

Chemphyschem. 2005 Sep 5;6(9):1786-8. No abstract available.

PMID:
16080222
31.

Exploring global motions and correlations in the ribosome.

Trylska J, Tozzini V, McCammon JA.

Biophys J. 2005 Sep;89(3):1455-63. Epub 2005 Jun 10.

32.

Coarse-grained models for proteins.

Tozzini V.

Curr Opin Struct Biol. 2005 Apr;15(2):144-50. Review.

PMID:
15837171
34.

Coherent dynamics of photoexcited green fluorescent proteins.

Cinelli RA, Tozzini V, Pellegrini V, Beltram F, Cerullo G, Zavelani-Rossi M, De Silvestri S, Tyagi M, Giacca M.

Phys Rev Lett. 2001 Apr 9;86(15):3439-42.

PMID:
11327990
35.

Spontaneous formation and stability of small GaP fullerenes

Tozzini V V, Buda F, Fasolino A.

Phys Rev Lett. 2000 Nov 20;85(21):4554-7.

PMID:
11082594

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