Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1998 1
2000 1
2001 1
2002 1
2005 1
2008 1
2014 1
2017 1
2020 2
2022 1
2024 1

Text availability

Article attribute

Article type

Publication date

Search Results

12 results

Results by year

Filters applied: . Clear all
Page 1
Polymer Folding Simulations from Hi-C Data.
Zhan Y, Giorgetti L, Tiana G. Zhan Y, et al. Methods Mol Biol. 2022;2301:259-265. doi: 10.1007/978-1-0716-1390-0_13. Methods Mol Biol. 2022. PMID: 34415540
In the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to the principle of maximum entropy to build a polymeric model based on the Hi-C data of the specific system one wants to study. The interactio …
In the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to …
MicroRNA-222 Regulates Melanoma Plasticity.
Lionetti MC, Cola F, Chepizhko O, Fumagalli MR, Font-Clos F, Ravasio R, Minucci S, Canzano P, Camera M, Tiana G, Zapperi S, Porta CAM. Lionetti MC, et al. J Clin Med. 2020 Aug 8;9(8):2573. doi: 10.3390/jcm9082573. J Clin Med. 2020. PMID: 32784455 Free PMC article.
Structure of the space of folding protein sequences defined by large language models.
Zambon A, Zecchina R, Tiana G. Zambon A, et al. Phys Biol. 2024 Jan 31;21(2). doi: 10.1088/1478-3975/ad205c. Phys Biol. 2024. PMID: 38237200 Free article.
Our findings indicate that these specialized algorithms can identify valleys with higher entropy compared to those found using traditional methods such as Monte Carlo Markov Chains. In a proof-of-concept case, we find that these highly entropic minima exhibit significant s …
Our findings indicate that these specialized algorithms can identify valleys with higher entropy compared to those found using traditional m …
Metal-organic frameworks as kinetic modulators for branched selectivity in hydroformylation.
Bauer G, Ongari D, Tiana D, Gäumann P, Rohrbach T, Pareras G, Tarik M, Smit B, Ranocchiari M. Bauer G, et al. Nat Commun. 2020 Feb 26;11(1):1059. doi: 10.1038/s41467-020-14828-6. Nat Commun. 2020. PMID: 32103008 Free PMC article.
This finding has a big potential in the production of aldehydes for the fine chemical industry. Monte Carlo and density functional theory simulations combined with kinetic models show that the micropores of MOFs with UMCM-1 and MOF-74 topologies increase the olefins densit …
This finding has a big potential in the production of aldehydes for the fine chemical industry. Monte Carlo and density functional th …
Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm.
Marini F, Camilloni C, Provasi D, Broglia RA, Tiana G. Marini F, et al. Gene. 2008 Oct 1;422(1-2):37-40. doi: 10.1016/j.gene.2008.06.003. Epub 2008 Jun 6. Gene. 2008. PMID: 18593595
Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing unders …
Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has p …
How likely are oscillations in a genetic feedback loop with delay?
Cola F, Marchetti F, Tiana G. Cola F, et al. Eur Phys J E Soft Matter. 2017 Aug;40(8):74. doi: 10.1140/epje/i2017-11563-y. Epub 2017 Aug 23. Eur Phys J E Soft Matter. 2017. PMID: 28828601 Free article.
We have developed an efficient sampling scheme of the parameter space, based on a Monte Carlo algorithm, and applied it to a two-node system with delay, characterised by a 8-dimension parameter space. ...
We have developed an efficient sampling scheme of the parameter space, based on a Monte Carlo algorithm, and applied it to a two-node …
Folding and aggregation of designed proteins.
Broglia RA, Tiana G, Pasquali S, Roman HE, Vigezzi E. Broglia RA, et al. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):12930-3. doi: 10.1073/pnas.95.22.12930. Proc Natl Acad Sci U S A. 1998. PMID: 9789017 Free PMC article.
Protein aggregation is studied by following the simultaneous folding of two designed identical 20-letter amino acid chains within the framework of a lattice model and using Monte Carlo simulations. It is found that protein aggregation is determined by elementary structures …
Protein aggregation is studied by following the simultaneous folding of two designed identical 20-letter amino acid chains within the framew …
Design and folding of dimeric proteins.
Tiana G, Broglia RA. Tiana G, et al. Proteins. 2002 Oct 1;49(1):82-94. doi: 10.1002/prot.10196. Proteins. 2002. PMID: 12211018
Dimerization is studied by following the evolution of two identical 20-letter amino acid chains within the framework of a lattice model and using Monte Carlo simulations. It is found that when design (evolution pressure) selects few, strongly interacting (conserved) amino …
Dimerization is studied by following the evolution of two identical 20-letter amino acid chains within the framework of a lattice model and …
Design of HIV-1-PR inhibitors that do not create resistance: blocking the folding of single monomers.
Broglia RA, Tiana G, Sutto L, Provasi D, Simona F. Broglia RA, et al. Protein Sci. 2005 Oct;14(10):2668-81. doi: 10.1110/ps.051670905. Protein Sci. 2005. PMID: 16195553 Free PMC article.
Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV-1-PR that successfully avoid the action of p-LES imply the destabilization of one or more LES and thus should lead to protein denaturation. Making use of Mon …
Aside from being specific and efficient, these inhibitors are expected not to induce resistance; in fact, mutations in HIV-1-PR that success …
Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale.
Capelli R, Paissoni C, Sormanni P, Tiana G. Capelli R, et al. J Chem Phys. 2014 May 21;140(19):195101. doi: 10.1063/1.4876219. J Chem Phys. 2014. PMID: 24852563
The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that they are expressible as thermal averages of some conformational properties. ...
The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that …
12 results