Zobrazeno 1 - 10
of 68
pro vyhledávání: '"Menichetti, Roberto"'
Allosteric regulation is a widespread strategy employed by several proteins to transduce chemical signals and perform biological functions. Metal sensor proteins are exemplary in this respect, e.g., in that they selectively bind and unbind DNA depend
Externí odkaz:
http://arxiv.org/abs/2409.03584
The analysis of complex systems such as neural networks is made particularly difficult by the overwhelming number of their interacting components. In the absence of prior knowledge, identifying a small but informative subset of network nodes on which
Externí odkaz:
http://arxiv.org/abs/2405.14531
Autor:
Giulini, Marco, Fiorentini, Raffaele, Tubiana, Luca, Potestio, Raffaello, Menichetti, Roberto
Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules. The development of low-resolution models takes the moves from the redu
Externí odkaz:
http://arxiv.org/abs/2403.08097
Coarse-grained (CG) models are simplified representations of soft matter systems that are commonly employed to overcome size and time limitations in computational studies. Many approaches have been developed to construct and parametrise such effectiv
Externí odkaz:
http://arxiv.org/abs/2202.10756
Simplified representations of macromolecules help in rationalising and understanding the outcome of atomistic simulations, and serve to the construction of effective, coarse-grained models. The number and distribution of coarse-grained sites bears a
Externí odkaz:
http://arxiv.org/abs/2106.08223
Autor:
Errica, Federico, Giulini, Marco, Bacciu, Davide, Menichetti, Roberto, Micheli, Alessio, Potestio, Raffaello
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD trajectories ind
Externí odkaz:
http://arxiv.org/abs/2007.08658
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out on the ba
Externí odkaz:
http://arxiv.org/abs/2004.03988
Publikováno v:
Phys. Rev. E 100, 033302 (2019)
The size of chemical compound space is too large to be probed exhaustively. This leads high-throughput protocols to drastically subsample and results in sparse and non-uniform datasets. Rather than arbitrarily selecting compounds, we systematically e
Externí odkaz:
http://arxiv.org/abs/1905.01897
Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive structure
Externí odkaz:
http://arxiv.org/abs/1805.10158
Publikováno v:
Biochemical and Biophysical Research Communications (2017)
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently proposed by Berea
Externí odkaz:
http://arxiv.org/abs/1710.02291