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16 papers
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
Toni Giorgino, Gianni De Fabritiis
Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to t…
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
Maciej Majewski, Adrià Pérez, Philipp Thölke +7
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships t…
A novel hotspot of gelsolin instability and aggregation propensity triggers a new mechanism of amyloidosis
Michela Bollati, Luisa Diomede, Toni Giorgino +14
The multidomain protein gelsolin (GSN) is composed of six homologous modules, sequentially named G1 to G6. Single point substitutions in this protein are responsible for AGel amylo…
Computational and Experimental Characterization of NF023, A Candidate Anticancer Compound Inhibiting cIAP2/TRAF2 Assembly
Federica Cossu, Luca Sorrentino, Elisa Fagnani +4
Protein-protein interactions are the basis of many important physiological processes and are currently promising, yet difficult, targets for drug discovery. In this context, inhibi…
TorchMD: A deep learning framework for molecular simulations
Stefan Doerr, Maciej Majewsk, Adrià Pérez +5
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved…
The structure of N184K amyloidogenic variant of gelsolin highlights the role of the H-bond network for protein stability and aggregation properties
Matteo de Rosa, Alberto Barbiroli, Francesco Bonì +8
Mutations in the gelsolin protein are responsible for a rare conformational disease known as AGel amyloidosis. Four of these mutations are hosted by the second domain of the protei…
High-resolution crystal structure of gelsolin domain 2 in complex with the physiological calcium ion
Michela Bollati, Emanuele Scalone, Francesco Bonì +4
The second domain of gelsolin (G2) hosts mutations responsible for a hereditary form of amyloidosis. The active form of gelsolin is Ca2+-bound; it is also a dynamic protein, hence…
Nanobody interaction unveils structure, dynamics and proteotoxicity of the Finnish-type amyloidogenic gelsolin variant
Toni Giorgino, Davide Mattioni, Amal Hassan +8
AGel amyloidosis, formerly known as familial amyloidosis of the Finnish-type, is caused by pathological aggregation of proteolytic fragments of plasma gelsolin. So far, four mutati…
Exploring the Role of Interdisciplinarity in Physics: Success, Talent and Luck
Alessandro Pluchino, Giulio Burgio, Andrea Rapisarda +4
Although interdisciplinarity is often touted as a necessity for modern research, the evidence on the relative impact of sectorial versus to interdisciplinary science is qualitative…
How to Differentiate Collective Variables in Free Energy Codes: Computer-Algebra Code Generation and Automatic Differentiation
Toni Giorgino
The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instan…
METAGUI 3: a graphical user interface for choosing the collective variables in molecular dynamics simulations
Toni Giorgino, Alessandro Laio, Alex Rodriguez
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis…
PLUMED-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts
Toni Giorgino
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take adv…
Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD
Toni Giorgino
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of bio…
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez, Fabian Paul, Toni Giorgino +2
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involv…
The APENEXT project
F. Bodin, P. Boucaud, N. Cabibbo +31
APENEXT is a new generation APE processor, optimized for LGT simulations. The project follows the basic ideas of previous APE machines and develops simple and cheap parallel system…
Status of APEmille
APE-Collaboration, :, A. Bartoloni +31
This paper presents the status of the APEmille project, which is essentially completed, as far as machine development and construction is concerned. Several large installations of…