Roadmap on methods and software for electronic structure based simulations in chemistry and materials, Volker Blum et al., Electron. Struct. 6, 042501
Locuaz: an in silico platform for protein binders optimization, GP Barletta, R Tandiana, M Soler, S Fortuna, W Rocchia, Bioinformatics 40 (8), btae492 2024
Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions, R Tandiana, GP Barletta, MA Soler, S Fortuna, W Rocchia, Journal of Chemical Theory and Computation 20 (6), 2630-2642 2024
Assessing nanobody interaction with SARS-CoV-2 Nsp9, G Esposito, Y Hunashal, M Percipalle, F Fogolari, T Venit, A Leonchiks, ..., Plos one 19 (5), e0303839 2024,
Statistical accuracy of molecular dynamics-based methods for sampling conformational ensembles of disordered proteins, A Bastida, J Zuniga, F Fogolari, MA Soler, Physical Chemistry Chemical Physics 2024,
The kth nearest neighbor method for estimation of entropy changes from molecular ensembles, F Fogolari, R Borelli, A Dovier, G Esposito, Wiley Interdisciplinary Reviews: Computational Molecular Science 14 (1), e1691 2024,
Roadmap on methods and software for electronic structure based simulations in chemistry and materials, V Blum, R Asahi, J Autschbach, C Bannwarth, G Bihlmayer, S Blügel, ..., Electronic Structure 2024,
Reactive natural deep eutectic solvents increase selectivity and efficiency of lipase catalyzed esterification of carbohydrate polyols, AR Buzatu, MA Soler, S Fortuna, O Ozkilinc, DM Dreavă, I Bîtcan, ..., Catalysis Today 426, 114373 2024,
Quantum ESPRESSO towards performance portability: GPU offload with OpenMP, FF Ruffino, L Bellentani, G Rossi, F Affinito, S Baroni, O Baseggio, ..., Procedia Computer Science 240, 52-60,
Lipase-catalysed esterification in a reactive natural deep eutectic solvent leads to lauroylcholine chloride rather than glucose ester, AR Buzatu, MA Soler, O Ozkilinc, S Fortuna, DM Dreavă, I Bîtcan, ..., Reaction Chemistry & Engineering 9, 2623 - 2634 (2024,)
2023
Quantum ESPRESSO: one further step towards the exascale, I. Carnimeo, F. Affinito, S. Baroni, O. Baseggio, L. Bellentani, R. Bertossa, P. Delugas, F. Ferrari Ruffino, S. Orlandini, F. Spiga, and P. Giannozzi, J. Chem. Theory Comput. (2023) (online at https://pubs.acs.org/doi/10.1021/acs.jctc.3c00249 )
Roadmap on Electronic Structure Codes in the Exascale Era, V Gavini, D Perez, X Gonze, M Giantomassi, M Torrent, L E Ratcliff, W Dawson, L Genovese, D R Bowler, T Miyazaki, A Nakata, L Truflandier, T D Kühne, C Plessl, R Schade, O Schütt, S Das, P Motamarri, A Gulans, A Buccheri, C Draxl, V Blum, M Rossi, S Kokott, M Scheffler, R M Richard, T L Windus, K-H Liou, M Dogan, J R Chelikowsky, F Gygi, J M Herbert, S Baroni, P Delugas, P Giannozzi, P Suryanarayana, Q Xu, J E Pask, M Govoni, V W-Z Yu, G Galli, Modelling and Simulation in Materials Science and Engineering 31, 06331 (2023)
Molecular electrostatics and pKa shifts calculations with the Generalized Born model. A tutorial through examples with Bluues2, M. A. Soler, O. Ozkilinc, Y. Hunashal, P. Giannozzi, G. Esposito and F. Fogolari , Comput. Phys. Commun. 287, 108716 (2023)
Replica-exchange optimization of antibody fragments, MA Soler, N Minovski, W Rocchia, S Fortuna, Computational Biology and Chemistry 103, 107819 2023
Description of conformational ensembles of disordered proteins by residue-local probabilities, A Bastida, J Zúñiga, B Miguel, MA Soler, Physical Chemistry Chemical Physics 25 (15), 10512-10524 2023
Exploring the role of cyclodextrins as a cholesterol scavenger: A molecular dynamics investigation of conformational changes and thermodynamics, M Ganjali Koli, F Fogolari, Scientific Reports 13 (1), 21765 2023
A comparison of mutual information, linear models and deep learning networks for protein secondary structure prediction, SSM Mahmoud, B Portelli, G D'Agostino, G Pollastri, G Serra, F Fogolari, Current Bioinformatics 18 (8), 631-646 2023
Novel IGFALS mutations with predicted pathogenetic effects by the analysis of AlphaFold structure, A Franzoni, F Baldan, N Passon, C Mio, D Driul, P Cogo, F Fogolari, ..., Endocrine 79 (2), 292-295 2023
2022
Mechanism and thermodynamics of adsorption of diclofenac on graphene-based nanomaterials, D Veclani, M Tolazzi, F Fogolari, A Melchior, Journal of Environmental Chemical Engineering 10 (6), 108789 (2022)
Novel IGFALS mutations with predicted pathogenetic effects by the analysis of AlphaFold structure, A Franzoni, F Baldan, N Passon, C Mio, D Driul, P Cogo, F Fogolari, Endocrine, 1-4 (2022)
Data Structures and Algorithms for k-th Nearest Neighbours Conformational Entropy Estimation, R Borelli, A Dovier, F Fogolari, Biophysica 2 (4), 340-352 (2022)
Biallelic ATOH1 gene variant in siblings with pontocerebellar hypoplasia, developmental delay, and hearing loss, T Višnjar, A Maver, K Writzl, O Maloku, G Bergant, H Jaklič, D Neubauer, F Fogolari , N P Meglič, B Peterlin, Neurology Genetics 8 (3), 1 (2022)
A novel de novo missense NIPA1 mutation causing hereditary spastic paraplegia, D Fabbro, C Mio, F Fogolari, G Damante, EUROPEAN JOURNAL OF HUMAN GENETICS 30 (SUPPL 1), 314-314 (2022)
The corona of protein–gold nanoparticle systems: the role of ionic strength, C Cantarutti, Y Hunashal, C La Rosa, M Condorelli, S Giorgetti, V Bellotti, F Fogolari, D Esposito, Physical Chemistry Chemical Physics 24 (3), 1630-1637
Engineering of metal-MoS2 contacts to overcome Fermi level pinning, P. Khakbaz, F. Driussi, P. Giannozzi, A. Gambi, D. Esseni, Solid-State Electronics 194, 108378 (2022).
Antibody Affinity Maturation Using Computational Methods: From an Initial Hit to Small-Scale Expression of Optimized Binders, B Medagli, MA Soler, R De Zorzi, S Fortuna, Computer-Aided Antibody Design, 333-359 2022
A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease, E Calì, SJ Lin, C Rocca, Y Sahin, A Al Shamsi, S El Chehadeh, ..., Genetics in Medicine 24 (10), 2194-2203 2022
Genotype–phenotype correlations and disease mechanisms in PEX13-related Zellweger spectrum disorders, P Borgia, S Baldassari, N Pedemonte, E Alkhunaizi, G D’Onofrio, ..., Orphanet Journal of Rare Diseases 17 (1), 286 2022
Antibody-antigen binding interface analysis in the big data era, PBPS Reis, GP Barletta, L Gagliardi, S Fortuna, MA Soler, W Rocchia, Frontiers in Molecular Biosciences 9, 945808 2022
2021
Simulation study of Fermi level depinning in metal-MoS2 contacts, P Khakbaz, F Driussi, P Giannozzi, A Gambi, D Esseni, Solid-State Electronics 184, 108039 (2021)
Measuring Shared Electrons in Extended Molecular Systems: Covalent Bonds from Plane-Wave Representation of Wave Function, G La Penna, D Tiana, P Giannozzi, Molecules 26 (13), 4044 (2021)
NMR‐Based Analysis of Nanobodies to SARS‐CoV‐2 Nsp9 Reveals a Possible Antiviral Strategy Against COVID‐19, G Esposito, Y Hunashal, M Percipalle, T Venit, MM Dieng, F Fogolari, ..., Advanced Biology 5 (12), 2101113 2021
A novel de novo NIPA1 missense mutation associated to hereditary spastic paraplegia, D Fabbro, C Mio, F Fogolari, G Damante, Journal of Human Genetics 66 (12), 1177-1180 2021
A novel de novo HDAC8 missense mutation causing Cornelia de Lange syndrome, C Mio, N Passon, F Fogolari, C Cesario, A Novelli, C Pittini, G Damante, Molecular Genetics & Genomic Medicine 9 (9), e1612 2021
Topologically non-trivial metal-organic assemblies inhibit β2-microglobulin amyloidogenesis, T Prakasam, Y Hunashal, C Cantarutti, S Giorgetti, G Faravelli, V Mondani, ..., Cell Reports Physical Science 2 (7) 2021
Optimal relabeling of water molecules and single-molecule entropy estimation, F Fogolari, G Esposito, Biophysica 1 (3), 279-296 2021
Structure of nanobody Nb23, M Percipalle, Y Hunashal, J Steyaert, F Fogolari, G Esposito, Molecules 26 (12), 3567 2021
Case Report: Novel Compound Heterozygous RNASEH2B Mutations Cause Aicardi–Goutières Syndrome, J Garau, S Masnada, F Dragoni, D Sproviero, F Fogolari, S Gagliardi, ..., Frontiers in Immunology 12, 672952 2021
Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the kth Nearest Neighbor Method, F Fogolari, G Esposito, B Tidor, Journal of chemical theory and computation 17 (5), 3039-3051 2021
Enhanced molecular dynamics method to efficiently increase the discrimination capability of computational protein–protein docking, N Scafuri, MA Soler, A Spitaleri, W Rocchia, Journal of Chemical Theory and Computation 17 (11), 7271-7280 2021
Mahmoud S. S. M., Esposito G., Serra G., Fogolari F. , Generalized Born radii computation using linear models and neural networks, Bioinformatics, 36, 1757-1764 (2020)
Mio C., Fogolari F., Pezzoli L., D’Elia A.V., Iascone M., Damante G., Missense NR2F1 variant in monozygotic twins affected with the Bosch–Boonstra–Schaaf optic atrophy syndrome, Molecular Genetics & Genomic Medicine, e1278 (2020)
Hunashal Y., Cantarutti C., Giorgetti S., Marchese L., Fogolari F., Esposito G., Insights into a protein-nanoparticle system by paramagnetic perturbation NMR spectroscopy, Molecules 25 (21) 5187 (2020).
Unit cell restricted Bloch functions basis for first-principle transport models: Theory and application, M. G. Pala, P. Giannozzi, D. Esseni, Phys. Rev. B102, 045410 (2020). DOI: https://doi.org/10.1103/PhysRevB.102.045410
Quantum ESPRESSO toward the exascale, P. Giannozzi, O. Baseggio, P. Bonfa’, D. Brunato, R. Car, I. Carnimeo, C. Cavazzoni, S. de Gironcoli, P. Delugas, F. Ferrari Ruffino, A. Ferretti, N. Marzari, I. Timrov, A. Urru, S. Baroni, J. Chem. Phys. 152, 154105 (2020). DOI: https://doi.org/10.1063/5.0005082
Investigation of structural, electronic and magnetic properties of breathing Metal-Organic Framework MIL-47 (Mn): a first principles approach, M. Hosseini, D.E.P. Vanpoucke, P. Giannozzi, M. Berahmanf, N. Hadipour, RSC Adv. 10, 4786-4794 (2020). DOI : https://doi.org/10.1039/C9RA09196C
2019
Giorgio V., Fogolari. F, Lippe G., Bernardi P., OSCP subunit of mitochondrial ATP synthase: Role in regulation of enzyme function and of its transition to a pore, British Journal of Pharmacology, 176, 4247-4257, 2019
Cantarutti C., Fogolari F., Hunashal Y., Ferrara V., Caragnano A., Beltrami A.P., Livi U., Sponga S., Esposito G., Assessing the Effect of Preservation in Heart Transplant Protocol: Cold Ischemia Versus Normothermic Perfusion, Biomarkers and Applications, 03:139, 2019
Improved understanding of metal-graphene contacts, F. Driussi, S. Venica, A. Gahoi, A. Gambi, P. Giannozzi, S. Kataria, M.C. Lemme, P. Palestri, D. Esseni, Microelectronic Engineering 216, 111035 (2019). DOI: https://doi.org/10.1016/j.mee.2019.111035.
Fast hybrid density-functional computations using plane-wave basis sets, I. Carnimeo, S. Baroni, P. Giannozzi, Electron. Struct. 1, 015009 (2019). DOI: https://doi.org/10.1088/2516-1075/aaf7d4
2018
Antoniel M., Jones K. A., Antonucci S., Spolaore B., Fogolari F., Petronilli V., Giorgio V., Di Lisa F., Forte M., Szabò I., Lippe G., Bernardi P., Protonation of the unique histidine in OSCP subunit of F-ATP synthase inhibits the permeability transition pore at acidic pH, EMBO Reports, 19, 257-268, 2018
Fogolari F., Corazza A., Esposito G., Free energy, enthalpy and entropy from implicit solvent end-point simulations, Frontiers in molecular biosciences, 5, 11, 2018.
Brancolini G., Maschio M. C., Corazza A., Cantarutti C., Fogolari F., Corni S., Esposito G., Citrate-stabilized gold nanoparticles interfere with amyloid fibril formation: β2-microglobulin D76N and Delta-N6 variants., Nanoscale, 10, 4793-4806, 2018.
Capuano A., Fogolari F., Bucciotti F., Spessotto P., Nicolosi P. A., Mucignat M. T., Cervi M., Esposito G., Colombatti A., Doliana R. The α4β1/EMILIN1 interaction discloses a novel and unique integrin-ligand type of engagement, Matrix Biology, 66, 50-66, 2018.
Cantarutti C., G. Raj, Fogolari F., Giorgetti S., Corazza A., Bellotti, V., Naumov P., Esposito G., Interference of citrate-stabilized gold nanoparticles on β2-microglobulin oligomeric association, Chemical Communications, 54, 5422-5425, 2018.
Dongmo Foumthuim C. J., Corazza A., Berni, R., Esposito G., Fogolari F., Dynamics and thermodynamics of transthyretin association from molecular dynamics simulations, BioMedResearch International, 2018, 7480749, 2018.
Fogolari F., Maloku O., Dongmo Foumthuim C. J., Corazza A., Esposito G., PDB2ENTROPY and PDB2TRENT: conformational and rotational-translational entropy from molecular ensembles, Journal of Chemical Information and Modeling, 58, 1319-1324, 2018.
Cantarutti C., Bertoncin P., Giorgetti S., Bellotti V., Fogolari. F., Esposito G., The interaction of β2-microglobulin and gold nanoparticles: impact of coating, charge and size, Journal of Materials Chemistry B, 6, 5964-5974, 2018
Quantum Crystallography: Current Developments and Future Perspectives, A. Genoni, L. Bucinsky, N. Claiser, J. Contreras-Garcia, B. Dittrich, P. M. Dominiak, E. Espinosa, C. Gatti, P. Giannozzi, J.-M. Gillet, D. Jayatilaka, P. Macchi, A. Ø. Madsen, L. J. Massa, C. F. Matta, K. M. Merz, Ph. N. H. Nakashima, H. Ott, U. Ryde, K. Schwarz, M. Sierka, S. Grabowsky, Chem. Eur. J. 24, 10881-10905 (2018), DOI: https://doi.org/10.1002/chem.201705952
DFT study of graphene doping due to metal contacts, P. Khakbaz, F. Driussi, A. Gambi, P. Giannozzi, S. Venica, D. Esseni, A. Gahoi, S. Kataria, M.C. Lemme, Proceedings of the 24th Int. Conference on Simulation of Semiconductor Processes and Devices (SISPAD) 2019, pp.279-282. DOI: https://doi.org/10.1109/SISPAD.2019.8870456
Software for quantum simulations of tomorrow, P. Giannozzi, Il Nuovo Saggiatore 35, n.5-6, p. 34-38 (2019). https://www.ilnuovosaggiatore.sif.it/article/213
