IIT Publications Search

Publications
2025
Rigoli M., Potestio R., Menichetti R.
A Multiscale Analysis of the CzrA Transcription Repressor Highlights the Allosteric Changes Induced by Metal Ion Binding
The Journal of Physical Chemistry B
DOI 10.1021/acs.jpcb.4c06106
Article Journal
2025
Soler M.A., Yakout R.B.A., Ozkilinc O., Esposito G., Rocchia W., Klein C., Fogolari F.
Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces
Molecules, vol. 30, (no. 1)
DOI 10.3390/molecules30010159
Article Journal
2025
Soler M. A., Yakout R. B. A., Ozkilinc O., Esposito G., Rocchia W., Klein C., Fogolari F.
Bluues_cplx: Electrostatics at Protein–Protein and Protein–Ligand Interfaces
Molecules, vol. 30, (no. 1), pp. 159
DOI 10.3390/molecules30010159
Article Journal
2025
Mak J.K., Bendandi A., Salim J.A., Mazoni I., de Moraes F.R., Borro L., Stortz F., Rocchia W., Neshich G., Minary P.
Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR–Cas9 off-target activity
NAR Genomics and Bioinformatics, vol. 7, (no. 2)
DOI 10.1093/nargab/lqaf054
2025
Abate C., Serra E., Rocchia W., Cavalli A., Decherchi S.
NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual
Journal of Chemical Information and Modeling
DOI 10.1021/acs.jcim.5c00821
Article Journal
2025
Di Florio V., Ansalone P., Siryk S.V., Decherchi S., de Falco C., Rocchia W.
NextGenPB: An analytically-enabled super resolution tool for solving the Poisson-Boltzmann equation featuring local (de)refinement
Computer Physics Communications, vol. 317
DOI 10.1016/j.cpc.2025.109816
Article Journal
2025
Jonnalagadda A., Agrawal A., Sharma A., Rocchia W., Succi S.
Towards nonlinear thermohydrodynamic simulations via the Onsager-regularized lattice-Boltzmann method
Physical Review Research
DOI 10.1103/1z5c-hnpn
Article in Press Journal
2024
Tandiana R., Barletta G.P., Soler M.A., Fortuna S., Rocchia W.
Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔG Predictions
Journal of Chemical Theory and Computation, vol. 20, (no. 6), pp. 2630-2642
DOI 10.1021/acs.jctc.3c01225
Article Journal
2024
Balasubramanian K.K., Di Salvo M., Rocchia W., Decherchi S., Crepaldi M.
Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective
IEEE Access
DOI 10.1109/ACCESS.2024.3389673
Article Journal
2024
Balasubramanian K. K., Salvo M. D., Rocchia W., Decherchi S., Crepaldi M.
Designing RISC-V Instruction Set Extensions for Artificial Neural Networks: An LLVM Compiler-Driven Perspective
IEEE Access
DOI 10.1109/ACCESS.2024.3389673
Article Journal
2024
Barletta G.P., Tandiana R., Soler M., Fortuna S., Rocchia W.
Locuaz: an in silico platform for protein binders optimization
Bioinformatics, vol. 40, (no. 8)
DOI 10.1093/bioinformatics/btae492
Article Journal
2024
Di Florio V., Giberti C., Rondoni L., Zhao H.
Microscopic state equation for oscillator chains
European Physical Journal Plus, vol. 139, (no. 7)
DOI 10.1140/epjp/s13360-024-05419-1
Article Journal
2024
Rondoni L., Di Florio V.
Probability Turns Material: The Boltzmann Equation
Entropy, vol. 26, (no. 2)
DOI 10.3390/e26020171
2024
Buzatu A.R., Soler M.A., Fortuna S., Ozkilinc O., Dreava D.M., Bitcan I., Badea V., Giannozzi P., Fogolari F., Gardossi L., Peter F., Todea A., Boeriu C.G.
Reactive natural deep eutectic solvents increase selectivity and efficiency of lipase catalyzed esterification of carbohydrate polyols
Catalysis Today, vol. 426
DOI 10.1016/j.cattod.2023.114373
Article Journal
2024
Bosio S., Bernetti M., Rocchia W., Masetti M.
Similarities and Differences in Ligand Binding to Protein and RNA Targets: The Case of Riboflavin
Journal of Chemical Information and Modeling, vol. 64, (no. 11), pp. 4570-4586
DOI 10.1021/acs.jcim.4c00420
Article Journal

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