IIT Publications Search

Publications
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
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
2023
Yang W., Rocchia W.
Biomolecular Electrostatic Phenomena: An Evergreen Field
Journal of Physical Chemistry B, vol. 127, (no. 18), pp. 3979-3981
DOI 10.1021/acs.jpcb.3c02158 Editorial Journal
2023
Balboni B., Masi M., Rocchia W., Girotto S., Cavalli A.
GSK-3β Allosteric Inhibition: A Dead End or a New Pharmacological Frontier?
International Journal of Molecular Sciences, vol. 24, (no. 8)
DOI 10.3390/ijms24087541 Review Journal
2023
Soler M.A., Minovski N., Rocchia W., Fortuna S.
Replica-exchange optimization of antibody fragments
Computational Biology and Chemistry, vol. 103
DOI 10.1016/j.compbiolchem.2023.107819 Article Journal
2023
Gagliardi L., Rocchia W.
SiteFerret: Beyond Simple Pocket Identification in Proteins
Journal of Chemical Theory and Computation, vol. 19, (no. 15), pp. 5242-5259
DOI 10.1021/acs.jctc.2c01306 Article Journal
2023
Douaki A., Stuber A., Hengsteler J., Momotenko D., Rogers D.M., Rocchia W., Hirst J.D., Nakatsuka N., Garoli D.
Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets
Chemical Communications, vol. 59, (no. 99), pp. 14713-14716
DOI 10.1039/d3cc04334g Article Journal
2022
Reis P.B.P.S., Bertolini M., Montanari F., Rocchia W., Machuqueiro M., Clevert D.-A.
A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven p KaPredictions in Proteins
Journal of Chemical Theory and Computation, vol. 18, (no. 8), pp. 5068-5078
DOI 10.1021/acs.jctc.2c00308 Article Journal
2022
Reis P.B.P.S., Barletta G.P., Gagliardi L., Fortuna S., Soler M.A., Rocchia W.
Antibody-Antigen Binding Interface Analysis in the Big Data Era
Frontiers in Molecular Biosciences, vol. 9
DOI 10.3389/fmolb.2022.945808 Article Journal
2022
Siryk S.V., Rocchia W.
Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment
Journal of Physical Chemistry B, vol. 126, (no. 49), pp. 10400-10426
DOI 10.1021/acs.jpcb.2c05564 Article Journal
2022
Raffo A., Gagliardi L., Fugacci U., Sagresti L., Grandinetti S., Brancato G., Biasotti S., Rocchia W.
Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics
Frontiers in Molecular Biosciences, vol. 9
DOI 10.3389/fmolb.2022.933924 Article Journal
2022
Ruiz-Rodriguez M.A., Cooper C.D., Rocchia W., Casalegno M., Lopez De Los Santos Y., Raos G.
Modeling of the Electrostatic Interaction and Catalytic Activity of [NiFe] Hydrogenases on a Planar Electrode
Journal of Physical Chemistry B, vol. 126, (no. 43), pp. 8777-8790
DOI 10.1021/acs.jpcb.2c05371 Article Journal