We are very excited to share our new paper on the Journal of Chemical Physics providing analytical expressions for the interactions of two charged dielectric spheres in a dielectric medium, using the linearised Poisson Boltzmann framework.
https://aip.scitation.org/doi/10.1063/5.0056120
This work, which models the interaction of charged particles in electrolytic solution, can find application both in the field of computational biophysics and of colloids.
Artemi Bendandi, co-tutored by Dr. Walter Rocchia, got her PhD in Physics cum laude, with a thesis on Electrostatic Interactions in Chromatin.
A series of webinars on the most recent and exciting research on the many different roles of electrostatics in biological systems is starting on Jan 13th 2021!
Check the Protein Electrostatics website for news and registration!
We have been awarded via the PRACE EU initiative with 19.7M of CPU hours on the MARCONI supercomputer at CINECA for working on the computational design of an anti-idiotypic antibody against an antigentic determinant of Dengue virus.
We have been awarded via the ISCRA initiative with 1.6M of CPU hours on the MARCONI supercomputer at CINECA for working on the design of a protein construct mimicking an antigenic determinant of Dengue virus.
Dr. Sara Fortuna of Unversity of Trieste is now affiliated with the IIT, for a collaboration with the CONCEPT Lab on enhanced sampling techniques applied to Computational Medicinal Chemistry.
Alternatives Research & Development Foundation (ARDF), which supports the development of alternative, non-animal methods in science, has awarded the Group of Sara Fortuna in Trieste university and Dr. Miguel Soler at the CONCEPT Lab with a grant for the project called "In silico design of customised high-affinity antibody fragments".
In this project, we aim to show that our developed computational protocols of binder design can compete and reduce or even avoid the demand for in vivo procedures for antibody discovery and maturation. We will develop high affinity antibody fragments for the molecular recognition of difficult immuno-targets, such as the isoform of the cancer biomarker HER2. This approach will advance over the current state-of-the-art techniques, being (i) more cost-effective; and (ii) capable of overcoming the difficulties in the selection of a specific binding site.
Dr. Rocchia was awarded the 2018 Emerging Technologies in Computational Chemistry prize at the 256th ACS national meeting 256th ACS national meeting in Boston.
In his presentation, Dr. Rocchia showed the tools developed for the automated analysis of pocket evolution along MD trajectories, the NanoShaper tool for buiding and analysing molecular surfaces and how these tools can contribute to another approach, which accelerates the protein-ligand binding process. We are very excited about this, which is an acknowledgment of the work done by all the collaborators involved in the different projects.
G. La Sala, S. Decherchi, M. De Vivo, and W. Rocchia. Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis ACS Central Science 2017 3 (9), 949-960
S. Decherchi, W. Rocchia. A general and robust ray casting based algorithm for triangulating surfaces at the nanoscale. PLoS ONE 8(4), e59744, 2013.
A. Spitaleri, S. Decherchi, A. Cavalli, and W. Rocchia. Fast Dynamic Docking Guided by Adaptive Electrostatic Bias: The MD-Binding Approach Journal of Chemical Theory and Computation 2018 14 (3), 1727-1736.
