My research activity focuses on the development and application of computational methods to study protein dynamics and its role in protein-ligand binding, protein-protein interactions, and protein design.
I obtained my PhD in Computational Chemistry at the University of Milan-Bicocca under the supervision of Prof. Laura Bonati. As part of her research group I contributed to the unveil the molecular mechanism of toxic response mediated by binding of dioxins to the Aryl hydrocarbon Receptor. In 2008 I was awarded a Marie Curie Inter European Fellowship to work at the MRC National Institute for Medical Research (NIMR) under the supervision of Dr. Willie R. Taylor and Dr. Jens Kleinjung. From 2011 to 2014 he was a BBSRC-funded postdoctoral research assistant in the group of Prof. Franca Fraternali at King’s College London working on methods to investigate allosteric regulation, and to analyse protein-protein interaction interfaces and networks.
During my career I developed and applied novel approaches combining structural bioinformatics and molecular simulation to address challenging biological questions, especially in relation to protein function, allosteric regulation and drug design. I introduced novel points of view in the definition of the limits and potential of molecular docking on theoretical models and in the use of molecular dynamics for drug design and medicinal chemistry. In particular, I developed an innovative computational method to detect local functional motions and to describe allosteric transmission in protein structures.
Most recently, in collaboration with Dr. Arianna Fornili (QMUL), I contributed to the development of a novel strategy for biasing the sampling of local states to drive the global conformational transitions in proteins. In collaboration with Dr. Shahid Khan (LBNL – Berkeley Lab) and Dr. Willie Taylor, I have contributed to explain the relationships between residue coevolution and molecular dynamics in two bacterial ring assemblies.
Newest selected publications
Pandini, A., Schulman, H. and Khan, S. (2019) 'Conformational coupling by trans-phosphorylation in calcium-calmodulin-dependent kinase II'. PLoS Computational Biology, 15 (5). pp. e1006796 - e1006796. ISSN: 1553-734X Open Access Link
Teletin, M., Czibula, G., Bocicor, M-I., Albert, S. and Pandini, A. (2018) 'Deep Autoencoders for Additional Insight into Protein Dynamics'.ICANN. Rhodes, Greece. 26 - 7 October. Springer International Publishing. pp. 79 - 89. ISSN: 0302-9743 Open Access Link
Motta, S., Minici, C., Corrada, D., Bonati, L. and Pandini, A. (2018) 'Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics'. PLoS Computational Biology, 14 (2). pp. e1006021 - e1006021. ISSN: 1553-734X Open Access Link
Tiberti, M., Pandini, A., Fraternali, F. and Fornili, A. (2017) 'In silico identification of rescue sites by double force scanning'. Bioinformatics, 34 (2). pp. 207 - 214. ISSN: 1367-4803 Open Access Link
Pernigo, S., Fukuzawa, A., Beedle, AEM., Holt, M., Round, A., Pandini, A., (2016) 'Binding of Myomesin to Obscurin-Like-1 to the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection'. Structure, 25 (1). pp. 107 - 120. ISSN: 1878-4186 Open Access Linket al.