Computational Methods for Protein Dynamics and Function

About

Proteins are the workhorses of the cell and their atomistic and molecular dynamics are at the core of their ability to perform biological functions. We have developed novel computational methods to investigate allosteric regulation, and to analyse protein-protein interfaces and networks.

Research papers

• Teletin, M., Czibula, G., Bocicor, M-I., Albert, S., Pandini, A. (2018) 'Deep Autoencoders for Additional Insight into Protein Dynamics'. Lecture Notes in Computer Science, 11140 pp. 79 - 89. ISSN: 0302-9743
• Tiberti, M., Pandini, A., Fraternali, F., Fornili, A. (2017) 'In silico identification of rescue sites by double force scanning'. Bioinformatics, Volume 34, Issue 2, pp. 207–214. ISSN: 1367-4803
• Pandini, A., Fornili, A. (2016) 'Using local states to drive the sampling of global conformations in proteins'.  Journal of Chemical Theory and Computation (2016), 12, 3, 1368-1379. ISSN: 1549-9618, 1549-9626
• Chung, SS., Pandini, A., Annibale, A., Coolen, ACC., Thomas, NSB., Fraternali, F. (2015) 'Bridging topological and functional information in protein interaction networks by short loops profiling'. Scientific Reports volume 5, pp. 8540. ISSN: 2045-2322
• Pandini, A., Fornili, A., Fraternali, F., Kleinjung, J. (2013) 'GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet'. Bioinformatics, 29:16, pp. 2053 - 2055. ISSN: 1367-4803
• Pandini, A., Fornili, A., Fraternali, F., Kleinjung, J. (2012) 'Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics'. FASEB Journal, 26:2, pp. 868 - 881. ISSN: 0892-6638
• Fraccalvieri, D., Pandini, A., Stella, F., Bonati, L. (2011) 'Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps'. BMC Bioinformatics, 12:158. ISSN: 1471-2105
• Bordogna, A., Pandini, A., Bonati, L. (2011) 'Predicting the accuracy of protein-ligand docking on homology models'. Journal of Computational Chemistry, 32 (1): 81 - 98. ISSN: 0192-8651, 1096-987X
• Pandini, A., Fornili, A., Kleinjung, J. (2010). 'Structural alphabets derived from attractors in conformational space'.  BMC Bioinformatics, 11. ISSN: 1471-2105
• Pandini, A., Mauri, G., Bordogna, A., Bonati, L. (2007) 'Detecting similarities among distant homologous proteins by comparison of domain flexibilities'. Protein Engineering, Design and Selection, 20:6, pp. 285 - 299. ISSN: 1741-0126