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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

Journal article

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

Conference paper

Motta, S., Minici, C., Corrada, D., Bonati, L. and Pandini, A. (2018) 'Ligand-induced perturbation of the HIF-2╬▒:ARNT dimer dynamics'. PLoS Computational Biology, 14 (2). pp. e1006021 - e1006021. ISSN: 1553-734X Open Access Link

Journal article

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

Journal article

Pernigo, S., Fukuzawa, A., Beedle, AEM., Holt, M., Round, A., Pandini, A., et al. (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 Link

Journal article

Pandini, A., Morcos, F. and Khan, S. (2016) 'The Gearbox of the Bacterial Flagellar Motor Switch'. Structure, 24 (7). pp. 1209 - 1220. ISSN: 0969-2126 Open Access Link

Journal article

Pandini, A. and Fornili, A. (2016) 'Using Local States to Drive the Sampling of Global Conformations in Proteins'. Journal of Chemical Theory and Computation, 12 (3). pp. 1368 - 1379. ISSN: 1549-9618 Open Access Link

Journal article

Pandini, A., Kleinjung, J., Rasool, S. and Khan, S. (2015) 'Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor'. PLoS One, 10 (11). pp. 1 - 1. ISSN: 1932-6203 Open Access Link

Journal article

Pandini, A., Kleinjung, J., Taylor, WR., Junge, W. and Khan, S. (2015) 'The Phylogenetic Signature Underlying ATP Synthase c-ring Compliance'. Biophysical Journal, 109 (5). pp. 975 - 987. ISSN: 1542-0086 Open Access Link

Journal article

Pernigo, S., Fukuzawa, A., Pandini, A., Holt, M., Kleinjung, J., Gautel, M. and et al. (2015) 'The crystal structure of the human titin:obscurin complex reveals a conserved yet specific muscle M-band zipper module'. Journal of Molecular Biology, 427 (4). pp. 718 - 736. ISSN: 0022-2836 Open Access Link

Journal article

Chung, SS., Pandini, A., Annibale, A., Coolen, AC., Thomas, NS. and Fraternali, F. (2015) 'Bridging topological and functional information in protein interaction networks by short loops profiling'. Scientific Reports, 5 (1). pp. 8540 - 8540. ISSN: 2045-2322 Open Access Link

Journal article

Buffa, P., Romano, C., Pandini, A., Massimino, M., Tirr├▓, E., Di Raimondo, F., et al. (2014) 'BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein'. FASEB Journal, 28 (3). pp. 1221 - 1236. ISSN: 0892-6638 Open Access Link

Journal article

Fornili, A., Pandini, A., Lu, H-C. and Fraternali, F. (2013) 'Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles'. Journal of Chemical Theory and Computation, 9 (11). pp. 5127 - 5147. ISSN: 1549-9618 Open Access Link

Journal article

Pandini, A., Fornili, A., Fraternali, F. and 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 Open Access Link

Journal article

Pandini, A., Fraccalvieri, D. and Bonati, L. (2013) 'Artificial Neural Networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry'. Current Topics in Medicinal Chemistry, 13 (5). pp. 642 - 651. ISSN: 1568-0266

Journal article

Fraccalvieri, D., Soshilov, AA., Karchner, SI., Franks, DG., Pandini, A., Bonati, L., et al. (2013) 'Comparative analysis of homology models of the Ah receptor ligand binding domain: Verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor'. Biochemistry, 52 (4). pp. 714 - 725. ISSN: 0006-2960 Open Access Link

Journal article

Pandini, A., Fornili, A., Fraternali, F. and 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 Open Access Link

Journal article

Fraccalvieri, D., Tiberti, M., Pandini, A., Bonati, L. and Papaleo, E. (2012) 'Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics'. Molecular BioSystems, 8 (10). pp. 2680 - 2691. ISSN: 1742-206X

Journal article

Fraccalvieri, D., Pandini, A., Stella, F. and Bonati, L. (2011) 'Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps'. BMC Bioinformatics, 12 (1). pp. 158 - 158. ISSN: 1471-2105 Open Access Link

Journal article

Bordogna, A., Pandini, A. and Bonati, L. (2011) 'Predicting the accuracy of protein-ligand docking on homology models'. Journal of Computational Chemistry, 32 (1). pp. 81 - 98. ISSN: 0192-8651 Open Access Link

Journal article

Pandini, A., Fornili, A. and Kleinjung, J. (2010) 'Structural alphabets derived from attractors in conformational space'. BMC Bioinformatics, 11 (1). pp. 97 - 97. ISSN: 1471-2105 Open Access Link

Journal article

Pandini, A., Soshilov, AA., Song, Y., Zhao, J., Bonati, L. and Denison, MS. (2009) 'Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis'. Biochemistry, 48 (25). pp. 5972 - 5983. ISSN: 0006-2960 Open Access Link

Journal article

Pandini, A., Mauri, G., Bordogna, A. and 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 Open Access Link

Journal article

Moro, G., Bonati, L., Bruschi, M., Cosentino, U., De Gioia, L., Fantucci, PC., et al. (2007) 'Computational approaches to shed light on molecular mechanisms in biological processes'. Theoretical Chemistry Accounts, 117 (5-6). pp. 723 - 741. ISSN: 1432-881X Open Access Link

Journal article

Pandini, A., Bonati, L., Fraternali, F. and Kleinjung, J. (2007) 'MinSet: A general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database'. Bioinformatics, 23 (4). pp. 515 - 516. ISSN: 1367-4803

Journal article

Pandini, A., Denison, MS., Song, Y., Soshilov, AA. and Bonati, L. (2007) 'Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis'. Biochemistry, 46 (3). pp. 696 - 708. ISSN: 0006-2960 Open Access Link

Journal article

Pandini, A. and Bonati, L. (2005) 'Conservation and specialization in PAS domain dynamics'. Protein Engineering, Design and Selection, 18 (3). pp. 127 - 137. ISSN: 1741-0126 Open Access Link

Journal article