COBIO
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
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
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. ISSN: 2045-2322 Open Access Link
Pernigo, S., Fukuzawa, A., Pandini, A., Holt, M., Kleinjung, J., Gautel, M. and et al. (2014) '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
Romano, C., Buffa, P., Pandini, A., Massimino, M., Tirro, E., Di Raimondo, F., et al. (2014) 'BCR-ABL residues interacting with Ponatinib are critical to preserve the tumorigenic potential of the oncoprotein'.Experimental Biology Meeting. San Diego, CA. 1 - 30 April. FEDERATION AMER SOC EXP BIOL. ISSN: 0892-6638
Buffa, P., Romano, C., Pandini, A., Massimino, M., Tirrò, 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
Pandini, A., Fornili, A., Fraternali, F. and Kleinjung, J. (2014) 'Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet'.58th Annual Meeting of the Biophysical-Society. San Francisco, CA. Elsevier BV. pp. 648a - 648a. ISSN: 0006-3495
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
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
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
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
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
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
Pandini, A., Fornili, A., Fraternali, F. and Kleinjung, J. (2012) 'Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics'.56th Annual Meeting of the Biophysical-Society. San Diego, CA. Elsevier BV. pp. 225a - 225a. ISSN: 0006-3495
Degroot, D., He, G., Fraccalvieri, D., Bonati, L., Pandini, A. and Denison, MS. (2011) 'AHR Ligands: Promiscuity in Binding and Diversity in Response', inThe AH Receptor in Biology and Toxicology. Wiley. pp. 63 - 79. ISBN 13: 9780470601822.
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. ISSN: 1471-2105 Open Access Link
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
Pandini, A., Fornili, A. and Kleinjung, J. (2010) 'Structural alphabets derived from attractors in conformational space'. BMC Bioinformatics, 11 (1). pp. 97. ISSN: 1471-2105 Open Access Link
Fornili, A., Pandini, A. and Fraternali, F. (2010) 'Interface Dynamics In Hub Proteins'. Elsevier BV. pp. 239a - 239a. ISSN: 0006-3495
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
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
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
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
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
Soshilov, A., Pandini, A., Bonati, L. and Denison, MS. (2006) 'Characterization of hsp90-binding to the the PASB domain of the Ah receptor'.Experimental Biology 2006 Meeting. San Francisco, CA. 7 - 5 April. FEDERATION AMER SOC EXP BIOL. pp. A963 - A963. ISSN: 0892-6638
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
Denison, MS., Pandini, A., Nagy, SR., Baldwin, EP. and Bonati, L. (2002) 'Ligand binding and activation of the Ah receptor'. Chemico-Biological Interactions, 141 (1-2). pp. 3 - 24. ISSN: 0009-2797