Gomaz, B., Pandini, A., Maršavelski, A. and Štefanić, Z. (2024) 'MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams'. Journal of Chemical Information and Modeling, 64 (15). pp. 5742 - 5748. ISSN: 1549-9596

Kliza, KW., Song, W., Pinzuti, I., Schaubeck, S., Kunzelmann, S., Kuntin, D., Fornili, A., Pandini, A., Hofmann, K., Garnett, JA., Stieglitz, B. and Husnjak, K. et al. (2024) 'N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling'. Cell Death Discovery, 10 (1). pp. 1 - 15. ISSN: 2058-7716 Open Access Link

Bibik, P., Alibai, S., Pandini, A. and Dantu, SC. (2024) 'PyCoM: a python library for large-scale analysis of residue-residue coevolution data'. Bioinformatics, 40 (4). pp. btae166. ISSN: 1367-4803 Open Access Link

Oues, N., Dantu, SC., Patel, RJ. and Pandini, A. (2023) 'MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations'. Bioinformatics, 39 (7). pp. btad427. ISSN: 1367-4803 Open Access Link

Morra, G., Meli, M., Moroni, E. and Pandini, A. (2023) 'Editorial: Computational drug discovery for targeting of protein-protein interfaces—Volume II'. Frontiers in Chemistry, 11. pp. 1 - 2. ISSN: 2296-2646 Open Access Link

Li, T., Motta, S., Stevens, AO., Song, S., Hendrix, E., Pandini, A. and He, Y. et al. (2022) 'Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex'. JACS Au, 2 (8). pp. 1935 - 1945. ISSN: 2691-3704 Open Access Link

Motta, S., Callea, L., Bonati, L. and Pandini, A. (2022) 'PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations'. Journal of Chemical Theory and Computation, 18 (3). pp. 1957 - 1968. ISSN: 1549-9618 Open Access Link

Cho, E., Rosa, M., Anjum, R., Mehmood, S., Soban, M., Mujtaba, M., Bux, K., Moin, ST., Tanweer, M., Dantu, S., Pandini, A., Yin, J., Ma, H., Ramanathan, A., Islam, B., Mey, ASJS., Bhowmik, D. and Haider, S. et al. (2021) 'Dynamic Profiling of β-Coronavirus 3CL M^proProtease Ligand-Binding Sites'. Journal of Chemical Information and Modeling, 61 (6). pp. 3058 - 3073. ISSN: 1549-9596 Open Access Link

Marchetti, F., Moroni, E., Pandini, A. and Colombo, G. (2021) 'Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics'. The Journal of Physical Chemistry Letters, 12 (15). pp. 3724 - 3732. ISSN: 1948-7185 Open Access Link

Motta, S., Pandini, A., Fornili, A. and Bonati, L. (2021) 'Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks'. Journal of chemical theory and computation, 17 (4). pp. 2080 - 2089. ISSN: 1549-9618 Open Access Link

Meli, M., Pandini, A. and Morra, G. (2021) 'Editorial: Computational Drug Discovery for Targeting of Protein-Protein Interfaces'. Frontiers in Chemistry, 9. pp. 1 - 2. ISSN: 2296-2646 Open Access Link

Wheatley, P., Gupta, S., Pandini, A., Chen, Y., Petzold, CJ., Ralston, CY., Blair, DF. and Khan, S. et al. (2020) 'Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM'. Biophysical Journal, 119 (6). pp. 1108 - 1122. ISSN: 0006-3495 Open Access Link

Akere, A., Chen, SH., Liu, X., Chen, Y., Dantu, SC., Pandini, A., Bhowmik, D. and Haider, S. et al. (2020) 'Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana Glycosyltransferases'. Biochemical Journal, 477 (15). pp. 2791 - 2805. ISSN: 0264-6021 Open Access Link

Portlock, TJ., Tyson, JY., Dantu, SC., Rehman, S., White, RC., McIntire, IE., Sewell, L., Richardson, K., Shaw, R., Pandini, A., Cianciotto, NP. and Garnett, JA. et al. (2020) 'Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System'. Frontiers in Molecular Biosciences, 7 (112). pp. 1 - 17. ISSN: 2296-889X Open Access Link

Motta, S., Pandini, A., Fornili, A. and Bonati, L. (2020) 'Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations'.64th Annual Meeting of the Biophysical-Society. San Diego, CA. 7 - 19 February. CELL PRESS. pp. 297A - 297A. ISSN: 0006-3495

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'.International Conference on Artificial Neural Networks ICANN 2018. 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., Garcia-Manyes, S., Gautel, M. and Steiner, RA. et al. (2016) 'Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection'. Structure, 25 (1). pp. 107 - 120. ISSN: 0969-2126 Open Access Link

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

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

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 Steiner, RA. 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

Buffa, P., Romano, C., Pandini, A., Massimino, M., Tirrò, E., Di Raimondo, F., Manzella, L., Fraternali, F. and Vigneri, PG. 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

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., Hahn, ME. and Denison, MS. 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

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

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., Pandini, A., Papaleo, E., Pitea, D., Saracino, GAA. and Zampella, G. 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

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