All Stories

  1. MDavocado: Analysis and Visualization of Protein Motion by Time-Dependent Angular Diagrams

    Article • Journal of Chemical Information and Modeling, July 2024, American Chemical Society (ACS)

    Dr Alessandro Pandini

  2. N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling

    Article • Cell Death Discovery, April 2024, Springer Science + Business Media

    Dr Alessandro Pandini

  3. PyCoM: a python library for large-scale analysis of residue–residue coevolution data

    Article • Bioinformatics, March 2024, Oxford University Press (OUP)

    Dr Alessandro Pandini

  4. MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations

    Article • Bioinformatics, July 2023, Oxford University Press (OUP)

    Dr Alessandro Pandini

  5. Editorial: Computational drug discovery for targeting of protein-protein interfaces—Volume II

    Article • Frontiers in Chemistry, March 2023, Frontiers

    Dr Alessandro Pandini

  6. Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex

    Article • JACS Au, August 2022, American Chemical Society (ACS)

    Dr Alessandro Pandini

  7. PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations

    Article • Journal of Chemical Theory and Computation, February 2022, American Chemical Society (ACS)

    Dr Alessandro Pandini

  8. Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

    Article • Journal of Chemical Information and Modeling, June 2021, American Chemical Society (ACS)

    Dr Alessandro Pandini

  9. Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics

    Article • The Journal of Physical Chemistry Letters, April 2021, American Chemical Society (ACS)

    Dr Alessandro Pandini

  10. Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks

    Article • Journal of Chemical Theory and Computation, March 2021, American Chemical Society (ACS)

    Dr Alessandro Pandini

  11. Editorial: Computational Drug Discovery for Targeting of Protein-Protein Interfaces

    Article • Frontiers in Chemistry, March 2021, Frontiers

    Dr Alessandro Pandini

  12. Allosteric Priming of E. coli CheY by the Flagellar Motor Protein FliM

    Article • Biophysical Journal, September 2020, Elsevier

    Dr Alessandro Pandini

  13. Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

    Article • Biochemical Journal, August 2020, Portland Press Ltd.

    Dr Alessandro Pandini

  14. Structure, Dynamics and Cellular Insight Into Novel Substrates of the Legionella pneumophila Type II Secretion System

    Article • Frontiers in Molecular Biosciences, June 2020, Frontiers

    Dr Alessandro Pandini, Dr Theo John Portlock

  15. Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

    Article • PLoS Computational Biology, May 2019, PLOS

    Dr Alessandro Pandini, Shahid Khan

  16. Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

    Article • PLoS Computational Biology, February 2018, PLOS

    Dr Alessandro Pandini

  17. In silico identification of rescue sites by double force scanning

    Article • Bioinformatics, August 2017, Oxford University Press (OUP)

    Dr Alessandro Pandini

  18. Binding of Myomesin to Obscurin-Like-1 at the Muscle M-Band Provides a Strategy for Isoform-Specific Mechanical Protection

    Article • Structure, January 2017, Elsevier

    Dr Alessandro Pandini

  19. The Gearbox of the Bacterial Flagellar Motor Switch

    Article • Structure, July 2016, Elsevier

    Dr Alessandro Pandini

  20. Using Local States To Drive the Sampling of Global Conformations in Proteins

    Article • Journal of Chemical Theory and Computation, March 2016, American Chemical Society (ACS)

    Dr Alessandro Pandini

  21. Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor

    Article • PLOS One, November 2015, PLOS

    Dr Alessandro Pandini

  22. The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance

    Article • Biophysical Journal, September 2015, Elsevier

    Dr Alessandro Pandini

  23. Bridging topological and functional information in protein interaction networks by short loops profiling

    Article • Scientific Reports, February 2015, Nature

    Dr Alessandro Pandini

  24. BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein

    Article • The FASEB Journal, December 2013, Federation of American Societies For Experimental Biology (FASEB)

    Dr Alessandro Pandini

  25. Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles

    Article • Journal of Chemical Theory and Computation, November 2013, American Chemical Society (ACS)

    Dr Alessandro Pandini

  26. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet

    Article • Bioinformatics, June 2013, Oxford University Press (OUP)

    Dr Alessandro Pandini

  27. Artificial Neural Networks for Efficient Clustering of Conformational Ensembles and their Potential for Medicinal Chemistry

    Article • Current Topics in Medicinal Chemistry, April 2013, Bentham Science Publishers

    Dr Alessandro Pandini

  28. 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

    Article • Biochemistry, January 2013, American Chemical Society (ACS)

    Dr Alessandro Pandini

  29. Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics

    Article • Molecular BioSystems, January 2012, Royal Society of Chemistry

    Dr Alessandro Pandini

  30. AHR Ligands: Promiscuity in Binding and Diversity in Response

    Article • November 2011, Wiley

    Dr Alessandro Pandini

  31. Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics

    Article • The FASEB Journal, November 2011, Federation of American Societies For Experimental Biology (FASEB)

    Dr Alessandro Pandini

  32. Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps

    Article • BMC Bioinformatics, January 2011, Springer Science + Business Media

    Dr Alessandro Pandini

  33. Predicting the accuracy of protein-ligand docking on homology models

    Article • Journal of Computational Chemistry, November 2010, Wiley

    Dr Alessandro Pandini

  34. Structural alphabets derived from attractors in conformational space

    Article • BMC Bioinformatics, January 2010, Springer Science + Business Media

    Dr Alessandro Pandini

  35. Detection of the TCDD Binding-Fingerprint within the Ah Receptor Ligand Binding Domain by Structurally Driven Mutagenesis and Functional Analysis

    Article • Biochemistry, June 2009, American Chemical Society (ACS)

    Dr Alessandro Pandini

  36. Detecting similarities among distant homologous proteins by comparison of domain flexibilities

    Article • Protein Engineering Design and Selection, June 2007, Oxford University Press (OUP)

    Dr Alessandro Pandini

  37. MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database

    Article • Bioinformatics, January 2007, Oxford University Press (OUP)

    Dr Alessandro Pandini

  38. Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis†

    Article • Biochemistry, January 2007, American Chemical Society (ACS)

    Dr Alessandro Pandini

  39. Computational approaches to shed light on molecular mechanisms in biological processes

    Article • Theoretical Chemistry Accounts, December 2006, Springer Science + Business Media

    Dr Alessandro Pandini

  40. Conservation and specialization in PAS domain dynamics

    Article • Protein Engineering Design and Selection, March 2005, Oxford University Press (OUP)

    Dr Alessandro Pandini

  41. Ligand binding and activation of the Ah receptor

    Article • Chemico-Biological Interactions, September 2002, Elsevier

    Dr Alessandro Pandini