Alessandro Pandini

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Research Interests

I am working on the development and application of methods for computational structural and synthetic biology with a particular interest in combining tools and algorithms from Structural Bioinformatics and Molecular Simulations:

  • Molecular Dynamics to compare functionally related proteins and to guide drug design studies
  • Structural and functional analysis of the Aryl hydrocarbon Receptor

Recent Publications

  • Pandini A, Kleinjung J, Taylor WR, Junge W, Khan S - The Phylogenetic Signature Underlying ATP Synthase c-ring Compliance
    Biophys J 109:975-987, 2015
    PubMed URL


  • Chung SS☯, Pandini A☯, Annibale A, Coolen ACC, Thomas NS, Fraternali F - Bridging Topological and Functional Information in Protein Interaction Networks by Short Loops Profiling
    Sci Rep 5:8540, 2015
    PubMed URL


  • Pernigo S, Fukuzawa A, Pandini A, Holt M, Kleinjung J, Gautel M, Steiner RA - The Crystal Structure of the Human Titin:Obscurin Complex Reveals a Conserved yet Specific Muscle M-Band Zipper Module
    J Mol Biol 427(4):718-736, 2015
    PubMedURL


  • Buffa P☯, Romano C☯, Pandini A☯, Massimino M, Tirrò E, Di Raimondo F, Manzella L, Fraternali F, Vigneri PG - BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein
    FASEB J 28(3):1221–1236, 2014
    PubMedURL


  • Fornili A, Pandini A, Lu H-C, Fraternali F - Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles
    J Chem Theory Comput 9(12):5127-5147, 2013
    PubMedURL


  • Pandini A*, Fornili A, Fraternali F, Kleinjung J - GSATools: analysis of allosteric communication and functional local motions using a Structural Alphabet
    Bioinformatics 29(16):2053-2055, 2013
    PubMed URL GSATools


  • Pandini A*, Fraccalvieri D, Bonati L - Artificial Neural Networks for Efficient Clustering of Conformational Ensembles and their Potential for Medicinal Chemistry
    Curr Top Med Chem 13(5):642-51, 2013
    PubMed URL


  • Pandini A☯*, Fornili A☯, Fraternali F, Kleinjung J - Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics
    FASEB J 26(2):868-81, 2012
    PubMed URL


equal contribution

* corresponding author

Other Selected Publications

  • Bordogna A, Pandini A, Bonati L - Predicting the accuracy of protein-ligand docking on homology models
    Journal of Computational Chemistry 32(1):81-98, 2011
    PubMed URL


  • Pandini A, Fornili A, Kleinjung J - Structural alphabets derived from attractors in conformational space
    BMC Bioinformatics 11(1):97, 2010
    PubMed URL Data


  • Pandini A, Soshilov A A, Song Y, Zhao J, Bonati L, Denison M S - Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis
    Biochemistry 48(25):5972-83, 2009
    PubMed URL


  • Pandini A, Mauri G, Bordogna A, Bonati L - Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    Protein Eng Des Sel 20(6):285-99, 2007
    PubMed URL


  • Pandini A, Bonati L, Fraternali F, Kleinjung J - MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database
    Bioinformatics 23(4):515-6, 2007
    PubMed URL Web server