1. Joseph A.P.
   Comparison of protein folds based on similarities in local backbone conformation.
   Doctorat de l'Université Paris Diderot - Paris 7 - Spécialité : Analyses de Génomes et Modélisation Moléculaire (2011) 244 p.
   
   
   Summary
   
   The rapidly increasing number of available protein structures necessitates fast and efficient tools for the comparison of protein folds. An efficient "sequence-like" structural alignment approach was developed by representing backbone conformation as a series of letters, with the use of Protein Blocks (PBs) [de Brevern et al. 2000, Joseph et al. 2010]. Classical Needleman-Wunsch dynamic programming was used and a dedicated PB substitution matrix was generated for scoring the alignment. Refined substitution matrices and an anchor based dynamic programming approach were used to improve the efficiency of this approach. For extending this approach to multiple structural alignment, a progressive strategy similar to that used in CLUSTALW, was adopted. The PB based pairwise (iPBA - http://www.dsimb.inserm.fr/dsimb_tools/ipba/index.php) and multiple (mulPBA) structure comparison approaches (mulPBA) was better than many other popular tools in more than 85% of alignments generated on benchmark datasets [Joseph et al. 2011, 2012, 2013]. This alignment strategy was also used to assess the performance of a fold recognition approach based on PB prediction. The influence of species specific data on sequence-structure relationship was also analysed using PBs [de Brevern et al. 2011]. The PB variations among homologous proteins were also studied in detail. Short studies on PolyProline II assignments [Mansiaux et al. 2011] and chameleon sequences [Ghozlane at al. 2009] were also carried out.
   
   

   Publications

   (10 papers, 1 book chapter)
   
   
1. Ghozlane A., Joseph A.P., Bornot A., de Brevern A.G.
   Analysis of protein chameleon sequence characteristics
   Bioinformation (2009) 3(9), 367-369.
   
   
2. Joseph A.P., Bornot A., de Brevern A.G.
   Local Structure Alphabets
   Protein Structure Prediction (2010)
   Huzefa Rangwala and George Karypis eds., Wiley, 75-106.
   
   
3. Joseph A.P., Agarwal G., Mahajan S., Gelly J.-C., Swapna L.S., Offmann B., Cadet F., Bornot A., Tyagi M., Valadié H., Schneider B., Etchebest C., Srinivasan N., de Brevern A.G.
   A short survey on Protein Blocks.
   Biophysical Reviews (2010) 2(3):137-145.
   
   
4. de Brevern A.G., Joseph A.P.
   Species Specific Amino Acid Sequence - Protein Local Structure Relationships: an analysis in the light of a structural alphabet.
   J. Theo. Biol. (2011) 51(2):493-507.
   
   
5. Mansiaux Y., Joseph A.P., Gelly J.-C., de Brevern A.G.
   Assignment of PolyProline II conformation and analysis of sequence - structure relationship
   PlosOne (2011) 6(3): e18401.
   
   
6. Joseph A.P., Srinivasan N., de Brevern A.G.
   Improvement of protein structure comparison using a structural alphabet
   Biochimie (2011) 93(9):1434-45.
   
   
7. J.-C. Gelly, Joseph A.P., Srinivasan N., de Brevern A.G.
   iPBA : A tool for protein structure comparison using sequence alignment strategies
   Nucleic Acid Res (2011) 39:W18-23.
   
   
8. Joseph A.P., Srinivasan N., de Brevern A.G.
   Cis-trans peptide variations in structurally similar proteins
   Amino Acids (2012) 43(3):1369-81.
   
   
9. Joseph A.P., Valadie H., Srinivasan N., de Brevern A.G.
   Local structural differences in homologous proteins: Specificities in different SCOP classes
   Plos One (2012) 7(6): e38805.
   
   
10. Joseph A.P., Srinivasan N., de Brevern A.G.
    Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies
    Biochimie (2012) 94:2025-34.
    
    
11. Léonard S.*, Joseph A.P.*, Srinivasan N., Gelly J.-C., de Brevern A.G.
    mulPBA : an efficient multiple protein structure alignment method based on a structural alphabet
    J Biol Struct Dyn (2013) in press.
    *: authors contribute equally.
    
    *: both authors contributed equally to this work.

Alexandre G. de Brevern
Last Modification : March 2024