Publications

(1) denotes co-first authorships, * denotes corresponding author.


  1. Gavin AC (1), Aloy P (1) et al. & Russell RB, Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. (2006) Nature, Accepted.

  2. Aloy P & Russell RB. Structural systems biology: modelling protein interactions and complexes. (2006) Nat Rev Mol Cell Biol, Accepted.

  3. Dopazo J & Aloy P. European bioinformatics becomes more omics. (2005) Genome Biol, Accepted.

  4. Shah P, Aloy P, Bork P & Russell RB. Structure similarity to bridge sequence space: new families on the bridges. (2005) Protein Sci. 14:1305-1314 PubMed

  5. Aloy P* & Russell RB. Structure-based systems biology: A zoom lens for the cell. (2005) FEBS Lett. 579 :1854-1858 (Systems Biology special issue.) PubMed

  6. Aloy P, Pichaud M & Russell RB. Protein complexes: Structure prediction challenges for the 21st century. (2005) Curr Opin Struct Biol. 15 :15-22 PubMed

  7. Stein A, Russell RB & Aloy P*. 3did: interacting domains of known three-dimensional structure. (2005) Nucleic Acids Res. 33 :D413-417 PubMed

  8. Hothorn M, Wolf S, Aloy P, Greiner S & Scheffzek K. Structural insights into the target-specificity of plant invertase and pectin methylesterase inhibitory proteins. (2004) Plant Cell 16 :3437-3447PubMed

  9. Aloy P & Russell RB. Ten thousand interactions for the molecular biologist. (2004) Nature Biotechnol. 22 :1317-1321 PubMed

  10. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M & Sali A. A structural perspective on protein-protein interactions and complexes. (2004) Curr Opin Struct Biol 14 :313-324 PubMed

  11. Copley RR, Aloy P, Russell RB & Telford MJ. Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans. (2004) Evol Dev 6 :164-169 PubMed

  12. Aloy P* & Russell RB. Taking the mystery out of biological networks. (2004) EMBO reports 5 :349-350 PubMed

  13. Aloy P, Bottcher B, Ceulemans H, Leutwein C, Mellwig C, Fischer S, Gavin AC, Bork P, Superti-Furga G, Serrano L & Russell RB. Structure-based assembly of protein complexes in yeast. (2004) Science 303 :2026-2029 PubMed

  14. Aloy P, Stark A, Hadley C & Russell RB. Predictions without templates: New folds, secondary structure and contacts in CASP5. (2003) PROTEINS: Struct. Funct. Genet., 53 : 436-456 PubMed

  15. Aloy P, Ceulemans H, Stark A & Russell RB. The relationship between sequence and inteaction divergence in proteins. (2003) J Mol Biol, 332 :989-998 PubMed

  16. Aloy P* & Russell RB. Understanding and predicting protein assemblies with 3D structures. (2003) Comp Funct Genom, 4 :410-415

  17. Aloy P* & Russell RB. InterPreTS: protein Interaction Prediction through Tertiary Structure. (2003) Bioinformatics 19 :161-162 PubMed

  18. Aloy P & Russell RB. The third dimension for protein interactions and complexes. (2002) Trends Biochem. Sci. 27 :633-638 PubMed

  19. Aloy P & Russell RB. Potential artefacts in protein-interaction networks. (2002) FEBS Lett. 530 :253-254 PubMed

  20. Torrents E, Aloy P, Gibert I & Rodriguez-Trelles F. Ribonucleotide reductases: divergent evolution of an ancient enzyme. (2002) J Mol Evol. 55:138-152 PubMed

  21. Aloy P, Ciccarelli FD, Leutwein C, Gavin AC, Superti-Furga G, Bork P, Boettcher B & Russell RB. A complex prediction: three-dimensional model of the yeast exosome. (2002) EMBO reports 3:628-635 PubMed

  22. Aloy P & Russell RB. Interrogating protein-interaction networks through structural biology. (2002) P Natl Acad Sci USA. 99:5896-5901 PubMed

  23. Aloy P, Oliva B, Querol E, Aviles FX & Russell RB. Structural similarity to link sequence space. New potential superfamilies and implications for structural genomics. (2002) Protein Sci. 11:1101-1116 PubMed

  24. Aloy P, Querol E, Aviles FX & Sternberg MJE. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. (2001) J Mol Biol. 311:395-408 PubMed

  25. Mas JM, Aloy P, Marti-Renom MA, Oliva B, de Llorens R, Aviles FX & Querol E. Classification of protein disulphide-bridge topologies. (2001) J Comput Aided Mol Des. 15:477-87. PubMed

  26. Aloy P(1), Companys V(1), Vendrell J, Aviles FX, Fricker LD, Coll M & Gomis-Ruth FX. The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases.(2001) J Biol Chem.276:16177-84. PubMed

  27. Aloy P, Mas JM, Marti-Renom MA, Querol E, Aviles FX & Oliva B. Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. (2000)  J Comput Aided Mol Des. 14 :83-92. PubMed

  28. Mas JM, Aloy P, Marti-Renom MA, Oliva B, Blanco-Aparicio C, Molina MA, de Llorens R, Querol E & Aviles FX. Protein similarities beyond disulphide bridge topology. (1998) J Mol Biol. 284:541-8. PubMed

  29. Aloy P, Moont G, Gabb HA, Querol E, Aviles FX & Sternberg MJE. Modelling repressor proteins docking to DNA. (1998) Proteins . 33:535-49. PubMed

  30. Sternberg MJ, Aloy P, Gabb HA, Jackson RM, Moont G, Querol E & Aviles FX. A computational system for modelling flexible protein-protein and protein-DNA docking. (1998) Proc Int Conf Intell Syst Mol Biol . 6:183-92. PubMed

  31. Martí-Renom MA, Mas JM, Aloy P, Querol E, Avilés FX & Oliva B. Statistical Analysis of the Loop-geometry on a Non-redundant Database of Proteins. (1998) J Mol  Model. 11: 347.

  32. Aloy P, Catasus L, Villegas V, Reverter D, Vendrell J & Aviles FX. Comparative analysis of the sequences and three-dimensional models of human procarboxypeptidases A1, A2 and B. (1998) Biol Chem . 379:149-55. PubMed

  33. Aloy P, Cedano J, Oliva B, Aviles FX & Querol E. 'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins. (1997) Comput Appl Biosci. 13:231-4. PubMed

  34. Cedano J, Aloy P, Perez-Pons JA & Querol E. Relation between amino acid composition and cellular location of proteins. (1997) J Mol Biol. 266:594-600.   PubMed

Book chapters

  1. Aloy P. Secondary structure prediction, protein interactions & complexes, In Dictionary of bioinformatics and computational biology, J. Hancock & M. Zvelebil, ed. John Wiley & Sons, 2004

  2. Aloy P, Oliva B & Russell RB. Structural Genomics & Structural Bioinformatics, In Bioinformatics and Genomes: Current Prespectives, M. Andrade, ed. Horizon Scientific Press, 2003

  3. Aloy P. Structure-based prediction of protein function. PhD Thesis, Barcelona Autonomous Univiersity, 2000