Structural bioinformatics
Patrick Aloy
Principal Investigator
ICREA Research Professor
Office Tel : +34 93 403 96 90
e-mail : paloy
irbbarcelona.org
Background
Modern molecular and cell biology no longer focus only on single macromolecules but now look into pathways, complexes or even entire organisms. The many genome-sequencing projects have provided a near complete list of the components present in an organism, and post-genomic projects have aimed to catalogue the relationships between them.
The emerging field of systems biology is now centered mainly on unravelling these relationships. For example, an understanding of metabolic and signalling pathways or gene-regulatory networks relies on detailed knowledge of protein–metabolite, protein–protein and protein–nucleic-acid interactions. However, a full understanding of how molecules interact can be attained only from three-dimensional (3D) structures, as these provide crucial atomic details about binding. These details allow a more rational design of experiments to disrupt an interaction and therefore to perturb any system in which the interaction is involved.
Research Lines
Our main scientific interests lie in the field of structural bioinformatics, in particular, the use of high-resolution 3D structures to reveal the molecular bases of how macromolecular complexes and cell networks operate. Structural information for interacting cellular components willimprove our understanding of the whole-cell framework at atomic level, thereby contributing to biological systems modelling.
Funding
This group receives financial support from the following sources:
- European Commission
- ICREA (Institució Catalana de Recerca i Estudis Avançats)(Catalan Institute of Research and Advanced Studies)
More info
Structural bioinformatics
3did Update: domain-domain and peptide-mediated interactions of known 3D structure
Stein A, Panjkovich A and Aloy P
Nucleic Acids Res, 37, D300-304 (2009)
A network medicine approach to human disease
Zanzoni A, Soler-López M and Aloy P
FEBS Lett (2009)
Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits
Pache RA and Aloy P
Proteomics, 8 (10), 1959-1964 (2008)
Towards a molecular characterisation of pathological pathways
Pache RA, Zanzoni A, Naval J, Mas JM and Aloy P
FEBS Lett, 582 (8), 1259-1265 (2008)
A molecular interpretation of genetic interactions in yeast
Stein A and Aloy P
FEBS Lett, 582 (8), 1245-1250 (2008)
Approved drug mimics of short peptide ligands from protein interaction motifs
Parthasarathi L, Casey F, Stein A, Aloy P and Shields DC
J Chem Inf Model, 48 (10), 1943-1948 (2008)
Contextual specificity in peptide-mediated protein interactions
Stein A and Aloy P
PLoS ONE, 3 (7), e2524 (2008)
Targeting and tinkering with interaction networks
Russell RB and Aloy P
Nat Chem Biol, 4 (11), 666-673 (2008)
Shaping the future of interactome networks
Aloy P
Genome Biol, 8 (10), 316 (2007)
Structural systems biology: modelling protein interactions
Aloy P and Russell RB
Nat Rev Mol Cell Biol, 7 (3), 188-197 (2006)
Proteome survey reveals modularity of the yeast cell machinery
Gavin AC, Aloy P et al
Nature, 440 (7084), 631-636 (2006)
Target selection for complex structural genomics
Bravo J and Aloy P
Curr Opin Struct Biol, 16 (3), 385-392 (2006)
Discovery and hypothesis generation through bioinformatics
Dopazo J and Aloy P
Genome Biol, 7 (2), 307 (2006)
Ten thousand interactions for the molecular biologist
Aloy P and Russell RB
Nat Biotechnol, 22 (10), 1317-1321 (2004)
Structure-based assembly of protein complexes in yeast
Aloy P et al
Science, 303 (5666), 2026-2029 (2004)
Interrogating protein-interaction networks through structural biology
Aloy P and Russell RB
Proc Natl Acad Sci USA, 99 (9), 5896-5901 (2002)
Structural bioinformatics
Patrick Aloy
Principal Investigator
ICREA Research Professor
Office Tel : +34 93 403 96 90
e-mail : paloyirbbarcelona.org
Postdoctoral Fellow
Andreas Zanzoni
tel + 34 93 403 96 89
andreas.zanzoniirbbarcelona.org
Roberto Mosca
tel +34 93 403 96 89
roberto.moscairbbarcelona.org
Guillermo Suñé
tel +34 93 403 93 89
guillermo.suneirbbarcelona.org
Albert Pujol
tel +34 93 403 96 89
albert.pujolirbbarcelona.org
Joan López
tel +34 93 403 96 89
joan.lopezirbbarcelona.org
PhD Student
Amelie Stein
tel + 34 93 403 96 89
asteinirbbarcelona.org
Roland Pache
tel + 34 93 403 96 89
roland.pacheirbbarcelona.org
Marc Duocastella
+34 93 403 9689
marc.duocastellairbbarcelona.org
Clara Berenguer Balaguer
tel +34 93 402 02 28
clara.berenguerirbbarcelona.org
MSc Student
Rodrigo Arroyo
tel. +34 93 402 02 28
rodrigo.arroyoirbbarcelona.org
Research Assistant
Verónica Martínez Ocaña
tel +34 93 403 96 90
veronica.martinezirbbarcelona.org
Lab Technician
Ricart Lluís i Mir
tel +34 93 402 02 28
ricart.lluisirbbarcelona.org
Structural bioinformatics
