Structural Bioinformatics and Network Biology
Patrick Aloy
Group Leader
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 and Network Biology
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
Stein A and Aloy P
PLoS Comput Biol, 6 (5), e1000789 (2010)
Unveiling the role of network and systems biology in drug discovery
Pujol A, Mosca R, Farrés J and Aloy P
Trends Pharmacol Sci, 31 (3), 115-123 (2010)
Structure of the FoxM1 DNA-recognition domain bound to a promoter sequence
Littler DR, Alvarez-Fernández M, Stein A, Hibbert RG, Heidebrecht T, Aloy P, Medema RH and Perrakis A
Nucleic Acids Res, 38 (13), 4527-4538 (2010)
Predicting protein-protein interaction specificity through the integration of three-dimensional structural information and the evolutionary record of protein domains
Panjkovich A and Aloy P
Mol Biosyst, 6 (4), 741-749 (2010)
Dynamic interactions of proteins in complex networks: a more structured view
Stein A, Pache RA, Bernadó P, Pons M and Aloy P
FEBS J, 276 (19), 5390-5405 (2009)
Splitting statistical potentials into meaningful scoring functions: testing the prediction of near-native structures from decoy conformations
Aloy P and Oliva B
BMC Struct Biol, 9, 71 (2009)
A network medicine approach to human disease
Zanzoni A, Soler-López M and Aloy P
FEBS Lett, 583 (11), 1759-1765 (2009)
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions
Pache RA, Babu MM and Aloy P
BMC Syst Biol, 3, 74 (2009)
Pushing structural information into the yeast interactome by high-throughput protein docking experiments
Mosca R, Pons C, Fernández-Recio J and Aloy P
PLoS Comput Biol, 5 (8), e1000490 (2009)
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)
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 and Network Biology
Patrick Aloy
Group Leader
ICREA Research Professor
Office Tel : +34 93 403 96 90
e-mail : paloyirbbarcelona.org
Research Associate
Roberto Mosca
tel +34 93 403 96 89
roberto.moscairbbarcelona.org
Research Assistant
José Luis Ruiz Camarero
tel + 34 93 403 96 89
jose.ruizirbbarcelona.org
Postdoctoral Fellows
Andreas Zanzoni
tel + 34 93 403 96 89
andreas.zanzoniirbbarcelona.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
Arnaud Ceol
tel + 34 93 403 96 89
arnaud.ceolirbbarcelona.org
Amelie Stein
tel +34 93 403 96 89
amelie.steinirbbarcelona.org
PhD Students
Roland Pache
tel + 34 93 403 96 89
roland.pacheirbbarcelona.org
Manuel Alejandro Alonso Tarajano
tel +34 93 403 96 89
manuel.alonsoirbbarcelona.org
Tiago Oliveira Botelho
tel +34 93 403 96 89
tiago.oliveirairbbarcelona.org
Rodrigo Arroyo
tel +34 93 402 02 28
rodrigo.arroyoirbbarcelona.org
Lab Technician
Ricart Lluís i Mir
tel +34 93 402 02 28
ricart.lluisirbbarcelona.org
Structural Bioinformatics and Network Biology
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