Structural Bioinformatics and Network Biology
Patrick Aloy
Group Leader
ICREA Research Professor
Office Tel : +34 93 40 39690
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
On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking
Feliu E, Aloy P and Oliva B
Protein Sci, 20 (3), 529-541 (2011)
A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks
Stein A, Rueda M, Panjkovich A, Orozco M and Aloy P
Structure, 19 (6), 881-889 (2011)
3did: identification and classification of domain-based interactions of known three-dimensional structure
Stein A, Céol A and Aloy P
Nucleic Acids Res, 39 (Database issue), D718-23. Epub 2010 (2011)
Interactome mapping suggests new mechanistic details underlying Alzheimer's disease
Soler-Lopez M, Zanzoni A, Lluis R, Stelzl U and Aloy P
Genome Res, 21 (3), 364-376 (2011)
Three-dimensional modeling of protein interactions and complexes is going 'omics
Stein A, Mosca R and Aloy P
Curr Opin Struc Biol, 21 (2), 200-208 (2011)
Systematic bioinformatics and experimental validation of yeast complexes reduces the rate of attrition during structural investigations
Brooks MA, Gewartowski K, Mitsiki E, Létoquart J, Pache RA, Billier Y, Bertero M, Corréa M, Czarnocki-Cieciura M, Dadlez M, Henriot V, Lazar N, Delbos L, Lebert D, Piwowarski J, Rochaix P, Böttcher B, Serrano L, Séraphin B, van Tilbeurgh H, Aloy P, Perrakis A and Dziembowski A
Structure, 18 (9), 1075-1082 (2010)
Revealing the molecular relationship between type 2 diabetes and the metabolic changes induced by a very-low-carbohydrate low-fat ketogenic diet
Farrés J, Pujol A, Coma M, Ruiz JL, Naval J, Mas JM, Molins A, Fondevila J and Aloy P
Nutr Metav (Lond), 7, 88 (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)
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
Stein A and Aloy P
PLoS Comput Biol, 6 (5), e1000789 (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)
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)
Uncovering new substrates for Aurora A kinase
Sardon T, Pache RA, Stein A, Molina H, Vernos I and Aloy P
EMBO Rep, 11 (12), 977-984 (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)
The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases.
Aloy P, Companys V, Vendrell J, Aviles FX, Fricker LD, Coll M, Gomis-Rüth FX.
J Biol Chem., 276 (19), 16177-16184 (2001)
Structural Bioinformatics and Network Biology
© Photos by Gianluca Battista/Massimiliano Minocri
Patrick Aloy
Group Leader
ICREA Research Professor
Office Tel : +34 93 40 39690
e-mail : paloyirbbarcelona.org
Research Associates
Andreas Zanzoni
tel +34 93 40 39689
e-mail: azanzoniirbbarcelona.org
Roberto Mosca
tel +34 93 40 39689
e-mail: roberto.moscairbbarcelona.org
Postdoctoral Fellows
Albert Pujol
tel +34 93 40 39689
e-mail: albert.pujolirbbarcelona.org
Arnaud Ceol
tel +34 93 40 39689
e-mail: arnaud.ceolirbbarcelona.org
Nahuai Badiola
tel +34 93 40 20228
e-mail: nahuai.badiolairbbarcelona.org
Samira Jaeger
tel +34 93 40 39689
e-mail: samira.jaegerirbbarcelona.org
PhD Students
Eva Capdevila
tel +34 93 40 39689
e-mail: eva.capdevilairbbarcelona.org
Manuel Alejandro Alonso
tel +34 93 40 39689
e-mail: manuel.alonsoirbbarcelona.org
Miquel Duran
tel +34 93 40 39689
e-mail: miquel.duranirbbarcelona.org
Rodrigo Arroyo
tel +34 93 40 20228
e-mail: rodrigo.arroyoirbbarcelona.org
Research Assistants
Jose Luis Ruiz
tel +34 93 40 39689
e-mail: jose.ruizirbbarcelona.org
Lab Technicians
Victor Alcalde
tel +34 93 40 39689
e-mail: victor.alcaldeirbbarcelona.org
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