Structural Bioinformatics and Network Biology / Patrick Aloy: Structural Bioinformatics and Network Biology / Structural & Computational Biology / IRB Barcelona

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.

Structural Bioinformatics and Network Biology Group Webpage

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

Selected publications

The role of structural disorder in the rewiring of protein interactions through evolution
Mosca R, Pache RA and Aloy P.
Mol Cell Proteomics, 7 (11), M111.01496 (2012)

Interactome mapping suggests new mechanistic details underlying Alzheimer's disease
Soler-López M, Zanzoni A, Lluís R, Stelzl U and Aloy P.
Genome Res, 3 (21), 364-76 (2011)

Uncovering new substrates for Aurora A kinase
Sardon T, Pache RA, Stein A, Molina H, Vernos I and Aloy P.
Embo Rep, 12 (11), 977-84 (2010)

Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures
Stein A and Aloy P.
Plos Comput Biol, 5 (6), e1000789 (2010)

All publications list

The proton-pump inhibitor lansoprazole enhances amyloid Beta production
Badiola N, Alcalde V, Pujol A, Münter LM, Multhaup G, Lleó A, Coma M, Soler-López M and Aloy P.
PLoS One, 3 (8), e58837 (2013)

Structural Systems Pharmacology: the role of 3D structures in next generation drug development
Duran-Frigola M, Mosca R, Aloy P
Chem Biol (2013)

Functional and Structural Analysis of C-Terminal BRCA1 Missense Variants
Quiles F, Fernández-Rodríguez J, Mosca R, Feliubadaló L, Tornero E, Brunet J, Blanco I, Capellá G, Pujana MA, Aloy P, Monteiro A, Lázaro C
PLoS One, 4 (8) (2013)

Analysis of chemical and biological features yields mechanistic insights into drug side effects
Duran-Frigola M and Aloy P.
Chem Biol, 4 (20), 594-603 (2013)

Interactome3D: adding structural details to protein networks
Mosca R, Céol A and Aloy P.
Nat Methods, 1 (10), 47-53 (2013)

A novel framework for the comparative analysis of biological networks
Pache RA and Aloy P.
PLoS One, 2 (7), e31220 (2012)

Towards Alzheimer's root cause: ECSIT as an integrating hub between oxidative stress, inflammation and mitochondrial dysfunction: Hypothetical role of the adapter protein ECSIT in familial and sporadic Alzheimer's disease pathogenesis
Soler-López M, Badiola N, Zanzoni A and Aloy P.
Bioessays, 7 (34), 532-41 (2012)

NetAligner--a network alignment server to compare complexes, pathways and whole interactomes
Pache RA, Céol A and Aloy P.
Nucleic Acids Res, Web Server (40), W157-61 (2012)

From protein interaction networks to novel therapeutic strategies
Jaeger S and Aloy P.
Iubmb Life, 6 (64), 529-37 (2012)

Recycling side-effects into clinical markers for drug repositioning
Duran-Frigola M and Aloy P.
Genome Med, 1 (4), 3 (2012)

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M and Hermjakob H.
Nat Methods, 7 (8), 528-9 (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, 6 (19), 881-9 (2011)

Three-dimensional modeling of protein interactions and complexes is going 'omics
Stein A, Mosca R and Aloy P.
Curr Opin Struc Biol, 2 (21), 200-8 (2011)

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, 3 (20), 529-41 (2011)

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites
Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M and Via A.
Nucleic Acids Res, Database i (39), D268-71 (2011)

3did: identification and classification of domain-based interactions of known three-dimensional structure
Stein A, Céol A and Aloy P.
Nucleic Acids Res, Database i (39), D718-23 (2011)

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 Metab (Lond) (7), 88 (2010)

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, 9 (18), 1075-82 (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, 13 (38), 4527-38 (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, 4 (6), 741-9 (2010)

Unveiling the role of network and systems biology in drug discovery
Pujol A, Mosca R, Farrés J and Aloy P.
Trends Pharmacol Sci, 3 (31), 115-23 (2010)

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)

Dynamic interactions of proteins in complex networks: a more structured view
Stein A, Pache RA, Bernadó P, Pons M and Aloy P.
Febs J, 19 (276), 5390-405 (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, 8 (5), e1000490 (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)

A network medicine approach to human disease
Zanzoni A, Soler-López M and Aloy P.
Febs Lett, 11 (583), 1759-65 (2009)

3did Update: domain-domain and peptide-mediated interactions of known 3D structure
Stein A, Panjkovich A and Aloy P.
Nucleic Acids Res, Database i (37), D300-4 (2009)

Targeting and tinkering with interaction networks
Russell RB and Aloy P
Nat Chem Biol, 11 (4), 666-73 (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, 10 (48), 1943-48 (2008)

Contextual specificity in peptide-mediated protein interactions
Stein A and Aloy P
PLoS ONE, 7 (3), e2524 (2008)

Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits
Pache RA and Aloy P
Proteomics, 10 (8), 1959-64 (2008)

Towards a molecular characterisation of pathological pathways
Pache RA, Zanzoni A, Naval J, Mas JM and Aloy P
FEBS Lett, 8 (582), 1259-65 (2008)

A molecular interpretation of genetic interactions in yeast
Stein A and Aloy P
FEBS Lett, 8 (582), 1245-50 (2008)

Shaping the future of interactome networks
Aloy P
Genome Biol (8), 316 (2007)

Discovery and hypothesis generation through bioinformatics
Dopazo J and Aloy P.
Genome Biol, 2 (7), 307 (2006)

Target selection for complex structural genomics
Bravo J and Aloy P
Curr Opin Struc Biol (16), 385-92 (2006)

Structural systems biology: modeling protein interactions
Aloy P and Russell RB
Nat Rev Mol Cell Biol (7), 188-97 (2006)

Proteome survey reveals modularity of the yeast cell machinery
Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB and Superti-Furga G
Nature (440), 631-36 (2006)

Structure-based assembly of protein complexes in yeast
Aloy P et al
Science, 303 (5666), 2026-2029 (2004)

Ten thousand interactions for the molecular biologist
Aloy P and Russell RB
Nat Biotechnol, 22 (10), 1317-1321 (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

Patrick Aloy
Group Leader
ICREA Research Professor

Office Tel : +34 93 40 39690

e-mail : paloyirbbarcelona.org

Research Associates
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

Jacopo Negroni
tel +34 93 40 39689
e-mail: jacopo.negroniirbbarcelona.org

Jofre Tenorio
tel +34 93 40 39689
e-mail: jofre.tenorioirbbarcelona.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

Laura Isús
tel +34 93 40 39689
e-mail: laura.isusirbbarcelona.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
Roger Olivella
tel +34 93 40 39689
e-mail: roger.olivellairbbarcelona.org

Lab Technicians
Victor Alcalde
tel +34 93 40 39689
e-mail: victor.alcaldeirbbarcelona.org

Visiting Students
Lydia Siragusa
tel +34 93 40 39689
e-mail: lydia.siragusairbbarcelona.org

Structural Bioinformatics and Network Biology

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7 June 2013
Scientific News
A 6-million euro European project to study stem cell aging
• Headed by EMBL in Germany, the consortium “SyStemAge” seeks to identify the molecular mechanisms behind aging and the consequences of this process, and also to propose biomarkers to combat age-related diseases.

• The consortium involves clinical researchers, biologists specialized in two types of blood cancer, systems biologists, and biotech managers.

• Patrick Aloy, researcher at IRB Barcelona, will integrate the biological and clinical data to build dynamic maps of genes and proteins involved in the processes addressed in this study.
17 December 2012
Scientific News
IRB Barcelona develops the first public-access resource that provides 3D information at molecular level for 12,000 protein interactions
Researchers have developed a platform that compiles all the atomic data, previously stored in diverse databases, on protein structures and protein interactions for eight organisms of relevance. They apply a singular homology-based modelling procedure.

Given the high reliability of the results it produces, the new tool, Interactome3D, has received the endorsement of Nature Methods, the journal that has published the project.
19 April 2013

An IRB Barcelona study contributes to the understanding and prevention of the side effects caused by drugs
- This is the first study that studies and quantifies 1,600 known adverse effects of drugs currently on the market.
- The scientists Miquel Duran and Patrick Aloy provide a description of the molecular processes responsible for more than 1,000 secondary effects.
- This knowledge, which is available to the scientific community, may be of great use to minimize and predict adverse effects during drug design.
8 May 2013
Le Monde
Preventing the unwanted effects of drugs
29 April 2013
Gaceta Médica
Researchers explain the cause of 1162 side effects
28 April 2013
ARA
Did you know that… drugs may have 1,600 side effects
17 December 2012
Diario Médico
The interactions between proteins, in one clic
23 November 2012
Institutional news
An international competition reaffirms the potential of bioinformatics in the diagnosis of disease
The team led by IRB Barcelona’s David Rossell and Patrick Aloy and by Anaxomics Biotech ranked among the best in the world for diagnosing and classifying patients in a blind test for four diseases.
26 April 2012
BioEssays
Video-abstracts: a new tool to make science more attractive
15 April 2011
Institute News
IRB Barcelona and the BSC renew and expand their joint research programme in order to further computational biology
IRB Barcelona and the BSC show their commitment to computational biology by renewing the Joint IRB-BSC Programme, which also doubles in the number of researchers involved.

The programme aims to position itself as an international leader in computational biology.