Patrick Aloy

发表

DynBench3D, a Web-Resource to Dynamically Generate Benchmark Sets of Large Heteromeric Protein Complexes.

Martino Bertoni, Patrick Aloy, P. Aloy, 2018, Journal of molecular biology.

An inter‐species protein–protein interaction network across vast evolutionary distance

Albert-László Barabási, Yu Xia, David E Hill, 2016, Molecular systems biology.

Using neighborhood cohesiveness to infer interactions between protein domains

José María Carazo, Carlos Oscar Sánchez Sorzano, Patrick Aloy, 2015, Bioinform..

InterPreTS: protein Interaction Prediction through Tertiary Structure

Robert B. Russell, Patrick Aloy, R. Russell, 2003, Bioinform..

A network biology approach to novel therapeutic estrategies

Patrick Aloy, 2017 .

Personalized cancer therapy prioritization based on driver alteration co-occurrence patterns

Patrick Aloy, Lidia Mateo, Miquel Duran-Frigola, 2020, Genome medicine.

Drug repositioning beyond the low-hanging fruits

Patrick Aloy, Lidia Mateo, Miquel Duran-Frigola, 2017 .

Novel Peptide-Mediated Interactions Derived from High-Resolution 3-Dimensional Structures

Patrick Aloy, Amelie Stein, P. Aloy, 2010, PLoS Comput. Biol..

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

Juan Fernández-Recio, Patrick Aloy, Roberto Mosca, 2009, PLoS Comput. Biol..

Bioactivity Profile Similarities to Expand the Repertoire of COVID-19 Drugs

Hugo Zaragoza, Martino Bertoni, Patrick Aloy, 2020, Journal of chemical information and modeling.

Eytan Ruppin, Xavier Barril, Gabriele Cruciani, 2017, PLoS Comput. Biol..

'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins

Baldomero Oliva, Francesc X. Avilés, Enrique Querol, 1997, Comput. Appl. Biosci..

Approved Drug Mimics of Short Peptide Ligands from Protein Interaction Motifs

Fergal P. Casey, Denis C. Shields, Patrick Aloy, 2008, J. Chem. Inf. Model..

Towards a detailed atlas of protein-protein interactions.

Tirso Pons, Alfonso Valencia, Arnaud Céol, 2013, Current opinion in structural biology.

Predictions without templates: New folds, secondary structure, and contacts in CASP5

Patrick Aloy, Robert B Russell, Alexander Stark, 2003, Proteins.

Nearest Neighbor Methods

Patrick Aloy, 2014 .

Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions.

M. Madan Babu, Patrick Aloy, Roland A. Pache, 2009, BMC systems biology.

3did: identification and classification of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, Amelie Stein, 2010, Nucleic Acids Res..

3did: interacting protein domains of known three-dimensional structure

Robert B. Russell, Patrick Aloy, Amelie Stein, 2004, Nucleic Acids Res..

3did Update: domain–domain and peptide-mediated interactions of known 3D structure

Alejandro Panjkovich, Patrick Aloy, Amelie Stein, 2008, Nucleic Acids Res..

NetAligner—a network alignment server to compare complexes, pathways and whole interactomes

Arnaud Céol, Patrick Aloy, Roland A. Pache, 2012, Nucleic Acids Res..

Understanding and Predicting Protein Assemblies With 3D Structures

Robert B. Russell, Patrick Aloy, R. Russell, 2003, Comparative and functional genomics.

A Computational System for Modeling Flexible Protein-Protein and protein-DNA Docking

Francesc X. Avilés, Enrique Querol, Michael J. E. Sternberg, 1998, ISMB.

3did: a catalog of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, Roberto Mosca, 2013, Nucleic Acids Res..

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

Julio Saez-Rodriguez, Wenyu Wang, Justin Guinney, 2021 .

Analysis of chemical and biological features yields mechanistic insights into drug side effects.

Patrick Aloy, Miquel Duran-Frigola, P. Aloy, 2013, Chemistry & biology.

A complex prediction: three‐dimensional model of the yeast exosome

Peer Bork, Patrick Aloy, Giulio Superti‐Furga, 2002, EMBO reports.

Assessing the applicability of template-based protein docking in the twilight zone.

Patrick Aloy, Roberto Mosca, P. Aloy, 2014, Structure.

3did: identification and classification of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, P. Aloy, 2010, Nucleic Acids Res..

Drug sensitivity in cancer cell lines is not tissue-specific

Patrick Aloy, Miquel Duran-Frigola, P. Aloy, 2015, Molecular Cancer.

Network-based proteomic approaches reveal the neurodegenerative, neuroprotective and pain-related mechanisms involved after retrograde axonal damage

Patrick Aloy, Francesco M. Mancuso, P. Aloy, 2015, Scientific Reports.

Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins

José M. Mas, Baldomero Oliva, Francesc X. Avilés, 1998 .

A structural perspective on proteinprotein interactions

Robert B. Russell, Frank Alber, Fred P. Davis, 2004 .

Shaping the future of interactome networks

Patrick Aloy, 2007, Genome Biology.

Systematic identification of molecular links between core and candidate genes in breast cancer.

Guillermo Suñé, Patrick Aloy, Miquel Duran-Frigola, 2015, Journal of molecular biology.

Baldomero Oliva, Enrique Querol, Patrick Aloy, 2002, Protein science : a publication of the Protein Society.

3did: a catalog of domain-based interactions of known three-dimensional structure

Arnaud Céol, Patrick Aloy, Roberto Mosca, 2013 .

The EHEC-host interactome reveals novel targets for the translocated intimin receptor

Peter Uetz, Roman Häuser, Patrick Aloy, 2014, Scientific Reports.

Contextual Specificity in Peptide-Mediated Protein Interactions

Patrick Aloy, P. Aloy, Amelie Stein, 2008, PloS one.

On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking

Elisenda Feliu, Patrick Aloy, P. Aloy, 2011, Protein science : a publication of the Protein Society.

Structural systems pharmacology: the role of 3D structures in next-generation drug development.

Patrick Aloy, Roberto Mosca, Miquel Duran-Frigola, 2013, Chemistry & biology.

Recycling side-effects into clinical markers for drug repositioning

Patrick Aloy, Miquel Duran-Frigola, 2012, Genome Medicine.

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution*

Patrick Aloy, Roberto Mosca, Roland A. Pache, 2012, Molecular & Cellular Proteomics.

The Proton-Pump Inhibitor Lansoprazole Enhances Amyloid Beta Production

Patrick Aloy, Montserrat Soler-López, Alberto Lleó, 2013, PloS one.

GOR Secondary‐Structure Prediction Method (Garnier–Osguthorpe–Robson Method)

Patrick Aloy, 2004 .

A chemo-centric view of human health and disease

Patrick Aloy, Miquel Duran-Frigola, David Rossell, 2014, Nature Communications.

Dynamic interactions of proteins in complex networks: a more structured view

Miquel Pons, Patrick Aloy, Pau Bernadó, 2009, The FEBS journal.

Incorporating high‐throughput proteomics experiments into structural biology pipelines: Identification of the low‐hanging fruits

Patrick Aloy, Roland A. Pache, P. Aloy, 2008, Proteomics.

The third dimension for protein interactions and complexes.

Patrick Aloy, Robert B Russell, R. Russell, 2002, Trends in biochemical sciences.

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Ashkan Golshani, Omar Wagih, John Parkinson, 2016, Cell reports.

Interrogating protein interaction networks through structural biology

Patrick Aloy, Robert B Russell, R. Russell, 2002, Proceedings of the National Academy of Sciences of the United States of America.

From protein interaction networks to novel therapeutic strategies

Patrick Aloy, P. Aloy, S. Jaeger, 2012, IUBMB life.

Ten thousand interactions for the molecular biologist

Patrick Aloy, Robert B Russell, R. Russell, 2004, Nature Biotechnology.

Target selection for complex structural genomics.

Patrick Aloy, Jerónimo Bravo, P. Aloy, 2006, Current opinion in structural biology.

A structural perspective on protein-protein interactions.

Frank Alber, Andrej Sali, Patrick Aloy, 2004, Current opinion in structural biology.

A Second-generation Protein–Protein Interaction Network of Helicobacter pylori*

Peter Uetz, Roman Häuser, Seesandra V Rajagopala, 2014, Molecular & Cellular Proteomics.

Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability

Aleksei Shkurin, Quaid Morris, Patrick Aloy, 2020, Molecular systems biology.

dSysMap: exploring the edgetic role of disease mutations

Jofre Tenorio-Laranga, Arnaud Céol, Patrick Aloy, 2015, Nature Methods.

Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans

Patrick Aloy, Richard R Copley, Robert B Russell, 2004, Evolution & development.

Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations

Patrick Aloy, Baldo Oliva, Baldo Oliva, 2009, BMC Structural Biology.

Residues Coevolution Guides the Systematic Identification of Alternative Functional Conformations in Proteins.

Modesto Orozco, Patrick Aloy, Roberto Mosca, 2016, Structure.

Pooled‐matrix protein interaction screens using Barcode Fusion Genetics

David E Hill, Marc Vidal, Laurence Pelletier, 2016, Molecular systems biology.

A reference map of the human protein interactome

Gary D. Bader, Yang Wang, Gary D Bader, 2019, bioRxiv.