Borja Pitarch, David Juan, Florencio Pazos. (2026). Detection of Specificity-Determining Positions in Protein Families. Methods Mol. Biol. 2979:49-63.
[PubMed:41174306] [HTML] [PDF]

Borja Pitarch, Mónica Chagoyen, Juan A G Ranea, Florencio Pazos. (2025). A review on Gene Ontology evaluations. Database (Oxford). 2025:baaf058.
[PubMed:40996702] [HTML] [PDF]

Elena Díaz-Santiago, Aurelio A. Moya-García, Jesús Pérez-García, Raquel Yahyaoui, Christine Orengo, Florencio Pazos, James R. Perkins, Juan A. G. Ranea. (2025). Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks. Front Pharmacol. 15:1470931.
[PubMed:39911831] [HTML] [PDF]

Borja Pitarch, Florencio Pazos. (2025). Deep Learning Approaches for the Prediction of Protein Functional Sites. Molecules. 30(2):214.
[PubMed:39860084] [HTML] [PDF]

Sergio Alias-Segura, Florencio Pazos, Mónica Chagoyen. (2024). Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes. Bioinformatics. 40(11):btae646.
[PubMed:39468724] [HTML] [PDF] [Code]

Manuel Garrido-Romero, Florencio Pazos, Elisa Sánchez-Martínez, ..., Mónica Chagoyen, ..., Jorge Novoa, ..., F Javier Moreno. (2024). Relevance of gut microbiome research in food safety assessment. Gut Microbes.16(1):2410476.
[PubMed:39360551] [HTML] [PDF]

Jorge Novoa, Javier López-Ibáñez, Mónica Chagoyen, Juan A.G. Ranea, Florencio Pazos. (2024). CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. Database (Oxford).2024:baae025.
[PubMed:38564426] [HTML] [PDF] [CoMentG Webserver]

Jorge Novoa, Antonio Fernandez-Dumont, E.N. Clare Mills, F. Javier Moreno & Florencio Pazos. (2024). Advancing the allergenicity assessment of new proteins using a text mining resource. Food Chem Toxicol. 187:114638.
[PubMed:38582341] [HTML] [PDF] [Browse Allergen Symptoms]

Cyrielle Payen, Annaelle Kerouanton, Jorge Novoa, Florencio Pazos, Carlos Benito, Martine Denis, Muriel Guyard, F. Javier Moreno, rianne Chemaly. (2023). Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach. Microorganisms. 11(6):1464.
[PubMed:37374967] [HTML] [PDF]

Jorge Novoa, Monica Chagoyen, Carlos Benito, F. Javier Moreno, Florencio Pazos. (2023). PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information. Genes. 14(4):942.
[PubMed:37107700] [HTML] [PDF] [PMIDigest software]

Javier Lopez-Ibańez, Florencio Pazos, Monica Chagoyen. (2023). MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis. Nucleic Acids Research. 51(W1):W305-W309.
[PubMed:37178003] [HTML] [PDF] [MBROLE 3.0 server]

Juan A.G. Ranea, James R. Perkins, Mónica Chagoyen, Elena Díaz-Santiago, Florencio Pazos. (2022). Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View. Genes. 13(6):1081.
[PubMed:35741843] [HTML] [PDF]

Florencio Pazos*, Mónica Chagoyen, Pedro Seoane & Juan A.G. Ranea. (2022). CoMent: Relationships Between Biomedical Concepts Inferred From the Scientific Literature. J. Mol. Biol. 434(11):167568.
[PubMed:35662459] [HTML] [PDF] [CoMent server]

Florencio Pazos. (2022). Computational prediction of protein functional sites-Applications in biotechnology and biomedicine. Adv Protein Chem Struct Biol.130:39-57.
[PubMed:35534114] [HTML] [PDF]

Florencio Pazos. (2021). Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity. Bioengineering 8(12):201.
[PubMed:34940354] [HTML] [PDF] [supplementary files] [Xdet software]

Javier Lopez-Ibañez, Florencio Pazos, Monica Chagoyen. (2021). Predicting biological pathways of chemical compounds with a profile-inspired approach. BMC Bioinformatics 22(1):320.
[PubMed:34118870] [HTML] [PDF] [iFragMent server]

Borja Pitarch, Juan A. G. Ranea, Florencio Pazos. (2021). Protein Residues Determining Interaction Specificity In Paralogous Families. Bioinformatics. 37(8):1076-1082.
[PubMed:33135068] [HTML] [PDF] [Xdet software] [script for generating interaction-based protein functional distances]

Fernando M. Jabato, Pedro Seoane, James R. Perkins, Elena Rojano, Adrián García Moreno, Mónica Chagoyen, Florencio Pazos, Juan A. G. Ranea. (2021). Systematic identification of genetic systems associated with phenotypes in patients with rare genomic copy number variations. Human Genetics. 140(3):457-475
[PubMed:32778951] [HTML] [PDF] [PhenFun software]

Juan Antonio Garcia-Martin, Max Chavarria, Victor de Lorenzo, Florencio Pazos. (2020). Concomitant prediction of environmental fate and toxicity of chemical compounds. Biology Methods and Protocols 5(1):bpaa025.
[PubMed:33376807] [HTML] [PDF] [BiodegPred server]

Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea. (2020). Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases. PLoS Genetics 16(10):e1009054.
[PubMed:33001999] [HTML] [PDF] [PhenCo software]

Florencio Pazos* & Mónica Chagoyen. (2019). Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology. Brief Bioinform. 20(4):1329-1336.
[PubMed:29351590] [HTML] [PDF]

Monica Chagoyen, Juan A G Ranea and Florencio Pazos. (2019). Applications of molecular networks in biomedicine. Biology Methods and Protocols. 4(1):bpz012.
[PubMed:32395629] [HTML] [PDF]

Rafael Torres-Perez, Juan A. Garcia-Martin, Lluis Montoliu, Juan C. Oliveros* and Florencio Pazos*. (2019). WeReview: CRISPR Tools - Live Repository of Computational Tools for Assisting CRISPR/Cas Experiments. Bioengineering. 6:63.
[PubMed:31349743] [HTML] [PDF] ["WeReview: CRISPR Tools" server]

Javier López-Ibáñez, Laura T Martín, Mónica Chagoyen & Florencio Pazos. (2019). Bacterial Feature Finder (BaFF) - a system for extracting features overrepresented in sets of prokaryotic organisms. Bioinformatics. 35(18):3482-3483.
[PubMed:30844057] [HTML] [PDF] [BaFF server]

Florencio Pazos*, Adrian Garcia-Moreno & Juan C. Oliveros. (2018). Automatic detection of genomic regions with informative epigenetic patterns. BMC Genomics. 19:847.
[PubMed:30486775] [HTML] [PDF]

Diego Garrido-Martín & Florencio Pazos. (2018). Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics. 19(1):67.
[PubMed:29482506] [HTML] [PDF]

Sara González-Pérez, Florencio Pazos & Mónica Chagoyen. (2017). Factors affecting interactome-based prediction of human genes associated with clinical signs. BMC Bioinformatics. 18(1):340.
[PubMed:28715999] [HTML] [PDF]

Adán Alpízar, Fabio Marino, Antonio Ramos-Fernández, Manuel Lombardía, Anita Jeko, Florencio Pazos, Alberto Paradela, César Santiago, Albert J. R. Heck and Miguel Marcilla. (2017). A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens. Molecular & Cellular Proteomics 16:181-193.
[PubMed:27920218] [HTML] [PDF]

Juan C. Oliveros, Mónica Franch, Daniel Tabas-Madrid, David San-León, Lluis Montoliu, Pilar Cubas and Florencio Pazos (2016). Breaking-Cas - interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res. 44:W267-W271.
[PubMed:27166368] [HTML] [PDF] [Breaking-Cas server]

Mónica Chagoyen and Florencio Pazos (2016). Characterization of clinical signs in the human interactome. Bioinformatics. 32(12)1761-1765.
[PubMed:26861820] [HTML] [PDF]

Sara Fernandez-Novo, Florencio Pazos and Mónica Chagoyen (2016). Rare disease relations through common genes and protein interactions. Mol Cell Probes. 30(3):178-181.
[PubMed:26995712] [HTML] [ODCs server]

Mónica Chagoyen, Javier López-Ibáñez and Florencio Pazos (2016). Functional Analysis of Metabolomics Data. Methods Mol Biol. 1415:399-406.
[PubMed:27115644] [HTML] [PDF] [List of tools] [MBROLE 2.0 server]

Javier López-Ibáñez, Florencio Pazos and Mónica Chagoyen (2016). MBROLE 2.0-functional enrichment of chemical compounds. Nucleic Acids Res. 44:W201-W204.
[PubMed:27084944] [HTML] [PDF] [MBROLE 2.0 server] [tools for analysing metabolomics data]

Mónica Chagoyen, Juan A. García-Martín and Florencio Pazos (2016). Practical analysis of specificity-determining residues in protein families. Briefings in Bioinformatics 17(2):255-261.
[PubMed:26141829] [HTML] [PDF] [JDet software] [Xdet and other tools]

Daniel López and Florencio Pazos (2015). Protein functional features are reflected in the patterns of mRNA translation speed. BMC Genomics. 16:513
[PubMed:26155933] [HTML] [PDF]

David Ochoa, David Juan, Valencia, A. and Florencio Pazos (2015). Detection of significant protein co-evolution. Bioinformatics. 31(13):2166-2173
[PubMed:25717190] [HTML] [PDF] [Summary] [pMT software] [E coli co-evolutionary network] [Mirrortree web server]

Isabel Monte, Mats Hamberg, Andrea Chini, Selena Gimenez-Ibanez, Gloria Garcia-Casado, Andrea Porzel, Florencio Pazos, Marta Boter and Roberto Solano (2014). Rational design of a ligand-based antagonist of jasmonate perception. Nature Chemical Biology. 10(8):671-676.
[PubMed:24997606] [HTML] [PDF]

David Ochoa and Florencio Pazos. (2014). Practical aspects of protein co-evolution. Frontiers in Cell and Developmental Biology. 2:14.
[PubMed:25364721] [HTML] [PDF] [mirrortree] [available tools for protein coevolution]

Mónica Chagoyen, José L. Carrascosa, Florencio Pazos* and José M. Valpuesta*. (2014). Molecular determinants of the ATP hydrolysis asymmetry of the CCT chaperonin complex. Proteins: Structure, Function, and Bioinformatics. 82(5):703-707.
[PubMed:24420718] [HTML] [PDF] [JDet software]

A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. de Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso and F. Cava. (2014). Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Cryst D. D70:79-90.
[PubMed:24419381] [HTML] [PDF] [JDet software]

Florencio Pazos, Natalia Pietrosemoli, Juan A. García-Martín and Roberto Solano. (2013). Protein intrinsic disorder in plants. Frontiers in Plant Science. 4:363.
[PubMed:24062761] [HTML] [PDF] [more info]

Daniel Lopez and Florencio Pazos (2013). COPRED: prediction of fold, GO molecular function and functional residues at the domain level. Bioinformatics. 29(14):1811-1812.
[PubMed:23720488] [HTML] [PDF] [more info] [COPRED web server]

David Juan, Florencio Pazos and Alfonso Valencia (2013). Emerging methods in protein co-evolution. Nature Reviews Genetics. 14(4):249-261.
[PubMed:23458856] [HTML] [PDF] [more info and available tools]

Daniel Lopez and Florencio Pazos (2013). Concomitant prediction of function and fold at the domain level with GO-based profiles. BMC Bioinformatics. 14(S3):S12.
[PubMed:23514233] [HTML] [PDF] [more info] [SCOP2GO resource] [COPRED web server]

Natalia Pietrosemoli, Juan A. García-Martín, Roberto Solano and Florencio Pazos (2013). Genome-Wide Analysis of Protein Disorder in Arabidopsis thaliana: Implications for Plant Environmental Adaptation. PLoS One. 8(2):e55524.
[PubMed:23408995] [HTML] [PDF] [more info]

David Ochoa, Ponciano García-Gutiérrez, David Juan, Alfonso Valencia and Florencio Pazos. (2013). Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions. Molecular Biosystems. 9(1):70-76.
[PubMed:23104128] [HTML] [PDF] [Summary] [Mirrortree and related programs] [Mirrortree web server]

Monica Chagoyen and Florencio Pazos (2013). Tools for the functional interpretation of metabolomic experiments. Briefings in Bioinformatics. 14(6):737-744.
[PubMed:23063930] [HTML] [PDF] [list of tools]

Natalia Pietrosemoli, Daniel Lopez, Aldo Segura-Cabrera and Florencio Pazos. (2012). Computational Prediction of Important Regions in Protein Sequences. IEEE Signal Processing Magazine. 29(6):143-147.
[HTML] [PDF] [Xdet and other tools] [JDet software]

Thilo Muth, Juan A. García-Martín, Antonio Rausell, David Juan, Alfonso Valencia and Florencio Pazos (2012). JDet: Interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. Bioinformatics. 28(4):584-586.
[PubMed:22171333] [HTML] [PDF] [JDet software]

Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia and Florencio Pazos (2011). Selection of organisms for the co-evolution-based study of protein interactions. BMC Bioinformatics. 12:363.
[PubMed:21910884] [HTML] [PDF] [Summary] [Mirrortree and related programs] [Mirrortree web server]

Mark N. Wass, Gloria Fuentes, Carles Pons, Florencio Pazos & Alfonso Valencia. (2011). Towards the prediction of protein interaction partners using physical docking. Mol Syst Biol. 7:469.
[PubMed:21326236] [HTML] [PDF] [Summary]

Monica Chagoyen & Florencio Pazos. (2011). MBRole: enrichment analysis of metabolomic data. Bioinformatics.27(5):730-731.
[Pubmed:21208985] [HTML] [PDF] [MBROLE server]

Zurita E, Chagoyen M, Cantero M, Alonso R, Gonzalez-Neira A, Lopez-Jimenez A, Lopez-Moreno JA, Landel CP, Benitez J, Pazos F, Montoliu L. (2011). Genetic polymorphisms among C57BL/6 mouse inbred strains. Transgenic Res. 20(3):481-489.
[Pubmed:20506040] [HTML] [PDF]

Juan C. Triviño & Florencio Pazos. (2010). Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds. BMC Syst Biol. 4:46.
[Pubmed:20406431] [HTML] [PDF]

David Ochoa & Florencio Pazos. (2010). Studying the co-evolution of protein families with the Mirrortree web server. Bioinformatics. 26(10):1370-1371.
[Pubmed:20363731] [HTML] [PDF] [MirrorTree Server] [mirrortree and related programs]

Antonio Rausell, David Juan, Florencio Pazos & Alfonso Valencia. (2010). Protein interactions and ligand binding: From protein subfamilies to functional specificity. Proc Natl Acad Sci USA. 107(5):1995-2000.
[PubMed:20133844] [HTML] [PDF] [TreeDet server]

Monica Chagoyen & Florencio Pazos. (2010). Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data. Bioinformatics. 26(3):378-384.
[PubMed:19965879] [HTML] [PDF] [Summary]

Daniel Lopez & Florencio Pazos. (2009). Gene ontology functional annotations at the structural domain level. Proteins. 76(3):598-607.
[PubMed:19241468] [HTML] [PDF] [more info] [Scop2go database]

Florencio Pazos & Alfonso Valencia. (2008). Protein co-evolution, co-adaptation and interactions. EMBO J. 27(20):2648-2655.
[PubMed:18818697] [HTML] [PDF] [mirrortree and related programs]

Florencio Pazos, David Juan, Jose M Izarzugaza, Eduardo Leon, Alfonso Valencia. (2008). Prediction of protein interaction based on similarity of phylogenetic trees. Methods Mol Biol. 484:523-535.
[PubMed:18592199] [HTML] [mirrortree/tol-mirrortree programs] [ECID system] [TSEMA web server]

David Juan, Florencio Pazos, Alfonso Valencia. (2008). Co-evolution and co-adaptation in protein networks. FEBS Lett. 582(8):1225-1230.
[PubMed:18282476] [HTML] [PDF]

Angela del Pozo, Florencio Pazos, Alfonso Valencia. (2008). Defining functional distances over gene ontology. BMC Bioinformatics. 9:50.
[PubMed:18221506] [HTML] [PDF]

Jose M. G. Izarzugaza, David Juan, Carles Pons, Florencio Pazos, Alfonso Valencia. (2008). Enhancing the prediction of protein pairings between interacting families using orthology information. BMC Bioinformatics. 9:35.
[PubMed:18215279] [HTML] [PDF] [TAG-TSEMA web server @CNIO]

Jung-Wook Bang, Derek J. Crockford, Elaine Holmes, Florencio Pazos, Michael J. E. Sternberg, Stephen H. Muggleton, Jeremy K. Nicholson. (2008). Integrative Top-Down System Metabolic Modeling in Experimental Disease States via Data-Driven Bayesian Methods. J Proteome Res. 7(2):497-503.
[PubMed:18179164] [HTML] [PDF]

David Juan, Florencio Pazos & Alfonso Valencia. (2008). High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA. 105(3):934-939.
[PubMed:18199838] [HTML] [PDF] [ECID system]

Gómez, MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A. (2007). The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol. 3:114.
[PubMed:17551509] [HTML] [PDF] [BDPserver]

Angel Carro, Michael Tress, David Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia & Ana Rojas (2006). TreeDet: A Web Server to Explore the Sequence Space. Nucleic Acids Research. 34:W110-W115.
[PubMed:16844971] [HTML] [PDF] [TreeDet web server]

Jose M. G. Izarzugaza, David Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia & Florencio Pazos. (2006). TSEMA: Interactive Prediction of Protein Pairings Between Interacting Families. Nucleic Acids Research. 34:W315-W319.
[PubMed:16845017] [HTML] [PDF] [TSEMA web server @CNIO]

Florencio Pazos, Antonio Rausell & Alfonso Valencia. (2006). Phylogeny-independent detection of functional residues. Bioinformatics. 22(12):1440-1448.
[PubMed:16551661] [HTML] [PDF] [Supplementary information] [MTreedet/Xdet programs]

Fleming K, Kelley LA, Islam SA, MacCallum RM, Muller A, Pazos F, Sternberg MJ. (2006). The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci. 361(1467):441-451.
[PubMed:16524832] [HTML]

Florencio Pazos & Jung-Wook Bang. (2006). Computational Prediction of Functionally Important Regions in Proteins. Current Bioinformatics. 1(1):15-23.
[HTML] [PDF]

Florencio Pazos, Juan A. G. Ranea, David Juan & Michael J. E. Sternberg. (2005). Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. Journal of Molecular Biology. 352(4):1002-1015.
[PubMed:16139301] [HTML] [PDF] [online additional material] [MirrorTree program]

Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost & Alfonso Valencia. (2005). EVAcon: a protein contact prediction evaluation service. Nucleic Acids Research. 33:W347-W351.
[PubMed:15980486] [HTML] [PDF] [EVA main site] [EVAcon]

Florencio Pazos, David Guijas, Alfonso Valencia & Victor De Lorenzo. (2005). MetaRouter: bioinformatics for bioremediation. Nucleic Acids Research. 33:D588-D592.
[PubMed:15608267] [HTML] [PDF] [MetaRouter server] [Additional information]

Florencio Pazos & Michael J. E. Sternberg. (2004). Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci USA. 101(41):14754-14759.
[PubMed:15456910] [HTML] [PDF]

Volker A. Eyrich, Dariusz Przybylski, Ingrid Y. Koh, Osvaldo Grana, Florencio Pazos, Alfonso Valencia & Burkhard Rost. (2003). CAFASP3 in the spotlight of EVA. Proteins. 53(S6): 548-560.
[PubMed:14579345] [HTML] [PDF] [EVA main site] [EVA spanish mirror]

Florencio Pazos, Alfonso Valencia & Victor De Lorenzo. (2003). The organization of the Microbial Biodegradation Network from a Systems-Biology perspective. EMBO Rep. 4(10):994-999.
[PubMed:12973298] [HTML] [PDF] [Representations of the network and additional data]

Monica Balsera, Juan Arellano, Florencio Pazos, Damian Devos, Alfonso Valencia & Javier De Las Rivas. (2003). A single-tryptophan embedded in a four alpha-helices bundle domain of PsbQ protein. Eur J Biochem. 270(19):3916-3927.
[PubMed:14511373] [HTML] [PDF]

Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Marti-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali & Burkhard Rost. (2003). EVA: evaluation of protein structure prediction servers. Nucleic Acids Research. 31(13):3311-3315.
[PubMed:12824315] [HTML] [PDF] [EVA main site] [EVA spanish mirror]

Antonio Maraver, Ana Oña, Fernando Abaitua, Dolores Gonzalez, Roberto Clemente, Jose A. Ruiz-Diaz, Jose R. Caston, Florencio Pazos & Jose F. Rodriguez. (2003). The Oligomerization Domain of VP3, the Scaffolding Protein of Infectious Bursal Disease Virus, Plays a Critical Role in Capsid Assembly. Journal of Virology. 77(11):6438-6449.
[PubMed:12743301] [HTML] [PDF]

Alfonso Valencia & Florencio Pazos. (2003). Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal. 44:411-426.
[PubMed:12647397] [Book web site]

Antonio del Sol, Florencio Pazos & Alfonso Valencia. (2003). Automatic Methods for Predicting Functionally Important Residues. Journal of Molecular Biology. 326(4):1289-1302.
[PubMed:12589769] [HTML] [PDF] [MTreedet program] [Treedet web server]

David de Juan, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Piero Fariselli & Rita Casadio. (2003). A neural network approach to evaluate fold recognition results. Proteins: Structure, Function and Genetics. 50(4):600-608.
[PubMed:12577266] [HTML] [PDF] [LIBELLULA server]

Alfonso Valencia & Florencio Pazos (2002). Computational methods for the prediction of protein interactions. Current Opinion in Structural Biology. 12(3):368-373.
[PubMed:12127457] [HTML] [PDF]

Piero Fariselli, Florencio Pazos, Alfonso Valencia & Rita Casadio (2002). Prediction of protein-protein interaction sites in heterocomplexes with neural networks. European Journal of Biochemistry. 269(5):1356-1361.
[PubMed:11874449] [PDF] [PS] [ISPRED server]

Florencio Pazos & Alfonso Valencia (2002). In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins: Structure, Function and Genetics 47(2): 219-227.
[PubMed:11933068] [HTML] [PDF] [E coli database of predicted interactions]

Daniel Fischer, Arne Elofsson, Leszek Rychlewski, Florencio Pazos, Alfonso Valencia, Burkhard Rost, Angel R. Ortiz, Roland L. Dunbrack Jr. (2001). CAFASP2: The second critical assessment of fully automated structure prediction methods. Proteins: Structure, Function and Genetics 45(S5): 171-183.
[PubMed:11835495] [HTML] [PDF] [CAFASP2 web site] [Contact prediction server]

Volker A. Eyrich, Marc A. Mart-Renom, Dariusz Przybylski, András Fiser, Florencio Pazos, Alfonso Valencia, Andrej Sali & Burkhard Rost (2001). EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 17(12):1242-1243.
[PubMed:11751240] [HTML] [PDF] [EVA main site] [EVA spanish mirror]

Florencio Pazos & Alfonso Valencia (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering. 14(9):609-614.
[PubMed:11707606] [HTML] [PDF] [MirrorTree program] [Multiple sequence alignments for E coli proteins]

Florencio Pazos, Pedro Heredia, Alfonso Valencia & Javier de las Rivas (2001). Threading Structural Model of the Manganese-Stabilizing Protein PsbO Reveals Presence of Two Possible beta-Sandwich Domains. Proteins: Structure, Funcion and Genetics. 45(4):372-381.
[PubMed:11746685] [HTML] [PDF] [PsbO model]

Florencio Pazos, Burkhard Rost and Alfonso Valencia (1999). A platform for integrating threading results with other information. Bioinformatics. 15(12):1062-1063.
[PubMed:10745999] [HTML] [PDF] [Threadlize software]

Florencio Pazos, Manuela Helmer Citterich, Gabriele Ausiello and Alfonso Valencia (1997). Correlated Mutations Contain Information About Protein-Protein Interaction. Journal of Molecular Biology. 271(4):511-523.
[PubMed:9281423] [HTML] [PDF]

Florencio Pazos, Osvaldo Olmea and Alfonso Valencia (1997). A graphical interface for correlated mutations and other structure prediction methods. CABIOS. 13(3):319-321.
[PubMed:9183539] [HTML] [PDF] [PlotCorr software]