B. Oliva

发表

Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction.

M. Sternberg, P. Bates, E. Querol, 1998, Journal of molecular biology.

Backup in gene regulatory networks explains differences between binding and knockout results

I. Simon, Z. Bar-Joseph, A. Gitter, 2009, Molecular systems biology.

Computational analysis of multimorbidity between asthma, eczema and rhinitis

D. Postma, E. Melén, J. González, 2017, PloS one.

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

Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details

E. Guney, B. Oliva, O. Fornes, 2012, Molecular informatics.

Classification of common functional loops of kinase super‐families

Baldomero Oliva, Enrique Querol, Narcis Fernandez-Fuentes, 2004, Proteins.

Integrating Structure to Protein-Protein Interaction Networks That Drive Metastasis to Brain and Lung in Breast Cancer

Ozlem Keskin, Emre Guney, Attila Gursoy, 2013, PloS one.

Transcription Factor NRF2 as a Therapeutic Target for Chronic Diseases: A Systems Medicine Approach

E. Guney, A. I. Rojo, Á. Valverde, 2018, Pharmacological Reviews.

Understanding Cancer Progression Using Protein Interaction Networks

E. Guney, R. Sanz-Pamplona, B. Oliva, 2012 .

Understanding allergic multimorbidity within the non-eosinophilic interactome

E. Melén, G. Koppelman, J. Bousquet, 2019, PloS one.

Genetic and functional characterization of disease associations explains comorbidity

E. Guney, C. Rubio-Perez, F. Sanz, 2017, Scientific Reports.

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets.

E. Guney, F. Sanz, L. Furlong, 2019, Journal of molecular biology.

TPMS technology to infer biomarkers of macular degeneration prognosis in in silico simulated prototype-patients under the study of heart failure treatment with sacubitril and valsartan

Albert Pujol, B. Oliva, N. Fernandez-Fuentes, 2019, bioRxiv.

Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization

E. Guney, B. Oliva, 2012, PloS one.

Proximal Pathway Enrichment Analysis for Targeting Comorbid Diseases via Network Endopharmacology

E. Guney, Jörg Menche, F. Sanz, 2018, Pharmaceuticals.

Targeting comorbid diseases via network endopharmacology

E. Guney, Jörg Menche, F. Sanz, 2018, bioRxiv.

Extending signaling pathways with protein-interaction networks. Application to apoptosis.

Kevin A. Robertson, E. Guney, P. Ghazal, 2012, Omics : a journal of integrative biology.

iFrag: A Protein-Protein Interface Prediction Server Based on Sequence Fragments.

E. Guney, B. Oliva, Javier García-García, 2017, Journal of molecular biology.

Virtual-organism toy-model as a tool to develop bioinformatics approaches of Systems Biology for medical-target discovery

E. Guney, Albert Pujol, B. Oliva, 2013, 1301.2528.

On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction

B. Oliva, O. Fornes, G. de las Cuevas, 2021, NAR genomics and bioinformatics.

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Matti Pirinen, Jukka Corander, Krister Wennerberg, 2016, Nature Communications.

Comparative modelling of protein structure and its impact on microbial cell factories

B. Oliva, Joan Planas-Iglesias, N. B. Centeno, 2005, Microbial cell factories.

Detecting remotely related proteins by their interactions and sequence similarity.

Baldomero Oliva, Enrique Querol, Narayanan Eswar, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Functional and topological characterization of transcriptional cooperativity in yeast

B. Oliva, D. Aguilar, 2012, BMC Research Notes.

Topological comparison of methods for predicting transcriptional cooperativity in yeast

Daniel Aguilar, B. Oliva, Baldo Oliva, 2008, BMC Genomics.

On the use of knowledge-based potentials for the evaluation of models of protein-protein, protein-DNA, and protein-RNA interactions.

Oriol Fornes, Jaume Bonet, Javier Garcia-Garcia, 2014, Advances in protein chemistry and structural biology.

A supersecondary structure library and search algorithm for modeling loops in protein structures

Baldomero Oliva, András Fiser, Narcis Fernandez-Fuentes, 2006, Nucleic acids research.

Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-β-glucanase by molecular dynamics simulations

R. Gargallo, E. Querol, B. Oliva, 2006, Journal of molecular modeling.

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence

A. Gursoy, B. Oliva, J. Bonet, 2012 .

Expression of endoplasmic reticulum stress proteins is a candidate marker of brain metastasis in both ErbB-2+ and ErbB-2- primary breast tumors.

M. J. van de Vijver, R. Sanz-Pamplona, V. Moreno, 2011, The American journal of pathology.

Arginine citrullination at the C-terminal domain controls RNA Polymerase transcription

Narcís Fernández Fuentes, M. Beato, B. Oliva, 2018 .

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population

J. Bertranpetit, B. Oliva, Sandra Walsh, 2020, Scientific Reports.

CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells.

G. Castellano, M. Beato, B. Oliva, 2012, Genes & development.

gene regulation in breast cancer cells CDK 2-dependent activation of PARP-1 is required for hormonal Material Supplemental

G. Castellano, M. Beato, B. Oliva, 2012 .

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin‐α7 mediated nuclear import pathway

B. Oliva, J. Bonet, Swantje Thiele, 2019, The FEBS journal.

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway

B. Oliva, J. Bonet, Swantje Thiele, 2018, bioRxiv.

A computer model-built structure of the T. congolense trypanothione reductase in complex with NADP

O. Tapia, E. Horjales, B. Oliva, 1992 .

The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins

Sebastian A. Leidel, S. Leidel, J. Pérez-Ortín, 2019, Nature Communications.

C-tail valine is a key residue for stabilization of complex between potato inhibitor and carboxypeptidase A.

E. Querol, F. X. Avilés, B. Oliva, 1994, The Journal of biological chemistry.

A collection of designed peptides to target SARS-Cov-2 – ACE2 interaction: PepI-Covid19 database

B. Oliva, N. Fernandez-Fuentes, R. Molina, 2020, bioRxiv.

FN 14 and GRP 94 expression are prognostic / predictive biomarkers of brain metastasis outcome that open up new therapeutic strategies

E. Guney, V. Moreno, B. Oliva, 2016 .

FN14 and GRP94 expression are prognostic/predictive biomarkers of brain metastasis outcome that open up new therapeutic strategies

E. Guney, V. Moreno, B. Oliva, 2015, Oncotarget.

Intramolecular trimerization, a novel strategy for making multispecific antibodies with controlled orientation of the antigen binding domains

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2016, Scientific Reports.

Prediction of a new class of RNA recognition motif

B. Oliva, F. Avilés, J. Bonet, 2011, Journal of molecular modeling.

Systems biology PIANA : protein interactions and network analysis

B. Oliva, R. Aragues, Daniel Jaeggi, 2006 .

Beyond tissueInfo: functional prediction using tissue expression profile similarity searches

F. Campagne, B. Oliva, L. Skrabanek, 2008, Nucleic acids research.

CACNA1A Mutations Causing Early Onset Ataxia: Profiling Clinical, Dysmorphic and Structural-Functional Findings

B. Oliva, C. Ortez, A. Martínez-Monseny, 2021, International journal of molecular sciences.

methods for the calculation of electrostatic interactions Comparison of the particle-particle particle-mesh and reaction field Molecular dynamics simulation of highly charged proteins :

R. Gargallo, P. Hünenberger, B. Oliva, 2003 .

Molecular dynamics simulation of highly charged proteins: Comparison of the particle‐particle particle‐mesh and reaction field methods for the calculation of electrostatic interactions

R. Gargallo, P. Hünenberger, B. Oliva, 2003, Protein science : a publication of the Protein Society.

The N-Terminal Phosphorylation of RB by p38 Bypasses Its Inactivation by CDKs and Prevents Proliferation in Cancer Cells.

F. Real, B. Oliva, Javier García-García, 2016, Molecular cell.

The antigen-binding fragment of human gamma immunoglobulin prevents amyloid β-peptide folding into β-sheet to form oligomers

B. Oliva, J. Bonet, R. Vicente, 2017, Oncotarget.

Human Albumin Impairs Amyloid β-peptide Fibrillation Through its C-terminus: From docking Modeling to Protection Against Neurotoxicity in Alzheimer's disease

B. Oliva, Javier García-García, J. Bonet, 2019, Computational and structural biotechnology journal.

Automated structure-based learning to model co-operativity and protein-DNA interactions in cis -regulatory modules

B. Oliva, O. Fornes, J. Bonet, 2022 .

An inhibitor of interaction between the transcription factor NRF2 and the E3 ubiquitin ligase adapter β-TrCP delivers anti-inflammatory responses in mouse liver

J. Encinar, A. I. Rojo, A. Cuadrado, 2022, Redox biology.

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

B. Oliva, O. Fornes, J. Bonet, 2019, bioRxiv.

Computational Analysis of Cysteine Substitutions Modelled on the α- and β-domains of Cd5,Zn2-Metallothionein 2

B. Oliva, M. Capdevila, P. González-Duarte, 1996 .

Positive selection in MAOA gene is human exclusive: determination of the putative amino acid change selected in the human lineage

K. Kidd, A. Andrés, J. Bertranpetit, 2004, Human Genetics.

Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency

B. Oliva, J. Bonet, S. Villegas, 2013, mAbs.

Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning

B. Oliva, N. Fernandez-Fuentes, J. Aguirre-Plans, 2022, Frontiers in Bioinformatics.

Protein kinase CK2-dependent phosphorylation of the human Regulators of Calcineurin reveals a novel mechanism regulating the calcineurin-NFATc signaling pathway.

B. Oliva, E. Itarte, Javier García-García, 2013, Biochimica et biophysica acta.

ADP-ribose derived Nuclear ATP is Required for Chromatin Remodeling and Hormonal Gene Regulation (97 charact)

M. Beato, A. Pohl, B. Oliva, 2014, bioRxiv.

MODELLER: A Program for Protein Structure Modeling

Baldomero Oliva, John P. Overington, Francisco Melo, 2013 .

RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

B. Oliva, O. Fornes, G. de las Cuevas, 2018, bioRxiv.

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

E. Guney, A. Gonzalez-Perez, F. Sanz, 2018, Front. Genet..

Molecular dynamics as a tool to help design mutants

O. Tapia, F. X. Avilés, B. Oliva, 1991 .

A molecular dynamics study of a model built Pro-36-Gly mutant derived from the potato carboxypeptidase A inhibitor protein.

O. Tapia, E. Querol, F. X. Avilés, 1991, Biochemical and biophysical research communications.

Molecular dynamics simulation as a tool to design mutant proteins: Comparative studies of the modelled potato carboxypeptidase A inhibitor and its Pro36→Gly mutant with the receptor-docked X-ray structure

O. Tapia, E. Querol, B. Oliva, 1991 .

Structure-based learning to model complex protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements

B. Oliva, O. Fornes, J. Bonet, 2022, bioRxiv.

The Gene Causing the Best's Macular Dystrophy (BMD) Encodes a Putative Ion Exchanger

E. Querol, B. Oliva, J. Cedano, 2001, DNA sequence : the journal of DNA sequencing and mapping.

Influence of $$ {\text{NH - }}{{\text{S}}^\gamma } $$ bonding interactions on the structure and dynamics of metallothioneins

B. Oliva, N. Romero-Isart, M. Vašák, 2010, Journal of molecular modeling.

Influence of NHS gamma bonding interactions on the structure and dynamics of metallothioneins

B. Oliva, N. Romero-Isart, 2019 .

Binding of excess cadmium(II) to Cd7-metallothionein from recombinant mouse Zn7-metallothionein 1. UV-VIS absorption and circular dichroism studies and theoretical location approach by surface accessibility analysis.

B. Oliva, R. Gonzàlez-Duarte, S. Atrian, 1997, Journal of inorganic biochemistry.

On the sensitivity of MD trajectories to changes in water‐protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field

O. Tapia, X. Daura, E. Querol, 1996, Proteins.

Role of motif B loop in allosteric regulation of RNA-dependent RNA polymerization activity.

B. Oliva, N. Verdaguer, D. Garriga, 2013, Journal of molecular biology.

Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span

A. Navarro, G. Muntané, P. Joshi, 2021, bioRxiv.

Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data.

Emre Guney, Joan Planas-Iglesias, Narcis Fernandez-Fuentes, 2020, Journal of molecular biology.

An ensemble learning approach for modeling the systems biology of drug-induced injury

Laura I. Furlong, Giulia Callegaro, Baldo Oliva, 2019, Biology direct.

Signatures of selection in the human olfactory receptor OR5I1 gene.

Anna Ramírez-Soriano, Francesc Calafell, Jaume Bertranpetit, 2007, Molecular biology and evolution.

Knowledge-based modeling of peptides at protein interfaces: PiPreD

Baldomero Oliva, Narcis Fernandez-Fuentes, B. Oliva, 2015, Bioinform..

Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription.

M. Beato, B. Oliva, D. Eick, 2019, Molecular cell.

Aberystwyth University Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription

M. Beato, B. Oliva, D. Eick, 2019 .

Arginine Citrullination at t he C-Terminal Domain Controls RNA Polymerase II Transcription Graphical

M. Beato, B. Oliva, D. Eick, 2018 .

Insight into the machinery that oils chromatin dynamics

M. Beato, B. Oliva, N. Fernandez-Fuentes, 2016, Nucleus.

TranScout: prediction of gene expression regulatory proteins from their sequences

Baldomero Oliva, Francesc X. Avilés, Enrique Querol, 2002, Bioinform..

Prediction and Comparison of SalmonellaHuman and SalmonellaArabidopsis Interactomes

Judith Klein-Seetharaman, Sylvia Schleker, Javier Garcia-Garcia, 2012, Chemistry & biodiversity.

Bcl-x(L)-mediated changes in metabolic pathways of breast cancer cells: from survival in the blood stream to organ-specific metastasis.

David Andreu, Cristina Chiva, Ramón Aragüés, 2005, The American journal of pathology.

Predicting cancer involvement of genes from heterogeneous data

Baldomero Oliva, Chris Sander, Ramon Aragues, 2008, BMC Bioinformatics.

BIPS: BIANA Interolog Prediction Server. A tool for protein–protein interaction inference

Baldomero Oliva, Judith Klein-Seetharaman, Javier García-García, 2012, Nucleic Acids Res..

ADP-ribose–derived nuclear ATP synthesis by NUDIX5 is required for chromatin remodeling

M. Beato, A. Pohl, B. Oliva, 2016, Science.

Analysis of the Robustness of Network-Based Disease-Gene Prioritization Methods Reveals Redundancy in the Human Interactome and Functional Diversity of Disease-Genes

Emre Guney, E. Guney, B. Oliva, 2014, PloS one.

Toward PWAS: discovering pathways associated with human disorders

Baldomero Oliva, Emre Guney, E. Guney, 2011, BMC Bioinformatics.

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.

Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI).

Baldomero Oliva, Josep Vendrell, B. Oliva, 2002, Journal of molecular biology.

A taxonomy of organ-specific breast cancer metastases based on a protein-protein interaction network.

Xavier Messeguer, Javier García-García, Rebeca Sanz-Pamplona, 2012, Molecular bioSystems.

A Transcriptome-proteome Integrated Network Identifies Endoplasmic Reticulum thiol oxidoreductase (ERp57) as a Hub that Mediates Bone Metastasis*

Emre Guney, Omar E. Olarte, Pablo Loza-Alvarez, 2013, Molecular & Cellular Proteomics.

Underexpression of transcriptional regulators is common in metastatic breast cancer cells overexpressing Bcl-xL.

Rebeca Sanz, Ramón Aragüés, Victor Moreno, 2006, Carcinogenesis.

Prediction of Protein-Protein Binding Affinities from Unbound Protein Structures.

B. Oliva, N. Fernandez-Fuentes, A. Meseguer, 2021, Methods in molecular biology.

On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2017, Bioinform..

GIANT: A Cytoscape Plugin for Modular Networks

Daniele Santoni, Alessandro Giuliani, Fabio Cumbo, 2014, PloS one.

'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..

OP-MOLB210219 4948..4961

A. Navarro, G. Muntané, P. Joshi, 2021 .

Characterization of the first described mutation of human red blood cell phosphoglycerate mutase.

P. de Atauri, B. Oliva, J. Carreras, 2005, Biochimica et biophysica acta.

ModLink+: improving fold recognition by using protein-protein interactions

Marc A. Martí-Renom, Baldomero Oliva, Jordi Espadaler, 2009, Bioinform..

Modeling the helicase domain of Brome mosaic virus 1a replicase

J. Díez, B. Oliva, D. Garriga, 2004, Journal of molecular modeling.

Understanding protein-protein interactions using local structural features.

Elisenda Feliu, Joan Planas-Iglesias, Baldo Oliva, 2013, Journal of molecular biology.

Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB)

Baldomero Oliva, Jordi Espadaler, Narcis Fernandez-Fuentes, 2007, Bioinformatics and biology insights.

Identification of function-associated loop motifs and application to protein function prediction

E. Querol, B. Oliva, F. Avilés, 2006, Bioinform..

ArchDB: automated protein loop classification as a tool for structural genomics

Baldomero Oliva, Francesc X. Avilés, Enrique Querol, 2004, Nucleic Acids Res..

A Collection of Designed Peptides to Target SARS-CoV-2 Spike RBD—ACE2 Interaction

B. Oliva, N. Fernandez-Fuentes, R. Molina, 2021, International journal of molecular sciences.

ArchDB 2014: structural classification of loops in proteins

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2013, Nucleic Acids Res..

PIANA: protein interactions and network analysis

Baldomero Oliva, Ramon Aragues, Daniel Jaeggi, 2006, Bioinform..

The Crystal Structure of a Cardiovirus RNA-Dependent RNA Polymerase Reveals an Unusual Conformation of the Polymerase Active Site

B. Coutard, B. Oliva, F. V. van Kuppeveld, 2014, Journal of Virology.

Stability and fluctuations of the potato carboxypeptidase A protein inhibitor fold: a molecular dynamics study.

O. Tapia, E. Querol, F. X. Avilés, 1991, Biochemical and biophysical research communications.

Classification of protein disulphide-bridge topologies

M. Martí-Renom, P. Aloy, E. Querol, 2001, J. Comput. Aided Mol. Des..

Targeting Importin-α7 as a Therapeutic Approach against Pandemic Influenza Viruses

B. Oliva, J. Bonet, E. Fodor, 2015, Journal of Virology.

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications

Baldomero Oliva, András Fiser, Jaume Bonet, 2014, Bio Algorithms Med Syst..

Generation and characterization of monospecific and bispecific hexavalent trimerbodies

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2013, mAbs.

In Vivo Tumor Targeting and Imaging with Engineered Trivalent Antibody Fragments Containing Collagen-Derived Sequences

B. Oliva, L. Álvarez-Vallina, J. Bonet, 2009, PloS one.

Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking

Baldomero Oliva, Simon J. Cockell, Richard M. Jackson, 2007, Bioinform..

Contribution of C-tail residues of potato carboxypeptidase inhibitor to the binding to carboxypeptidase A A mutagenesis analysis.

E. Querol, F. X. Avilés, B. Oliva, 2000, European journal of biochemistry.

Multivalent antibodies: when design surpasses evolution.

Baldomero Oliva, Jaume Bonet, B. Oliva, 2010, Trends in biotechnology.

Functional pathways shared by liver and lung metastases: a mitochondrial chaperone machine is up-regulated in soft-tissue breast cancer metastasis

Rebeca Sanz, Ramón Aragüés, Rosette Lidereau, 2007, Clinical & Experimental Metastasis.

Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops

Baldomero Oliva, Enrique Querol, Michael J E Sternberg, 2005, Proteins.

In-silico simulated prototype-patients using TPMS technology to study a potential adverse effect of sacubitril and valsartan

Valentin Junet, Joaquim Aguirre-Plans, Baldo Oliva, 2020, PloS one.

In-silico drug repurposing study predicts the combination of pirfenidone and melatonin as a promising candidate therapy to reduce SARS-CoV-2 infection progression and respiratory distress caused by cytokine storm

J. Farrés, À. Olvera, B. Oliva, 2020, PloS one.

InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.

Oriol Fornes, Joan Planas-Iglesias, Jaume Bonet, 2016, Biochemical Society transactions.

Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships

Baldomero Oliva, Jordi Espadaler, Oriol Romero-Isart, 2005, Bioinform..

CAPS-DB: a structural classification of helix-capping motifs

Baldomero Oliva, Narcis Fernandez-Fuentes, Joan Segura, 2011, Nucleic Acids Res..

Biological pathways contributing to organ-specific phenotype of brain metastatic cells.

B. Oliva, S. Boluda, À. Sierra, 2008, Journal of proteome research.

Corrigendum to “An inhibitor of interaction between the transcription factor NRF2 and the E3 ubiquitin ligase adapter β-TrCP delivers anti-inflammatory responses in mouse liver” [Redox Biol. 55 (2022) 102396/PMID: 35839629]

J. Encinar, A. I. Rojo, A. Cuadrado, 2022, Redox biology.

M. Martí-Renom, P. Aloy, E. Querol, 1998, Journal of molecular biology.

Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features

Daniel Aguilar, B. Oliva, Baldo Oliva, 2012, PloS one.

Calculation of the group-based pressure in molecular simulations. II. Numerical tests and application to liquid water

Baldomero Oliva, Philippe H. Hünenberger, P. Hünenberger, 2002 .

Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design

Baldomero Oliva, Joan Segura, Joan Planas-Iglesias, 2014, Bioinform..

GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms

Baldomero Oliva, Emre Guney, Javier García-García, 2014, Bioinform..

Biana: a software framework for compiling biological interactions and analyzing networks

Baldomero Oliva, Emre Guney, Javier García-García, 2010, BMC Bioinformatics.

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Marc A. Martí-Renom, Baldomero Oliva, Andrej Sali, 2007, PLoS Comput. Biol..

The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins

S. Leidel, J. Pérez-Ortín, J. Díez, 2019, Nature Communications.

Amyloid-β Peptide Nitrotyrosination Stabilizes Oligomers and Enhances NMDAR-Mediated Toxicity

N. Inestrosa, B. Oliva, J. Bonet, 2016, The Journal of Neuroscience.

Red cell glucose phosphate isomerase (GPI): a molecular study of three novel mutations associated with hereditary nonspherocytic hemolytic anemia

B. Oliva, E. Beutler, J. Carreras, 2006, Human mutation.

Glucose phosphate isomerase deficiency: enzymatic and familial characterization of Arg346His mutation.

B. Oliva, J. Vives Corrons, J. Carreras, 2005, Biochimica et biophysica acta.

Phospho-mimicking Atf1 mutants bypass the transcription activating function of the MAP kinase Sty1 of fission yeast

B. Oliva, J. Ayté, Laura Sánchez-Mir, 2017, Current Genetics.

Deciphering the role of the signal- and Sty1 kinase-dependent phosphorylation of the stress-responsive transcription factor Atf1 on gene activation

B. Oliva, J. Ayté, Laura Sánchez-Mir, 2017, The Journal of Biological Chemistry.

Prediction of enzyme function by combining sequence similarity and protein interactions

Marc A. Martí-Renom, Baldomero Oliva, Francesc X. Avilés, 2008, BMC Bioinformatics.

Comparative modelling of protein structure and its impact on microbial cell factories

B. Oliva, Joan Planas-Iglesias, N. B. Centeno, 2005, Microbial cell factories.

Model Formulation: Training Multidisciplinary Biomedical Informatics Students: Three Years of Experience

Baldomero Oliva, Victor Maojo, Erik M. van Mulligen, 2008, J. Am. Medical Informatics Assoc..

Revealing Shared Proteins and Pathways in Cardiovascular and Cognitive Diseases Using Protein Interaction Network Analysis

Raul Vicente, J. García-Ojalvo, O. Keskin, 2023, bioRxiv.

Comparative modelling of protein structure and its impact on microbial cell factories

B. Oliva, Joan Planas-Iglesias, N. B. Centeno, 2005 .

Analysis of electrostatic contributions to the selectivity of interactions between RING‐finger domains and ubiquitin‐conjugating enzymes

B. Oliva, T. Thomson, J. Scheper, 2009, Proteins.

An automated classification of the structure of protein loops.

Baldomero Oliva, Francesc X. Avilés, Enrique Querol, 1997, Journal of molecular biology.

iLoops: a protein-protein interaction prediction server based on structural features

Baldomero Oliva, Javier García-García, Joan Planas-Iglesias, 2013, Bioinform..

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Suleiman A. Khan, Michael A. Goren, Donna E. Dillenberger, 2016, Nature Communications.

Integration and Prediction of PPI Using Multiple Resources from Public Databases

Baldo Oliva, Ramón Aragüés, Javier Garcia-Garcia, 2008 .

Backup in gene regulatory networks explains differences between binding and knockout results

I. Simon, Z. Bar-Joseph, A. Gitter, 2009, Molecular systems biology.

Theoretical study of the role of arginine 127 in the water-promoted mechanism of peptide cleavage by carboxypeptidase A

B. Oliva, Àngels González-Lafont, J. M. Lluch, 1998 .

The N-Terminal Phosphorylation of RB by p38 Bypasses Its Inactivation by CDKs and Prevents Proliferation in Cancer Cells.

F. Real, B. Oliva, Javier García-García, 2016, Molecular cell.

GUILDify v2.0: A Tool to Identify Molecular Networks Underlying Human Diseases, Their Comorbidities and Their Druggable Targets.

E. Guney, F. Sanz, L. Furlong, 2019, Journal of molecular biology.

Evaluation of Computationally Designed Peptides against TWEAK, a Cytokine of the Tumour Necrosis Factor Ligand Family

B. Oliva, À. Sierra, D. Andreu, 2021, International journal of molecular sciences.