Ligand-induced changes in the binding sites of proteins. - Xavier Fradera; Xavier de la Cruz; Carlos H. Tomich P. Silva; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (Bioinform., 2002)

Continuum and discrete calculation of fractional contributions to solvation free energy. - Antonio Morreale; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (J. Comput. Chem., 2003)

Hydration Free Energy in Macromolecules. - Antonio Morreale; Xavier de la Cruz; Tim Meyer; Josep Lluis Gelpí; F. Javier Luque; Modesto Orozco (Spanish Bioinformatics Conference, 2004)

Comparison of Active Centers of Proteins: The Kinesin Family as a Test Case. - Antoni Valencia; Martín Pérez; Adam Hospital; Joan Carles Fernández; Elena Manresa; Robert Soliva; Josep Lluis Gelpí; Modesto Orozco (Spanish Bioinformatics Conference, 2004)

PMUT: a web-based tool for the annotation of pathological mutations on proteins. - Carles Ferrer-Costa; Josep Lluis Gelpí; Leire Zamakola; Ivan Parraga; Xavier de la Cruz; Modesto Orozco (Bioinform., 2005)

A consensus view of protein dynamics. - Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco (Proc. Natl. Acad. Sci. USA, 2007)

FlexServ: an integrated tool for the analysis of protein flexibility. - Jordi Camps; Oliver Carrillo; Agustí Emperador; Laura Orellana; Adam Hospital; Manuel Rueda; Damjan Cicin-Sain; Marco D'Abramo; Josep Lluis Gelpí; Modesto Orozco (Bioinform., 2009)

Enabling HMMER for the Grid with COMP Superscalar. - Enric Tejedor; Rosa M. Badia; Romina Royo; Josep Lluis Gelpí (ICCS, 2010)

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. - Adam Hospital; Pau Andrio; Carlos Fenollosa; Damjan Cicin-Sain; Modesto Orozco; Josep Lluis Gelpí (Bioinform., 2012)

NAFlex: a web server for the study of nucleic acid flexibility. - Adam Hospital; Ignacio Faustino; Rosana Collepardo-Guevara; Carlos González; Josep Lluis Gelpí; Modesto Orozco (Nucleic Acids Res., 2013)

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale. - Michela Candotti; Alberto Pérez; Carles Ferrer-Costa; Manuel Rueda; Tim Meyer; Josep Lluis Gelpí; Modesto Orozco (PLoS Comput. Biol., 2013)

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. - Adam Hospital; Pau Andrio; Cesare Cugnasco; Laia Codó; Yolanda Becerra 001; Pablo D. Dans; Federica Battistini; Jordi Torres; Josep Ramón Goñi; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2016)

Four simple recommendations to encourage best practices in research software. - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. - Víctor López-Ferrando; Andrea M. Gazzo; Xavier de la Cruz; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2017)

Metadata to Describe Genomic Information. - Jaime Delgado; Daniel Naro; Silvia Llorente; Josep Lluis Gelpí; Romina Royo (MIE, 2018)

Towards FAIR principles for research software. - Anna-Lena Lamprecht; Leyla J. García; Mateusz Kuzak; Carlos Martinez-Ortiz; Ricardo Arcila; Eva Martin Del Pico; Victoria Dominguez Del Angel; Stephanie van de Sandt; Jon C. Ison; Paula Andrea Martínez; Peter McQuilton; Alfonso Valencia; et al. (Data Sci., 2020)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows. - Jorge Ejarque; Pau Andrio; Adam Hospital; Javier Conejero; Daniele Lezzi; Josep Lluis Gelpí; Rosa M. Badia (e-Science, 2022)

BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. - Genís Bayarri; Pau Andrio; Adam Hospital; Modesto Orozco; Josep Lluis Gelpí (Bioinform., 2022)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations. - Genís Bayarri; Pau Andrio; Adam Hospital; Modesto Orozco; Josep Lluis Gelpí (Nucleic Acids Res., 2022)

High-Throughput Prediction of the Impact of Genetic Variability on Drug Sensitivity and Resistance Patterns for Clinically Relevant Epidermal Growth Factor Receptor Mutations from Atomistic Simulations. - Aristarc Suriñach; Adam Hospital; Yvonne Westermaier; Luis Jordà; Sergi Orozco-Ruiz; Daniel Beltrán; Francesco Colizzi; Pau Andrio; Robert Soliva; Martí Municoy; Josep Lluis Gelpí; Modesto Orozco (J. Chem. Inf. Model., 2023)

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows. - Genís Bayarri; Pau Andrio; Josep Lluis Gelpí; Adam Hospital; Modesto Orozco (PLoS Comput. Biol., 2024)

Identity resolution of software metadata using Large Language Models. - Eva Martin Del Pico; Josep Lluis Gelpí; Salvador Capella-Gutiérrez (CoRR, 2025)