Exploring the Universe of Protein Structures beyond the Protein Data Bank. - Pilar Cossio; Antonio Trovato; Fabio Pietrucci; Flavio Seno; Amos Maritan; Alessandro Laio (PLoS Comput. Biol., 2010)

BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures. - Edoardo Sarti; Stefano Zamuner; Pilar Cossio; Alessandro Laio; Flavio Seno; Antonio Trovato (Comput. Phys. Commun., 2013)

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. - Pilar Cossio; David Rohr; Fabio Baruffa; Markus Rampp; Volker Lindenstruth; Gerhard Hummer (Comput. Phys. Commun., 2017)

Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. - Rodrigo Ochoa; Alessandro Laio; Pilar Cossio (J. Chem. Inf. Model., 2019)

An automated protocol for modelling peptide substrates to proteases. - Rodrigo Ochoa; Mikhail D. Magnitov; Roman A. Laskowski; Pilar Cossio; Janet M. Thornton (BMC Bioinform., 2020)

Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. - Isaias Lans; Karen Palacio-Rodríguez; Claudio N. Cavasotto; Pilar Cossio (J. Comput. Aided Mol. Des., 2020)

Need for Cross-Validation of Single Particle Cryo-EM. - Pilar Cossio (J. Chem. Inf. Model., 2020)

In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. - Isaias Lans; Ernesto Anoz-Carbonell; Karen Palacio-Rodríguez; José Antonio Aínsa; Milagros Medina; Pilar Cossio (PLoS Comput. Biol., 2020)

PARCE: Protocol for Amino acid Refinement through Computational Evolution. - Rodrigo Ochoa; Miguel A. Soler; Alessandro Laio; Pilar Cossio (Comput. Phys. Commun., 2021)

Protocol for iterative optimization of modified peptides bound to protein targets. - Rodrigo Ochoa; Pilar Cossio; Thomas Fox (J. Comput. Aided Mol. Des., 2022)

Simulation-based inference of single-molecule force spectroscopy. - Lars Dingeldein; Pilar Cossio; Roberto Covino (Mach. Learn. Sci. Technol., 2023)

CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM. - Minkyu Jeon; Rishwanth Raghu; Miro Astore; Geoffrey Woollard; Ryan Feathers; Alkin Kaz; Sonya M. Hanson; Pilar Cossio; Ellen D. Zhong (NeurIPS, 2024)

Cryo-em images are intrinsically low dimensional. - Luke Evans; Octavian-Vlad Murad; Lars Dingeldein; Pilar Cossio; Roberto Covino; Marina Meila (CoRR, 2025)