Publications of Pilar Cossio

Palacio-Rodriguez, K.; Vroylandt, H.; Stelzl, L. S.; Pietrucci, F.; Hummer, G.; Cossio, P.: Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 13 (32), pp. 7490 - 7496 (2022)

Ochoa, R.; Lunardelli, V. A. S.; Rosa, D. S.; Laio, A.; Cossio, P.: Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol. Frontiers in immunology 13, 862851 (2022)

Rocha-Roa, C.; Orjuela, J. D.; Leidy, C.; Cossio, P.; Aponte-Santamaría, C.: Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models. FEBS Letters 595 (21), pp. 2701 - 2714 (2021)

Giraldo-Barreto, J.; Ortiz, S.; Thiede, E. H.; Palacio-Rodriguez, K.; Carpenter, B.; Barnett, A. H.; Cossio, P.: A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments. Scientific Reports 11 (1), 13657 (2021)

Nome, R. A.; Cossio, P.; Z, Y.: Editorial: Integrating Timescales From Molecules Up. Frontiers in Chemistry 9, 680533 (2021)

Ochoa, R.; Laskowski, R. A.; Thornton, J. M.; Cossio, P.: Impact of Structural Observables From Simulations to Predict the Effect of Single-Point Mutations in MHC Class II Peptide Binders. Frontiers in Molecular Biosciences 8, 636562 (2021)

Ochoa, R.; Cossio, P.: PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 26 (6), 1664 (2021)

Ochoa, R.; Soler, M. A.; Laio, A.; Cossio, P.: PARCE: Protocol for Amino acid Refinement through Computational Evolution. Computer Physics Communications 260, 107716 (2021)

Ochoa, R.; Magnitov, M.; Laskowski, R. A.; Cossio, P.; Thornton, J. M.: An automated protocol for modelling peptide substrates to proteases. BMC Bioinformatics 21 (1), 586 (2020)

Lans, I.; Palacio-Rodríguez, K.; Cavasotto, C. N.; Cossio, P.: Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles. Journal of Computer-Aided Molecular Design 34 (10), pp. 1063 - 1077 (2020)

Lans, I.; Anoz-Carbonell, E.; Palacio-Rodríguez, K.; Aínsa, J. A.; Medina, M.; Cossio, P.: In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target. PLoS Computational Biology 16 (8), e1007898 (2020)

Ortiz , S.; Stanisic, L.; Rodriguez , B. A.; Rampp, M.; Hummer, G.; Cossio, P.: Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 4, 100032 (2020)

Cossio, P.: Need for Cross-Validation of Single Particle Cryo-EM. Journal of Chemical Information and Modeling 60 (5), pp. 2413 - 2418 (2020)

Covino, R.; Woodside, M. T.; Hummer, G.; Szabo, A.; Cossio, P.: Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. The Journal of Chemical Physics 151 (15), 154115 (2019)

Ochoa, R.; Laio, A.; Cossio, P.: Predicting the Affinity of Peptides to Major Histocompatibility Complex Class II by Scoring Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 59 (8), pp. 3464 - 3473 (2019)

Palacio-Rodríguez, K.; Lans, I.; Cavasotto, C. N.; Cossio, P.: Exponential consensus ranking improves the outcome in docking and receptor ensemble docking. Scientific Reports 9, 5142, pp. 1 - 14 (2019)

Cossio, P.; Allegretti, M.; Mayer, F.; Müller, V.; Vonck, J.; Hummer, G.: Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase. Microscopy 67 (5), pp. 266 - 273 (2018)

Lans, I.; Seco, J.; Serrano, A.; Burbano, R.; Cossio, P.; Daza, M. C.; Medina, M.: The Dimer-of-Trimers Assembly Prevents Catalysis at the Transferase Site of Prokaryotic FAD Synthase. Biophysical Journal 115 (6), pp. 988 - 995 (2018)

Cossio, P.; Hummer, G.: Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 49, pp. 162 - 168 (2018)

Cossio, P.; Hummer, G.; Szabo, A.: Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 148 (12), 123309 (2018)