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viernes, 29 de marzo 2024
29/03/2024
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Publications

1.Likelihood-based structural analysis of electron microscopy images
P. Cossio, and G. Hummer. Current Opinion in Structural Biology. Vol 49, 162-168. 2018.

2.Transition paths in single-molecule force spectroscopy. 
P. Cossio, G. Hummer, and A. Szabo. Journal of Chemical Physics. Vol. 148, 123309. 2018. 

3. Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. 
M. Sebastián, E. Anoz-Carbonell, B. Gracia, P. Cossio, J.A. Aínsa, I. Lans, M. Medina. Journal of enzyme inhibition and medicinal chemistry. Vol. 33, 241-254, 2018.

4. Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids.
R. Ochoa, M. Soler, A. Laio and P. Cossio. Physical Chemistry Chemical Physics. Vol. 20, 25901-25909. 2018.

5. The dimer-of-trimers assembly preventsăcatalysis at the transferase siteăof prokaryotic FAD Synthase.
I. Lans, J. Seco, A. Serrano, R. Burbano, P. Cossio, M. C. Daza, and M. Medina. Biophysical Journal. Vol 115, 988-995. 2018.

6. Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase.
P. Cossio, M. Allegretti, F. Mayer, V. Mueller, J. Vonck and G. Hummer. Microscopy. 10.1093/jmicro/dfy033, 2018.

7. Predicting the affinity of peptides to MHC Class II by scoring molecular dynamics simulations.
R. Ochoa, A. Laio and P. Cossio. J. Chem. Inf. Model. accepted. 2019

8. Exponential consensus ranking improves the outcome in docking and receptor ensemble docking.
K. Palacio-Rodriguez, I. Lans, C. N. Cavasotto, and P. Cossio. Scientific Reports. Vol. 9, 5142-5156. 2019

9. Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors. R.
Covino, M. T. Woodside, G. Hummer, A. Szabo, and P. Cossio. J. Chem. Phys. Vol. 151, 154115. 2019.

10.Validation tests for cryo-EM maps using an independent particle set
S Ortiz, L Stanisic, BA Rodriguez, M Rampp, G Hummer, P Cossio, Journal of structural biology: X 4, 100032, 2020.

11. Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II
R Ochoa, A Laio, P Cossio, Biophysical Journal 118 (3), 359a, 2020.

12. Need for Cross-Validation of Single Particle Cryo-EM
P Cossio, Journal of chemical information and modeling 60 (5), 2413-2418, 2020.

13. In silico discovery and biological validation of ligands of FAD synthase, a promising new antimicrobial target
I Lans, E Anoz-Carbonell, K Palacio-Rodríguez, JA Aínsa, M Medina, et al PLoS computational biology 16 (8), e1007898, 2020.

14. Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles
I Lans, K Palacio-Rodríguez, CN Cavasotto, P Cossio, Journal of computer-aided molecular design 34 (10), 1063-1077, 2020.

15. An automated protocol for modelling peptide substrates to proteases
R Ochoa, M Magnitov, RA Laskowski, P Cossio, JM Thornton BMC bioinformatics 21 (1), 1-20, 2021.

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

17. PARCE: Protocol for amino acid refinement through computational evolution
R Ochoa, MA Soler, A Laio, P Cossio, Computer Physics Communications 260, 107716, 2021.

18. Impact of structural observables from simulations to predict the effect of single-point mutations in MHC class II peptide binders
R Ochoa, RA Laskowski, JM Thornton, P Cossio, Front. Mol. Biosci. 8: 636562., 2021

19. Integrating Timescales From Molecules Up
RA Nome, P Cossio, Frontiers Media SA, 2021.

20. A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments
J Giraldo-Barreto, S Ortiz, EH Thiede, K Palacio-Rodriguez, B Carpenter, et al Scientific Reports 11 (1), 1-15, 2021.

 

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