Publikationen des Max-Planck-Institutes für Biophysik

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Zeitschriftenartikel (19)

2021
Zeitschriftenartikel
Ochoa, R.; Cossio, P.: PepFun: Open Source Protocols for Peptide-Related Computational Analysis. Molecules 26 (6), 1664 (2021)
2020
Zeitschriftenartikel
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)
Zeitschriftenartikel
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), S. 1063 - 1077 (2020)
Zeitschriftenartikel
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)
Zeitschriftenartikel
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)
Zeitschriftenartikel
Cossio, P.: Need for Cross-Validation of Single Particle Cryo-EM. Journal of Chemical Information and Modeling 60 (5), S. 2413 - 2418 (2020)
2019
Zeitschriftenartikel
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)
Zeitschriftenartikel
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), S. 3464 - 3473 (2019)
Zeitschriftenartikel
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, S. 1 - 14 (2019)
2018
Zeitschriftenartikel
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), S. 266 - 273 (2018)
Zeitschriftenartikel
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), S. 988 - 995 (2018)
Zeitschriftenartikel
Cossio, P.; Hummer, G.: Likelihood-based structural analysis of electron microscopy images. Current Opinion in Structural Biology 49, S. 162 - 168 (2018)
Zeitschriftenartikel
Cossio, P.; Hummer, G.; Szabo, A.: Transition paths in single-molecule force spectroscopy. The Journal of Chemical Physics 148 (12), 123309 (2018)
Zeitschriftenartikel
Sebastián, M.; Anoz-Carbonell, E.; Gracia, B.; Cossio, P.; Aínsa, J. A.; Lans, I.; Medina, M.: Discovery of antimicrobial compounds targeting bacterial type FAD synthetases. Journal of Enzyme Inhibition and Medicinal Chemistry 33 (1), S. 241 - 254 (2018)
2017
Zeitschriftenartikel
Cossio, P.; Rohr, D.; Baruffa, F.; Rampp, M.; Lindenstruth, V.; Hummer, G.: BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Computer Physics Communications 210 (01), S. 163 - 171 (2017)
2016
Zeitschriftenartikel
Cossio, P.; Hummer, G.; Szabo, A.: Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophysical Journal 111 (4), S. 832 - 840 (2016)
2015
Zeitschriftenartikel
Cossio, P.; Hummer, G.; Szabo, A.: On artifacts in single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 112 (46), S. 14248 - 14253 (2015)
2014
Zeitschriftenartikel
Ceballos, J. A.; Giraldo, M. A.; Cossio, P.: Effects of a disulfide bridge prior to amyloid formation of the ABRI peptide. RSC Advances 4, S. 36923 - 36928 (2014)
2013
Zeitschriftenartikel
Cossio, P.; Hummer, G.: Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Journal of Structural Biology 184 (3), S. 427 - 437 (2013)

Konferenzbeitrag (1)

2020
Konferenzbeitrag
Ochoa, R.; Laio, A.; Cossio, P.: Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II. 64th Annual Meeting of the Biophysical-Society, San Diego, CA, 15. Februar 2020 - 19. Februar 2020. Biophysical Journal 118 (3), Supplement 1 Aufl., S. 359A (2020)
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