Cragnolini, T.; Beton, J.; Topf, M. Cryo-EM Structure and B-Factor Refinement with Ensemble
Representation. 2022, No. Ccc, 1–40. DOI: 10.1101/2022.06.08.495259
HM Britt, T Cragnolini, S Khatun, A Hatimy, J James, N Page, JP Williams, C Hughes, R Denny,
K Thalassinos, J PC Vissers, “Evaluation of Acquisition Modes for Semi-Quantitative Analysis by
Targeted and Untargeted Mass Spectrometry”, Rapid Communications in Mass Spectrometry,
DOI: 10.1002/rcm.9308
2021
Martinez-Zapien D., Legrand P., McEwen A.G., Proux F., Cragnolini T., Pasquali S., Dock-Bregeon A.-C., “The crystal structure of the 5functional domain of the transcription riboregulator 7SK”, Nucleic acids research
Cragnolini T., Kryshtafovych A., Topf M., ``Cryo‐EM targets in CASP14'', Proteins. DOI: 10.1002/prot.26216}
Britt H., Cragnolini T., Thalassinos K., ``Integration of mass spectrometry data for structural biology'', Chemical Reviews.
Charles Eldrid, Aisha Ben-Younis, Jakub Ujma, Hannah Britt, Tristan Cragnolini, Symeon Kalfas, Dale Cooper-Shepherd, Nick Tomczyk, Kevin Giles, Mike Morris, Rehana Akter, Daniel Raleigh, and Konstantinos Thalassinos, ``Cyclic Ion Mobility–Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase'', J. Am. Soc. Mass Spectrom. DOI: 10.1021/jasms.1c00018
Cragnolini T., Sahota H., Joseph A., Sweeney A., Malhotra S., Vasishtan D., Topf M., ``TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows'', Acta Crystallographica Section D. DOI: 10.1107/S2059798320014928
2020
Cragnolini T., Sweeney A., Topf M., ``Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps'', Methods. Mol. Biol. DOI: 10.1007/978-1-0716-0966-8_9.
2019
Kimchi O., Cragnolini T., Brenner M.P., Colwell L., ``A polymer physics framework for the entropy of arbitrary pseudoknots'', Biophysical journal. DOI: 10.1016/j.bpj.2019.06.037
Kryshtafovych A., Malhotra S., Monastyrskyy B., Cragnolini T., Joseph A., Chiu W., Topf M., ``Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results'', Proteins. DOI: 10.1002/prot.25817}
2017
Cragnolini T., Chakraborty D., Šponer J., Derreumaux P., Pasquali P., “Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch”, The Journal of Chemical Physics
2016
Martinez-Zapien D., Legrand P., McEwen A.G., Proux F., Cragnolini T., Pasquali S., Dock-Bregeon A.-C., “The crystal structure of the 5functional domain of the transcription riboregulator 7SK”, Nucleic acids research
Stadlbauer P., Mazzanti L., Cragnolini T., Wales D.J., Derreumaux P., Pasquali S., Šponer J., “Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes”, Journal of Chemical Theory and Computation
2015
Cragnolini T., Laurin Y., Derreumaux P., Pasquali P., “Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings”, Journal of Chemical Theory and Computation
Cragnolini T., Derreumaux P., Pasquali S., “Ab initio RNA folding”, Journal of Physics: Condensed Matter.
2014
Doutreligne S., Cragnolini T., Pasquali S., Derreumaux P., Baaden M., “UnityMol: Interactive scientific visualization for integrative biology”, Large Data Analysis and Visualization (LDAV), 2014 IEEE 4th Symposium
Laurent B., Chavent M., Cragnolini T., Dahl A.C.E., Derreumaux P., Sansom M.S.P., Baaden M. “Epock: speedy analysis of protein pocket dynamics”, Bioinformatics.
Tiwari S.P., Fuglebakk E., Hollup S.M., Skjærven L., Cragnolini T., Grindhaug S.H., Tekle K.M. and Reuter N., “WEBnm@ v2.0: Web server and services for comparing protein flexibility”, BMC Bioinformatics.
Sterpone F., Melchionna S., Tuffery P., Pasquali S., Mousseau N., Cragnolini T., Chebaro Y., St-Pierre J.-F., Kalimeri M., Barducci A., Laurin Y., Tek A., Baaden M., Nguyen P.H. and Derreumaux P., “The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems”, Chemical Society Reviews.
2013
Cragnolini T., Derreumaux P., and Pasquali S. “Coarse-grained simulations of RNA and DNA duplexes.”, The Journal of Physical Chemistry B.
