T. Cragnolini

发表

Coarse-grained simulations of RNA and DNA duplexes.

P. Derreumaux, S. Pasquali, T. Cragnolini, 2013, The journal of physical chemistry. B.

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

D. Wales, J. Šponer, P. Derreumaux, 2016, Journal of chemical theory and computation.

The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK

S. Pasquali, F. Proux, Pierre Legrand, 2017, Nucleic acids research.

Cyclic Ion Mobility–Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase

D. Raleigh, K. Thalassinos, K. Giles, 2021, Journal of the American Society for Mass Spectrometry.

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Marc Baaden, Samuela Pasquali, Maria Kalimeri, 2014, Chemical Society reviews.

Evaluation of Acquisition Modes for the Quantitative Analysis of Cross-Linked Peptides by Targeted and Untargeted Mass Spectrometry

K. Thalassinos, R. Denny, T. Cragnolini, 2020 .

Cyclic Ion Mobility–Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase

D. Raleigh, K. Thalassinos, K. Giles, 2020, Journal of the American Society for Mass Spectrometry.

Cryo-EM structure and B-factor refinement with ensemble representation

M. Topf, T. Cragnolini, J. Beton, 2022, bioRxiv.

Integrating model simulation tools and cryo‐electron microscopy

M. Topf, A. Sweeney, T. Cragnolini, 2022, WIREs Computational Molecular Science.

Integration of Mass Spectrometry Data for Structural Biology.

K. Thalassinos, T. Cragnolini, Hannah M. Britt, 2021, Chemical reviews.

TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows

M. Topf, D. Vasishtan, S. Malhotra, 2021, Acta crystallographica. Section D, Structural biology.

Cryo‐EM targets in CASP14

M. Topf, T. Cragnolini, A. Kryshtafovych, 2021, Proteins.

Cryo‐electron microscopy targets in CASP13: Overview and evaluation of results

Wah Chiu, Andriy Kryshtafovych, Bohdan Monastyrskyy, 2019, Proteins.

Automated Modeling and Validation of Protein Complexes in Cryo-EM Maps.

M. Topf, A. Sweeney, T. Cragnolini, 2020, Methods in molecular biology.

A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.

Lucy J. Colwell, Lucy J Colwell, Michael P Brenner, 2019, Biophysical journal.

RNA structure prediction including pseudoknots through direct enumeration of states

Lucy J. Colwell, Michael P. Brenner, Tristan Cragnolini, 2018, bioRxiv.

The coarse-grained HiRE-RNA model for de novo calculations of RNA free energy surfaces, folding pathways and complex structure prediction

P. Derreumaux, S. Pasquali, T. Cragnolini, 2014, 1404.0568.

WEBnm@ v2.0: Web server and services for comparing protein flexibility

Lars Skjærven, Nathalie Reuter, Edvin Fuglebakk, 2014, BMC Bioinformatics.

Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.

Samuela Pasquali, Philippe Derreumaux, Tristan Cragnolini, 2015, Journal of chemical theory and computation.

Ab initio RNA folding

Samuela Pasquali, Philippe Derreumaux, Tristan Cragnolini, 2014, Journal of physics. Condensed matter : an Institute of Physics journal.

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.

Samuela Pasquali, David J Wales, Philippe Derreumaux, 2017, The Journal of chemical physics.

Epock: rapid analysis of protein pocket dynamics

Matthieu Chavent, Marc Baaden, Mark S. P. Sansom, 2014, Bioinform..

Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations

D. Raleigh, K. Thalassinos, T. Cragnolini, 2022, Analytical chemistry.

Evaluation of acquisition modes for semi‐quantitative analysis by targeted and untargeted mass spectrometry

J. Vissers, K. Thalassinos, R. Denny, 2022, Rapid communications in mass spectrometry : RCM.

UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules

Marc Baaden, Samuela Pasquali, Antoine Taly, 2015, 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR).