Samuela Pasquali
Samuela Pasquali
University of Paris
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Amyloid β protein and Alzheimer’s disease: When computer simulations complement experimental studies
J Nasica-Labouze, PH Nguyen, F Sterpone, O Berthoumieu, NV Buchete, ...
Chemical reviews 115 (9), 3518-3563, 2015
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
HH Gan, S Pasquali, T Schlick
Nucleic acids research 31 (11), 2926-2943, 2003
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
F Sterpone, S Melchionna, P Tuffery, S Pasquali, N Mousseau, ...
Chemical Society Reviews 43 (13), 4871-4893, 2014
HiRE-RNA: a high resolution coarse-grained energy model for RNA
S Pasquali, P Derreumaux
The journal of physical chemistry B 114 (37), 11957-11966, 2010
The coarse-grained OPEP force field for non-amyloid and amyloid proteins
Y Chebaro, S Pasquali, P Derreumaux
The Journal of Physical Chemistry B 116 (30), 8741-8752, 2012
Analysis of protein sequence/structure similarity relationships
HH Gan, RA Perlow, S Roy, J Ko, M Wu, J Huang, S Yan, A Nicoletta, ...
Biophysical journal 83 (5), 2781-2791, 2002
Folding and aggregation of designed proteins
RA Broglia, G Tiana, S Pasquali, HE Roman, E Vigezzi
Proceedings of the National Academy of Sciences 95 (22), 12930-12933, 1998
Coarse-grained simulations of RNA and DNA duplexes
T Cragnolini, P Derreumaux, S Pasquali
The Journal of Physical Chemistry B 117 (27), 8047-8060, 2013
Epock: rapid analysis of protein pocket dynamics
B Laurent, M Chavent, T Cragnolini, ACE Dahl, S Pasquali, ...
Bioinformatics 31 (9), 1478-1480, 2015
Coarse-grained HiRE-RNA model for ab initio RNA folding beyond simple molecules, including noncanonical and multiple base pairings
T Cragnolini, Y Laurin, P Derreumaux, S Pasquali
Journal of chemical theory and computation 11 (7), 3510-3522, 2015
Coarse-grained simulations complemented by atomistic molecular dynamics provide new insights into folding and unfolding of human telomeric G-quadruplexes
P Stadlbauer, L Mazzanti, T Cragnolini, DJ Wales, P Derreumaux, ...
Journal of Chemical Theory and Computation 12 (12), 6077-6097, 2016
UnityMol: interactive scientific visualization for integrative biology
S Doutreligne, T Cragnolini, S Pasquali, P Derreumaux, M Baaden
2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV), 109-110, 2014
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
S Pasquali, HH Gan, T Schlick
Nucleic acids research 33 (4), 1384-1398, 2005
Ten simple rules to create a serious game, illustrated with examples from structural biology
M Baaden, O Delalande, N Ferey, S Pasquali, J Waldispühl, A Taly
PLoS computational biology 14 (3), e1005955, 2018
Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin
FLB Da Silva, S Pasquali, P Derreumaux, LG Dias
Soft Matter 12 (25), 5600-5612, 2016
The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK
D Martinez-Zapien, P Legrand, AG McEwen, F Proux, T Cragnolini, ...
Nucleic acids research 45 (6), 3568-3579, 2017
Protein-RNA complexation driven by the charge regulation mechanism
FLB da Silva, P Derreumaux, S Pasquali
Biochemical and biophysical research communications 498 (2), 264-273, 2018
Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch
T Cragnolini, D Chakraborty, J Šponer, P Derreumaux, S Pasquali, ...
The Journal of Chemical Physics 147 (15), 2017
Structural transitions in the RNA 7SK 5′ hairpin and their effect on HEXIM binding
K Röder, G Stirnemann, AC Dock-Bregeon, DJ Wales, S Pasquali
Nucleic acids research 48 (1), 373-389, 2020
Impact of thermostats on folding and aggregation properties of peptides using the optimized potential for efficient structure prediction coarse-grained model
YG Spill, S Pasquali, P Derreumaux
Journal of chemical theory and computation 7 (5), 1502-1510, 2011
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