Marco Pasi
Marco Pasi
Laboratoire de Biologie et Pharmacologie Appliquée - ENS Paris-Saclay
Verified email at ens-paris-saclay.fr - Homepage
TitleCited byYear
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
C Blanchet, M Pasi, K Zakrzewska, R Lavery
Nucleic acids research 39 (suppl_2), W68-W73, 2011
1222011
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, T Cheatham III, ...
Nucleic acids research 42 (19), 12272-12283, 2014
1212014
Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin‐like serine‐proteases
E Papaleo, M Pasi, L Riccardi, I Sambi, P Fantucci, LD Gioia
FEBS letters 582 (6), 1008-1018, 2008
612008
Analyzing ion distributions around DNA
R Lavery, JH Maddocks, M Pasi, K Zakrzewska
Nucleic acids research 42 (12), 8138-8149, 2014
582014
xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures.
M Pasi, M Tiberti, A Arrigoni, E Papaleo
Journal of chemical information and modeling 52 (7), 1865-1874, 2012
522012
Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics
M Pasi, JH Maddocks, R Lavery
Nucleic acids research 43 (4), 2412-2423, 2015
472015
PaLaCe: A coarse-grain protein model for studying mechanical properties
M Pasi, R Lavery, N Ceres
Journal of chemical theory and computation 9 (1), 785-793, 2013
432013
Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations
E Papaleo, M Pasi, M Tiberti, L De Gioia
PLoS One 6 (9), 2011
352011
Molecular determinants of enzyme cold adaptation: Comparative structural and computational studies of cold-and warm-adapted enzymes
E Papaleo, M Tiberti, G Invernizzi, M Pasi, V Ranzani
Current Protein and Peptide Science 12 (7), 657-683, 2011
332011
Dynamic properties of a psychrophilic α-amylase in comparison with a mesophilic homologue
M Pasi, L Riccardi, P Fantucci, L De Gioia, E Papaleo
The Journal of Physical Chemistry B 113 (41), 13585-13595, 2009
252009
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA
D Petkevičiūtė, M Pasi, O Gonzalez, JH Maddocks
Nucleic acids research 42 (20), e153-e153, 2014
232014
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding
J Li, JM Sagendorf, TP Chiu, M Pasi, A Perez, R Rohs
Nucleic acids research 45 (22), 12877-12887, 2017
212017
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics
M Pasi, R Lavery
Nucleic acids research 44 (11), 5450-5456, 2016
192016
The role of unconventional hydrogen bonds in determining BII propensities in B-DNA
A Balaceanu, M Pasi, PD Dans, A Hospital, R Lavery, M Orozco
The journal of physical chemistry letters 8 (1), 21-28, 2017
132017
DNA minicircles clarify the specific role of DNA structure on retroviral integration
M Pasi, D Mornico, S Volant, A Juchet, J Batisse, C Bouchier, V Parissi, ...
Nucleic acids research 44 (16), 7830-7847, 2016
122016
A protein solvation model based on residue burial
N Ceres, M Pasi, R Lavery
Journal of chemical theory and computation 8 (6), 2141-2144, 2012
102012
Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles
M Pasi, K Zakrzewska, JH Maddocks, R Lavery
Nucleic acids research 45 (7), 4269-4277, 2017
72017
Hospital A., Lavery R., Orozco M
A Balaceanu, M Pasi, PD Dans
The role of unconventional hydrogen bonds in determining BII propensities in …, 2017
62017
Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA
O Gonzalez, M Pasi, D Petkeviciute, J Glowacki, JH Maddocks
Multiscale Modeling & Simulation 15 (3), 1073-1107, 2017
52017
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules
PD Dans, A Balaceanu, M Pasi, AS Patelli, D Petkevičiūtė, J Walther, ...
Nucleic acids research 47 (21), 11090-11102, 2019
22019
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