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Pablo Ricardo Arantes
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Gaussian accelerated molecular dynamics: Principles and applications
J Wang, PR Arantes, A Bhattarai, RV Hsu, S Pawnikar, YM Huang, ...
Wiley Interdisciplinary Reviews: Computational Molecular Science 11 (5), e1521, 2021
1292021
Natural plant alkaloid (emetine) inhibits HIV-1 replication by interfering with reverse transcriptase activity
ALC Valadão, CM Abreu, JZ Dias, P Arantes, H Verli, A Tanuri, ...
Molecules 20 (6), 11474-11489, 2015
812015
Fighting COVID-19 using molecular dynamics simulations
PR Arantes, A Saha, G Palermo
ACS Central Science 6 (10), 1654-1656, 2020
582020
Structural basis for Cas9 off-target activity
M Pacesa, CH Lin, A Cléry, A Saha, PR Arantes, K Bargsten, MJ Irby, ...
Cell 185 (22), 4067-4081. e21, 2022
542022
Making it rain: cloud-based molecular simulations for everyone
PR Arantes, MD Polêto, C Pedebos, R Ligabue-Braun
Journal of Chemical Information and Modeling 61 (10), 4852-4856, 2021
432021
Molecular dynamics reveals a DNA-Induced dynamic switch triggering activation of CRISPR-Cas12a
A Saha, PR Arantes, RV Hsu, YB Narkhede, M Jinek, G Palermo
Journal of chemical information and modeling 60 (12), 6427-6437, 2020
432020
Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters
M Rossetti, R Merlo, N Bagheri, D Moscone, A Valenti, A Saha, ...
Nucleic acids research 50 (14), 8377-8391, 2022
402022
Electrospun PVA-Dacarbazine nanofibers as a novel nano brain-implant for treatment of glioblastoma: in silico and in vitro characterization
L Steffens, AM Morás, PR Arantes, K Masterson, Z Cao, M Nugent, ...
European Journal of Pharmaceutical Sciences 143, 105183, 2020
382020
Establishing the allosteric mechanism in CRISPR‐Cas9
Ł Nierzwicki, PR Arantes, A Saha, G Palermo
Wiley Interdisciplinary Reviews: Computational Molecular Science 11 (3), e1503, 2021
372021
Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9
L Nierzwicki, KW East, UN Morzan, PR Arantes, VS Batista, GP Lisi, ...
Elife 10, e73601, 2021
242021
Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
Ł Nierzwicki, KW East, JM Binz, RV Hsu, M Ahsan, PR Arantes, E Skeens, ...
Nature catalysis 5 (10), 912-922, 2022
192022
Emerging methods and applications to decrypt allostery in proteins and nucleic acids
PR Arantes, AC Patel, G Palermo
Journal of molecular biology, 167518, 2022
182022
Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods
A Saha, PR Arantes, G Palermo
Current opinion in structural biology 75, 102400, 2022
132022
In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination
C Pedebos, PR Arantes, GM Giesel, H Verli
Glycobiology 25 (11), 1183-1195, 2015
132015
Structural basis for reduced dynamics of three engineered HNH endonuclease lys-to-ala mutants for the clustered regularly interspaced short palindromic repeat (CRISPR …
J Wang, E Skeens, PR Arantes, F Maschietto, B Allen, GW Kyro, GP Lisi, ...
Biochemistry 61 (9), 785-794, 2022
102022
mM; Palermo, G.; Miao, Y. Gaussian accelerated molecular dynamics: Principles and applications
J Wang, PR Arantes, A Bhattarai, RV Hsu, S Pawnikar, Y Huang
WIREs Comput. Mol. Sci 11, e1521, 2021
92021
Development of GROMOS-compatible parameter set for simulations of chalcones and flavonoids
PR Arantes, MD Polêto, EBO John, C Pedebos, BI Grisci, M Dorn, ...
The Journal of Physical Chemistry B 123 (5), 994-1008, 2019
92019
Structural and dynamic insights into the HNH nuclease of divergent Cas9 species
HB Belato, MD Alexandra, L Nierzwicki, PR Arantes, G Jogl, G Palermo, ...
Journal of Structural Biology 214 (1), 107814, 2022
82022
Huang, Y. m. M.; Palermo, G.; Miao, Y., Gaussian accelerated molecular dynamics: Principles and applications
J Wang, PR Arantes, A Bhattarai, RV Hsu, S Pawnikar
Wiley Interdisciplinary Reviews: Computational Molecular Science 11, e1521, 2021
72021
Machines on genes through the computational microscope
S Sinha, C Pindi, M Ahsan, PR Arantes, G Palermo
Journal of chemical theory and computation 19 (7), 1945-1964, 2023
62023
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