| 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 | 152 | 2021 |
| 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 | 90 | 2015 |
| 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 | 72 | 2022 |
| Fighting COVID-19 using molecular dynamics simulations PR Arantes, A Saha, G Palermo ACS Central Science 6 (10), 1654-1656, 2020 | 63 | 2020 |
| 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 | 58 | 2021 |
| 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 | 55 | 2022 |
| 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 | 47 | 2020 |
| 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 | 44 | 2020 |
| 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 | 41 | 2021 |
| 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 | 30 | 2021 |
| 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 | 26 | 2022 |
| Emerging methods and applications to decrypt allostery in proteins and nucleic acids PR Arantes, AC Patel, G Palermo Journal of molecular biology 434 (17), 167518, 2022 | 24 | 2022 |
| 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 | 19 | 2022 |
| An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a A Saha, M Ahsan, PR Arantes, M Schmitz, C Chanez, M Jinek, G Palermo Nature Communications 15 (1), 1473, 2024 | 14 | 2024 |
| 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 | 13 | 2015 |
| 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 | 11 | 2022 |
| 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 | 10 | 2022 |
| Development of GROMOS-compatible parameter set for simulations of chalcones and flavonoids PR Arantes, MD Poleto, EBO John, C Pedebos, BI Grisci, M Dorn, H Verli The Journal of Physical Chemistry B 123 (5), 994-1008, 2019 | 10 | 2019 |
| New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity AM Molina Vargas, S Sinha, R Osborn, PR Arantes, A Patel, S Dewhurst, ... Nucleic acids research 52 (2), 921-939, 2024 | 9 | 2024 |
| GPU-enhanced DFTB metadynamics for efficiently predicting free energies of biochemical systems A Kumar, PR Arantes, A Saha, G Palermo, BM Wong Molecules 28 (3), 1277, 2023 | 9 | 2023 |
