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Pablo Ricardo Arantes, Ph.D - Publications

Affiliations: 
2019- Department of Bioengineering University of California, Riverside, Riverside, CA, United States 
Area:
Computational Chemistry, Molecular Dynamics, Genome Editing Technology
Website:
https://pablo-arantes.github.io/pabloarantes/
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Saha A, Ahsan M, Arantes PR, Schmitz M, Chanez C, Jinek M, Palermo G. An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a. Nature Communications. 15: 1473. PMID 38368461 DOI: 10.1038/s41467-024-45762-6  0.373
2023 Molina Vargas AM, Sinha S, Osborn R, Arantes PR, Patel A, Dewhurst S, Hardy DJ, Cameron A, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity. Nucleic Acids Research. PMID 38033324 DOI: 10.1093/nar/gkad1132  0.64
2023 Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a. Nucleic Acids Research. PMID 38033317 DOI: 10.1093/nar/gkad1127  0.647
2023 Wang J, Maschietto F, Qiu T, Arantes PR, Skeens E, Palermo G, Lisi GP, Batista VS. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal. PMID 37936350 DOI: 10.1016/j.bpj.2023.11.005  0.608
2023 Vargas AMM, Osborn R, Sinha S, Arantes PR, Patel A, Dewhurst S, Palermo G, O'Connell MR. New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity. Biorxiv : the Preprint Server For Biology. PMID 37547020 DOI: 10.1101/2023.07.26.550755  0.644
2023 Sinha S, Molina Vargas AM, Arantes PR, Patel A, O'Connell MR, Palermo G. RNA-mediated Allosteric Activation in CRISPR-Cas13a. Biorxiv : the Preprint Server For Biology. PMID 37546822 DOI: 10.1101/2023.07.27.550797  0.65
2023 Sinha S, Pindi C, Ahsan M, Arantes PR, Palermo G. Machines on Genes through the Computational Microscope. Journal of Chemical Theory and Computation. PMID 36947696 DOI: 10.1021/acs.jctc.2c01313  0.612
2023 Kumar A, Arantes PR, Saha A, Palermo G, Wong BM. GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems. Molecules (Basel, Switzerland). 28. PMID 36770943 DOI: 10.3390/molecules28031277  0.732
2023 Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Frontiers in Molecular Biosciences. 9: 1072733. PMID 36699705 DOI: 10.3389/fmolb.2022.1072733  0.673
2022 Nierzwicki Ł, East KW, Binz JM, Hsu RV, Ahsan M, Arantes PR, Skeens E, Pacesa M, Jinek M, Lisi GP, Palermo G. Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR-Cas9. Nature Catalysis. 5: 912-922. PMID 36778082 DOI: 10.1038/s41929-022-00848-6  0.686
2022 Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M. Structural basis for Cas9 off-target activity. Cell. 185: 4067-4081.e21. PMID 36306733 DOI: 10.1016/j.cell.2022.09.026  0.76
2022 Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Research. PMID 35822842 DOI: 10.1093/nar/gkac578  0.767
2022 Saha A, Arantes PR, Palermo G. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Current Opinion in Structural Biology. 75: 102400. PMID 35689914 DOI: 10.1016/j.sbi.2022.102400  0.788
2022 Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry. PMID 35420793 DOI: 10.1021/acs.biochem.2c00127  0.683
2022 Arantes PR, Patel AC, Palermo G. Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids. Journal of Molecular Biology. 167518. PMID 35240127 DOI: 10.1016/j.jmb.2022.167518  0.646
2021 Nierzwicki L, East KW, Morzan UN, Arantes PR, Batista VS, Lisi GP, Palermo G. Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9. Elife. 10. PMID 34908530 DOI: 10.7554/eLife.73601  0.627
2021 Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YM, Palermo G, Miao Y. Gaussian accelerated molecular dynamics (GaMD): principles and applications. Wiley Interdisciplinary Reviews. Computational Molecular Science. 11. PMID 34899998 DOI: 10.1002/wcms.1521  0.636
2021 Belato HB, D'Ordine AM, Nierzwicki L, Arantes PR, Jogl G, Palermo G, Lisi GP. Structural and dynamic insights into the HNH nuclease of divergent Cas9 species. Journal of Structural Biology. 214: 107814. PMID 34871741 DOI: 10.1016/j.jsb.2021.107814  0.669
2021 Arantes PR, Polêto MD, Pedebos C, Ligabue-Braun R. Making it Rain: Cloud-Based Molecular Simulations for Everyone. Journal of Chemical Information and Modeling. 61: 4852-4856. PMID 34595915 DOI: 10.1021/acs.jcim.1c00998  0.707
2021 Nierzwicki Ł, Arantes PR, Saha A, Palermo G. Establishing the allosteric mechanism in CRISPR-Cas9. Wiley Interdisciplinary Reviews. Computational Molecular Science. 11. PMID 34322166 DOI: 10.1002/wcms.1503  0.791
2021 Narkhede YB, Gautam AK, Hsu RV, Rodriguez W, Zewde NT, Harrison RES, Arantes PR, Gaieb Z, Gorham RD, Kieslich C, Morikis D, Sahu A, Palermo G. Role of Electrostatic Hotspots in the Selectivity of Complement Control Proteins Toward Human and Bovine Complement Inhibition. Frontiers in Molecular Biosciences. 8: 618068. PMID 33829039 DOI: 10.3389/fmolb.2021.618068  0.561
2020 Arantes PR, Saha A, Palermo G. Fighting COVID-19 Using Molecular Dynamics Simulations. Acs Central Science. 6: 1654-1656. PMID 33140032 DOI: 10.1021/acscentsci.0c01236  0.755
2020 Saha A, Arantes PR, Hsu RV, Narkhede YB, Jinek M, Palermo G. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. Journal of Chemical Information and Modeling. PMID 33107304 DOI: 10.1021/acs.jcim.0c00929  0.782
2020 Arantes PR, Pedebos C, Polêto MD, Pol-Fachin L, Verli H. The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains. Journal of Chemical Information and Modeling. 60: 631-643. PMID 31769974 DOI: 10.1021/Acs.Jcim.9B00904  0.763
2019 Arantes PR, Polêto MD, John EBO, Pedebos C, Grisci BI, Dorn M, Verli H. Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids. The Journal of Physical Chemistry. B. PMID 30624922 DOI: 10.1021/Acs.Jpcb.8B10139  0.764
2018 Arantes PR, Pérez-Sánchez H, Verli H. Antithrombin conformational modulation by D-myo-inositol 3,4,5,6-tetrakisphosphate (TMI), a novel scaffold for the development of antithrombotic agents. Journal of Biomolecular Structure & Dynamics. 36: 4045-4056. PMID 29173042 DOI: 10.1080/07391102.2017.1407259  0.634
2015 Pedebos C, Arantes PR, Giesel GM, Verli H. In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination. Glycobiology. 25: 1183-95. PMID 26220543 DOI: 10.1093/glycob/cwv053  0.541
2015 Chaves Valadão AL, Abreu CM, Dias JZ, Arantes P, Verli H, Tanuri A, de Aguiar RS. Natural Plant Alkaloid (Emetine) Inhibits HIV-1 Replication by Interfering with Reverse Transcriptase Activity. Molecules (Basel, Switzerland). 20: 11474-89. PMID 26111177 DOI: 10.3390/molecules200611474  0.534
2014 Schachter J, Valadao AL, Aguiar RS, Barreto-de-Souza V, Rossi AD, Arantes PR, Verli H, Quintana PG, Heise N, Tanuri A, Bou-Habib DC, Persechini PM. 2´,3´-Dialdehyde of ATP, ADP, and adenosine inhibit HIV-1 reverse transcriptase and HIV-1 replication. Current Hiv Research. 12: 347-58. PMID 25174839  0.514
2014 Arantes PR, Sachett LG, Graebin CS, Verli H. Conformational characterization of ipomotaosides and their recognition by COX-1 and 2. Molecules (Basel, Switzerland). 19: 5421-33. PMID 24879586 DOI: 10.3390/molecules19045421  0.571
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