| Scalable molecular dynamics on CPU and GPU architectures with NAMD JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ... The Journal of Chemical Physics 153 (4), 044130, 2020 | 1815 | 2020 |
| Enhanced sampling techniques in molecular dynamics simulations of biological systems RC Bernardi, MCR Melo, K Schulten Biochimica et Biophysica Acta (BBA)-General Subjects 1850 (5), 872-877, 2015 | 723 | 2015 |
| NAMD goes quantum: an integrative suite for hybrid simulations MCR Melo, RC Bernardi, T Rudack, M Scheurer, C Riplinger, JC Phillips, ... Nature methods 15 (5), 351-354, 2018 | 184 | 2018 |
| Accelerating antibiotic discovery through artificial intelligence MCR Melo, JRMA Maasch, C de la Fuente-Nunez Communications biology 4 (1), 1050, 2021 | 96 | 2021 |
| Fundamental behaviors emerge from simulations of a living minimal cell ZR Thornburg, DM Bianchi, TA Brier, BR Gilbert, TM Earnest, MCR Melo, ... Cell 185 (2), 345-360. e28, 2022 | 94 | 2022 |
| Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories MCR Melo, RC Bernardi, C De La Fuente-nunez, Z Luthey-Schulten The Journal of Chemical Physics 153 (13), 134104, 2020 | 83 | 2020 |
| Mining for encrypted peptide antibiotics in the human proteome MDT Torres, MCR Melo, L Flowers, O Crescenzi, E Notomista, ... Nature Biomedical Engineering 6 (1), 67-75, 2022 | 73 | 2022 |
| Direction Matters: Monovalent Streptavidin/Biotin Complex under Load SM Sedlak, LC Schendel, MCR Melo, DA Pippig, Z Luthey-Schulten, ... Nano letters 19 (6), 3415-3421, 2018 | 56 | 2018 |
| A tethered ligand assay to probe SARS-CoV-2: ACE2 interactions MS Bauer, S Gruber, A Hausch, PSFC Gomes, LF Milles, T Nicolaus, ... Proceedings of the National Academy of Sciences 119 (14), e2114397119, 2022 | 36 | 2022 |
| Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly CH Chen, MCR Melo, N Berglund, A Khan, C de la Fuente-Nunez, ... Current Opinion in Structural Biology 61, 160-166, 2020 | 33 | 2020 |
| Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning JRMA Maasch, MDT Torres, MCR Melo, C de la Fuente-Nunez Cell Host & Microbe 31 (8), 1260-1274. e6, 2023 | 26 | 2023 |
| Population FBA predicts metabolic phenotypes in yeast P Labhsetwar, MCR Melo, JA Cole, Z Luthey-Schulten PLoS computational biology 13 (9), e1005728, 2017 | 23 | 2017 |
| GSAFold: A new application of GSA to protein structure prediction MCR Melo, RC Bernardi, TVA Fernandes, PG Pascutti Proteins: Structure, Function, and Bioinformatics 80 (9), 2305-2310, 2012 | 17 | 2012 |
| Kinetic Modelling of the Genetic Information Processes in a Minimal Cell ZR Thornburg, MCR Melo, D Bianchi, TA Brier, C Crotty, M Breuer, ... Frontiers in Molecular Biosciences 6, 130, 2019 | 15 | 2019 |
| Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections MCR Melo, DEB Gomes, RC Bernardi Journal of the American Chemical Society 145 (1), 70-77, 2022 | 11 | 2022 |
| Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome RC Bernardi, HL Doden, MCR Melo, S Devendran, RM Pollet, SM Mythen, ... BioRxiV, 2020.06. 12.149468, 2020 | 10 | 2020 |
| NAMD User’s guide R Bernardi, M Bhandarkar, A Bhatele, E Bohm, R Brunner, F Buelens, ... Urbana, Illinois, USA Theor. Comput. Biophys. Group, Beckman Institute, Univ …, 2018 | 10 | 2018 |
| Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection. C Zhang, A Verma, Y Feng, MC dos Reis Melo, M McQuillan, M Hansen, ... | 8 | 2021 |
| Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike MCR Melo, RC Bernardi Biophysical Journal 122 (14), 2833-2840, 2023 | 5 | 2023 |
| Bridging the gap between in vitro and in silico single-molecule force spectroscopy DEB Gomes, MCR Melo, PSFC Gomes, RC Bernardi bioRxiv, 2022.07. 14.500151, 2022 | 4 | 2022 |
Rafael C BernardiAssistant Professor - Department of Physics at Auburn UniversityVerified email at auburn.edu
