Search Results - "Melo, Marcelo"

Enhanced sampling techniques in molecular dynamics simulations of biological systems by Bernardi, Rafael C., Melo, Marcelo C.R., Schulten, Klaus

“…Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often…”
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Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories by Melo, Marcelo C R, Bernardi, Rafael C, de la Fuente-Nunez, Cesar, Luthey-Schulten, Zaida

“…Molecular interactions are essential for regulation of cellular processes from the formation of multi-protein complexes to the allosteric activation of…”
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Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike by Melo, Marcelo C.R., Bernardi, Rafael C.

“…Over a century ago, physicists started broadly relying on theoretical models to guide new experiments. Soon thereafter, chemists began doing the same. Now,…”
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Direction Matters: Monovalent Streptavidin/Biotin Complex under Load by Sedlak, Steffen M, Schendel, Leonard C, Melo, Marcelo C. R, Pippig, Diana A, Luthey-Schulten, Zaida, Gaub, Hermann E, Bernardi, Rafael C

“…Novel site-specific attachment strategies combined with improvements of computational resources enable new insights into the mechanics of the monovalent…”
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Accelerating antibiotic discovery through artificial intelligence by Melo, Marcelo C. R., Maasch, Jacqueline R. M. A., de la Fuente-Nunez, Cesar

“…By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the host-pathogen evolutionary arms race. As pathogens evolve…”
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Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning by Maasch, Jacqueline R.M.A., Torres, Marcelo D.T., Melo, Marcelo C.R., de la Fuente-Nunez, Cesar

“…Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect…”
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Mining for encrypted peptide antibiotics in the human proteome by Torres, Marcelo D. T., Melo, Marcelo C. R., Flowers, Laurice, Crescenzi, Orlando, Notomista, Eugenio, de la Fuente-Nunez, Cesar

“…The emergence of drug-resistant bacteria calls for the discovery of new antibiotics. Yet, for decades, traditional discovery strategies have not yielded new…”
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Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections by Melo, Marcelo C. R., Gomes, Diego E. B., Bernardi, Rafael C.

“…The unbinding pathway of a protein complex can vary significantly depending on biochemical and mechanical factors. Under mechanical stress, a complex may…”
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Fundamental behaviors emerge from simulations of a living minimal cell by Thornburg, Zane R., Bianchi, David M., Brier, Troy A., Gilbert, Benjamin R., Earnest, Tyler M., Melo, Marcelo C.R., Safronova, Nataliya, Sáenz, James P., Cook, András T., Wise, Kim S., Hutchison, Clyde A., Smith, Hamilton O., Glass, John I., Luthey-Schulten, Zaida

“…We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory…”
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Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern by Bauer, Magnus S., Gruber, Sophia, Hausch, Adina, Melo, Marcelo C. R., Gomes, Priscila S. F. C., Nicolaus, Thomas, Milles, Lukas F., Gaub, Hermann E., Bernardi, Rafael C., Lipfert, Jan

“…Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to the cellular receptor angiotensin-converting enzyme 2…”
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Population FBA predicts metabolic phenotypes in yeast by Labhsetwar, Piyush, Melo, Marcelo C R, Cole, John A, Luthey-Schulten, Zaida

“…Using protein counts sampled from single cell proteomics distributions to constrain fluxes through a genome-scale model of metabolism, Population flux balance…”
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A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions by Bauer, Magnus S, Gruber, Sophia, Hausch, Adina, Gomes, Priscila S F C, Milles, Lukas F, Nicolaus, Thomas, Schendel, Leonard C, Navajas, Pilar López, Procko, Erik, Lietha, Daniel, Melo, Marcelo C R, Bernardi, Rafael C, Gaub, Hermann E, Lipfert, Jan

“…SignificanceIn the dynamic environment of the airways, where SARS-CoV-2 infections are initiated by binding to human host receptor ACE2, mechanical stability…”
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A new species of Characidium Reinhardt (Characiformes: Crenuchidae) from the Río Huallaga, central Peruvian Amazon, with a review of secondary sexual characters in the genus by Teixeira, Tulio F., Melo, Marcelo R. S.

“…Characidium pumarinri n. sp. is described from the affluents of Río Huallaga, a tributary of Río Marañón that drains the eastern slopes of the Andes, in the…”
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Extraction of Eucalyptus leaves using solvents of distinct polarity. Cluster analysis and extracts characterization by Rodrigues, Vítor H., de Melo, Marcelo M.R., Portugal, Inês, Silva, Carlos M.

“…[Display omitted] •Extraction of Eucalyptus globulus leaves, with/without preliminary dewaxing.•Solvents: methanol, ethanol, dichloromethane, pure & modified…”
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Supercritical fluid extraction of sterols from Eichhornia crassipes biomass using pure and modified carbon dioxide. Enhancement of stigmasterol yield and extract concentration by Martins, Pedro F., de Melo, Marcelo M.R., Sarmento, Pedro, Silva, Carlos M.

“…•SFE of sterols, particularly stigmasterol, from stalks and leaves of Eichhornia crassipes.•Experimental conditions tested: 200–300bar, 0.0–5.0wt.% ethanol…”
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Another piece of the living fossil puzzle: A new species of Polymixia Lowe, 1836 (Polymixiiformes: Polymixiidae) from the western South Atlantic by De Cia Caixeta, Heloísa, Oliveira, Claudio, Melo, Marcelo Roberto Souto de

“…The family Polymixiidae is an ancient group of acanthomorph fish, often regarded as living fossils. Currently, there are 11 valid species allocated in the…”
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Enzymatic Potential of Filamentous Fungi as a Biological Pretreatment for Acidogenic Fermentation of Coffee Waste by Pereira, Joana, Cachinho, Ana, de Melo, Marcelo M. R., Silva, Carlos M., Lemos, Paulo C., Xavier, Ana M. R. B., Serafim, Luísa S.

“…Spent coffee grounds (SCGs) are a promising substrate that can be valorized by biotechnological processes, such as for short-chain organic acid (SCOA)…”
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Tray drying of medical cannabis inflorescences at industrial scale: Kinetics measurement and modeling towards the implementation of statistical process control by de Melo, Marcelo M.R., Águas, Fernando, Nascimento, João

“…The production of medical cannabis in compliance with the guidelines of Good Manufacturing Practice requires a science-based control strategy for the process…”
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Supercritical fluid extraction of Eucalyptus globulus leaves. Experimental and modelling studies of the influence of operating conditions and biomass pretreatment upon yields and kinetics by Rodrigues, Vítor H., de Melo, Marcelo M.R., Portugal, Inês, Silva, Carlos M.

“…•SFE of Eucalyptus globulus leaves, with and without biomass preatreatments.•Optimization of pressure and cosolvent content for bulk extract and TTA…”
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Impact of a Pretreatment Step on the Acidogenic Fermentation of Spent Coffee Grounds by Pereira, Joana, de Melo, Marcelo M R, Silva, Carlos M, Lemos, Paulo C, Serafim, Luísa S

“…Acidogenic fermentation (AF) is often applied to wastes to produce short-chain organic acids (SCOAs)-molecules with applications in many industries. Spent…”
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