Search Results - "Amaro, E."

Systematic description of COVID-19 pandemic using exact SIR solutions and Gumbel distributions by Amaro, J. E.

“…An epidemiological study is carried out in several countries analyzing the first wave of the COVID-19 pandemic using the SIR model and Gumbel distribution. The…”
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POVME 3.0: Software for Mapping Binding Pocket Flexibility by Wagner, Jeffrey R, Sørensen, Jesper, Hensley, Nathan, Wong, Celia, Zhu, Clare, Perison, Taylor, Amaro, Rommie E

“…We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring…”
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POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics by Durrant, Jacob D, Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E

“…Analysis of macromolecular/small-molecule binding pockets can provide important insights into molecular recognition and receptor dynamics. Since its release in…”
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SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma by Andreano, Emanuele, Piccini, Giulia, Licastro, Danilo, Casalino, Lorenzo, Johnson, Nicole V., Paciello, Ida, Monego, Simeone Dal, Pantano, Elisa, Manganaro, Noemi, Manenti, Alessandro, Manna, Rachele, Casa, Elisa, Hyseni, Inesa, Benincasa, Linda, Montomoli, Emanuele, Amaro, Rommie E., McLellan, Jason S., Rappuoli, Rino

“…To investigate the evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the immune population, we coincupi bated the authentic virus…”
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Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning by Votapka, Lane W, Amaro, Rommie E

“…The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine…”
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Modeling Energy Communities with Collective Photovoltaic Self-Consumption: Synergies between a Small City and a Winery in Portugal by Pontes Luz, Guilherme, Amaro e Silva, Rodrigo

“…The recently approved regulation on Energy Communities in Europe is paving the way for new collective forms of energy consumption and production, mainly based…”
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A glycan gate controls opening of the SARS-CoV-2 spike protein by Sztain, Terra, Ahn, Surl-Hee, Bogetti, Anthony T., Casalino, Lorenzo, Goldsmith, Jory A., Seitz, Evan, McCool, Ryan S., Kearns, Fiona L., Acosta-Reyes, Francisco, Maji, Suvrajit, Mashayekhi, Ghoncheh, McCammon, J. Andrew, Ourmazd, Abbas, Frank, Joachim, McLellan, Jason S., Chong, Lillian T., Amaro, Rommie E.

“…SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded ‘down’ to an…”
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The flexibility of ACE2 in the context of SARS-CoV-2 infection by Barros, Emilia P., Casalino, Lorenzo, Gaieb, Zied, Dommer, Abigail C., Wang, Yuzhang, Fallon, Lucy, Raguette, Lauren, Belfon, Kellon, Simmerling, Carlos, Amaro, Rommie E.

“…The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human…”
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Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein by Casalino, Lorenzo, Gaieb, Zied, Goldsmith, Jory A, Hjorth, Christy K, Dommer, Abigail C, Harbison, Aoife M, Fogarty, Carl A, Barros, Emilia P, Taylor, Bryn C, McLellan, Jason S, Fadda, Elisa, Amaro, Rommie E

“…The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and…”
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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs by Wagner, Jeffrey R, Lee, Christopher T, Durrant, Jacob D, Malmstrom, Robert D, Feher, Victoria A, Amaro, Rommie E

“…Allosteric drug development holds promise for delivering medicines that are more selective and less toxic than those that target orthosteric sites. To date,…”
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An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes by Bernetti, Mattia, Masetti, Matteo, Recanatini, Maurizio, Amaro, Rommie E, Cavalli, Andrea

“…Unveiling the mechanistic features of drug-target binding is of central interest in biophysics and drug discovery. Herein, we address this challenge by…”
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SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding by Votapka, Lane W, Jagger, Benjamin R, Heyneman, Alexandra L, Amaro, Rommie E

“…We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to…”
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Developing a two-dimensional landscape model of opportunities for penetrative passing in association football - Stage I by Passos, Pedro, Amaro E Silva, Rodrigo, Gomez-Jordana, Luís, Davids, Keith

“…This study investigated a method for modelling a landscape of opportunities for penetrative passing completed on the ground by ball carriers in association…”
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Effect of urban shadowing on the potential of solar‐powered vehicles by Brito, Miguel Centeno, Amaro e Silva, Rodrigo, Pera, David, Costa, Ivo, Boutov, Dmitri

“…Abstract Solar‐powered vehicles have the potential to reduce CO 2 emissions, operational costs and charging frequency needs of electric vehicles. This…”
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Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds by Lee, Christopher T, Comer, Jeffrey, Herndon, Conner, Leung, Nelson, Pavlova, Anna, Swift, Robert V, Tung, Chris, Rowley, Christopher N, Amaro, Rommie E, Chipot, Christophe, Wang, Yi, Gumbart, James C

“…Predicting the rate of nonfacilitated permeation of solutes across lipid bilayers is important to drug design, toxicology, and signaling. These rates can be…”
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D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings by Gaieb, Zied, Parks, Conor D., Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Walters, W. Patrick, Lambert, Millard H., Nevins, Neysa, Bembenek, Scott D., Ameriks, Michael K., Mirzadegan, Tara, Burley, Stephen K., Amaro, Rommie E., Gilson, Michael K.

“…The Drug Design Data Resource aims to test and advance the state of the art in protein–ligand modeling by holding community-wide blinded, prediction…”
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Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B by Shi, Ke, Carpenter, Michael A, Banerjee, Surajit, Shaban, Nadine M, Kurahashi, Kayo, Salamango, Daniel J, McCann, Jennifer L, Starrett, Gabriel J, Duffy, Justin V, Demir, Özlem, Amaro, Rommie E, Harki, Daniel A, Harris, Reuben S, Aihara, Hideki

“…Crystal structures of human APOBEC3A and a chimera of APOBEC3B and APOBEC3A bound to ssDNA reveal an unanticipated ‘U-shaped’ binding mode and provide insight…”
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Computational approaches to mapping allosteric pathways by Feher, Victoria A, Durrant, Jacob D, Van Wart, Adam T, Amaro, Rommie E

“…•Advances in computational methods for allosteric pathways are reviewed.•New methods are able to replicate many but not all experimental results.•Each method…”
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D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies by Gaieb, Zied, Liu, Shuai, Gathiaka, Symon, Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Feher, Victoria A., Walters, W. Patrick, Kuhn, Bernd, Rudolph, Markus G., Burley, Stephen K., Gilson, Michael K., Amaro, Rommie E.

“…The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures…”
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Aneuploidy increases resistance to chemotherapeutics by antagonizing cell division by Replogle, John Michael, Zhou, Wen, Amaro, Adrianna E., McFarland, James M., Villalobos-Ortiz, Mariana, Ryan, Jeremy, Letai, Anthony, Yilmaz, Omer, Sheltzer, Jason, Lippard, Stephen J., Ben-David, Uri, Amon, Angelika

“…Aneuploidy, defined as whole chromosome gains and losses, is associated with poor patient prognosis in many cancer types. However, the condition causes…”
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