Search Results - "Pedebos, Conrado"

Simulations of the spike: molecular dynamics and SARS-CoV-2 by Pedebos, Conrado, Khalid, Syma

“…This month’s Under the Lens discusses a few of the growing number of recent molecular simulation studies that have made substantial contributions towards our…”
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The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli by Pedebos, Conrado, Smith, Iain Peter Shand, Boags, Alister, Khalid, Syma

“…The periplasm of Gram-negative bacteria is a complex, highly crowded molecular environment. Little is known about how antibiotics move across the periplasm and…”
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Structural Basis for Silicic Acid Uptake by Higher Plants by van den Berg, Bert, Pedebos, Conrado, Bolla, Jani R., Robinson, Carol V., Baslé, Arnaud, Khalid, Syma

“…[Display omitted] •NIP channels mediate uptake of metalloids such as silicic acid in plants.•The first structure of a NIP metalloid porin is reported.•OsNIP2;1…”
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Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms by Böhning, Jan, Ghrayeb, Mnar, Pedebos, Conrado, Abbas, Daniel K., Khalid, Syma, Chai, Liraz, Bharat, Tanmay A. M.

“…Many bacteria in nature exist in multicellular communities termed biofilms, where cells are embedded in an extracellular matrix that provides rigidity to the…”
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Polymyxin B1 within the E. coli cell envelope: insights from molecular dynamics simulations by Weerakoon, Dhanushka, Petrov, Kamen, Pedebos, Conrado, Khalid, Syma

“…Polymyxins are used as last-resort antibiotics, where other treatments have been ineffectual due to antibiotic resistance. However, resistance to polymyxins…”
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CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space by Shkurti, Ardita, Styliari, Ioanna Danai, Balasubramanian, Vivek, Bethune, Iain, Pedebos, Conrado, Jha, Shantenu, Laughton, Charles A

“…CoCo (“complementary coordinates”) is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the…”
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Rocio Virus Encephalitis: In Silico Evidence for Drug Repurposing by Sagini, João Pedro, Arantes, Pablo Ricardo, Pedebos, Conrado, Ligabue-Braun, Rodrigo

“…Arboviral diseases have a high incidence in Brazil and constitute a serious public health problem. Rocio virus (ROCV) is an arbovirus belonging to the family…”
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Atomic model and micelle dynamics of QS-21 saponin by Pedebos, Conrado, Pol-Fachin, Laércio, Pons, Ramon, Teixeira, Cilâine V, Verli, Hugo

“…QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical…”
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Predicting the Behaviour of Antibiotics in a Virtual E. coli Cell Envelope by Khalid, Syma, Pedebos, Conrado

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The Antimicrobial Peptide Polymyxin B1 Encounters Many Molecular Obstacles in the Periplasm En Route to the Inner Membrane of E. Coli by Khalid, Syma, Pedebos, Conrado

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The effects of biomolecular crowding on the behaviour of polymyxin antibiotics within the E. coli cell envelope by Smith, Iain P.S., Pedebos, Conrado, Khalid, Syma

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Spatial organisation of the E. coli outer membrane from multiscale computer simulations by Khalid, Syma, Prakaash, Dheeraj, Pedebos, Conrado, Okada, Kiyoshiro

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Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli: Insights from Molecular Dynamics by Smith, Iain P. S., Pedebos, Conrado, Khalid, Syma

“…The cell envelope of Gram-negative bacteria is a crowded tripartite architecture that separates the cell interior from the external environment. Two membranes…”
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Making it Rain: Cloud-Based Molecular Simulations for Everyone by Arantes, Pablo R, Polêto, Marcelo D, Pedebos, Conrado, Ligabue-Braun, Rodrigo

“…We present a user-friendly front-end for running molecular dynamics (MD) simulations using the OpenMM toolkit on the Google Colab framework. Our goals are (1)…”
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Polymyxin B1 in the Escherichia coli inner membrane: A complex story of protein and lipopolysaccharide-mediated insertion by Weerakoon, Dhanushka, Marzinek, Jan K., Pedebos, Conrado, Bond, Peter J., Khalid, Syma

“…The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for “last-resort” antibiotics such as polymyxins. However, the…”
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Complexity matters: Polymyxins and the E. coli cell envelope by Smith, Iain P.S., Pedebos, Conrado, Khalid, Syma

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The solute carrier SPNS2 recruits PI(4,5)P2 to synergistically regulate transport of sphingosine-1-phosphate by Tang, Haiping, Li, Huanyu, Prakaash, Dheeraj, Pedebos, Conrado, Qiu, Xingyu, Sauer, David B., Khalid, Syma, Duerr, Katharina, Robinson, Carol V.

“…Solute carrier spinster homolog 2 (SPNS2), one of only four known major facilitator superfamily (MFS) lysolipid transporters in humans, exports…”
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Interactions of polymyxin B1 with the gram-negative inner membrane: A simulation study by Weerakoon, Dhanushka, Marzinek, Jan K., Bond, Peter J., Pedebos, Conrado, Khalid, Syma

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Structure determination needs to go viral by de Bastos Balbe e Gutierres, Matheus, Pedebos, Conrado, Bacaicoa-Caruso, Paula, Ligabue-Braun, Rodrigo

“…Viral diseases are expected to cause new epidemics in the future, therefore, it is essential to assess how viral diversity is represented in terms of deposited…”
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Computational microbiology of bacteria: Advancements in molecular dynamics simulations by Khalid, Syma, Brandner, Astrid F, Juraschko, Nikolai, Newman, Kahlan E, Pedebos, Conrado, Prakaash, Dheeraj, Smith, Iain P S, Waller, Callum, Weerakoon, Dhanushka

“…Microbiology is traditionally considered within the context of wet laboratory methodologies. Computational techniques have a great potential to contribute to…”
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