Publications by authors named "Conrado Pedebos"

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Making it Rain: Cloud-Based Molecular Simulations for Everyone.
Pablo R Arantes, Marcelo D Polêto, Conrado Pedebos, Rodrigo Ligabue-Braun

J Chem Inf Model· October 2021

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eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems.
Pablo Ricardo Arantes, Rodrigo Ligabue-Braun, Conrado Pedebos

J Chem Inf Model· December 2025

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From venoms to vanity: Exploring animal toxins as cosmeceuticals.
Pamela Rodrigues Sampaio, Antonio Vicente Peruzzo Neto, Elisa Beatriz de Oliveira John, Conrado Pedebos, Rodrigo Ligabue-Braun

Toxicon· November 2025

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Diacylation of Peptides Enables the Construction of Functional Vesicles for Drug-Carrying Liposomes.
Christy J Cho, Sangyoon Kang, Conrado Pedebos, Syma Khalid, Roberto J Brea

Angew Chem Int Ed Engl· May 2025

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Polymyxin B1 in the Escherichia coli inner membrane: A complex story of protein and lipopolysaccharide-mediated insertion.
Dhanushka Weerakoon, Jan K Marzinek, Conrado Pedebos, Peter J Bond, Syma Khalid

J Biol Chem· October 2024

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

J Phys Chem B· March 2024

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

Amino Acids· January 2024

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Computational microbiology of bacteria: Advancements in molecular dynamics simulations.
Syma Khalid, Astrid F Brandner, Nikolai Juraschko, Kahlan E Newman, Conrado Pedebos

Structure· November 2023

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The solute carrier SPNS2 recruits PI(4,5)P to synergistically regulate transport of sphingosine-1-phosphate.
Haiping Tang, Huanyu Li, Dheeraj Prakaash, Conrado Pedebos, Xingyu Qiu

Mol Cell· August 2023

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Lipids mediate supramolecular outer membrane protein assembly in bacteria.
Melissa N Webby, Abraham O Oluwole, Conrado Pedebos, Patrick G Inns, Anna Olerinyova

Sci Adv· November 2022

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Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms.
Jan Böhning, Mnar Ghrayeb, Conrado Pedebos, Daniel K Abbas, Syma Khalid

Nat Commun· November 2022

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Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein.
Lorena Zuzic, Firdaus Samsudin, Aishwary T Shivgan, Palur V Raghuvamsi, Jan K Marzinek, Conrado Pedebos

Structure· August 2022

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

Nat Rev Microbiol· April 2022

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Polymyxin B1 within the ell envelope: insights from molecular dynamics simulations.
Dhanushka Weerakoon, Kamen Petrov, Conrado Pedebos, Syma Khalid

Biophys Rev· December 2021

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Structural Basis for Silicic Acid Uptake by Higher Plants.
Bert van den Berg, Conrado Pedebos, Jani R Bolla, Carol V Robinson, Arnaud Baslé

J Mol Biol· October 2021

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Modifying the catalytic preference of alpha-amylase toward n-alkanes for bioremediation purposes using in silico strategies.
Éderson Sales Moreira Pinto, Bruno César Feltes, Conrado Pedebos, Márcio Dorn

J Comput Chem· August 2021

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The hitchhiker's guide to the periplasm: Unexpected molecular interactions of polymyxin B1 in E. coli.
Conrado Pedebos, Iain Peter Shand Smith, Alister Boags, Syma Khalid

Structure· May 2021

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Evolution of an Amniote-Specific Mechanism for Modulating Ubiquitin Signaling via Phosphoregulation of the E2 Enzyme UBE2D3.
Monica Roman-Trufero, Constance M Ito, Conrado Pedebos, Indiana Magdalou, Yi-Fang Wang

Mol Biol Evol· July 2020

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The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains.
Pablo R Arantes, Conrado Pedebos, Marcelo D Polêto, Laércio Pol-Fachin, Hugo Verli

J Chem Inf Model· February 2020

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CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.
Ardita Shkurti, Ioanna Danai Styliari, Vivek Balasubramanian, Iain Bethune, Conrado Pedebos

J Chem Theory Comput· April 2019

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Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids.
Pablo R Arantes, Marcelo D Polêto, Elisa B O John, Conrado Pedebos, Bruno I Grisci

J Phys Chem B· February 2019

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Dynamics of DDB2-DDB1 complex under different naturally-occurring mutants in Xeroderma Pigmentosum disease.
Bruno César Feltes, Conrado Pedebos, Diego Bonatto, Hugo Verli

Biochim Biophys Acta Gen Subj· December 2018

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The role of Zn2+, dimerization and N-glycosylation in the interaction of Auxin-Binding Protein 1 (ABP1) with different auxins.
Cibele Tesser da Costa, Conrado Pedebos, Hugo Verli, Arthur Germano Fett-Neto

Glycobiology· December 2017

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In silico Investigation of the PglB Active Site Reveals Transient Catalytic States and Octahedral Metal Ion Coordination.
Conrado Pedebos, Pablo Ricardo Arantes, Guilherme Menegon Giesel, Hugo Verli

Glycobiology· November 2015

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Atomic model and micelle dynamics of QS-21 saponin.
Conrado Pedebos, Laércio Pol-Fachin, Ramon Pons, Cilâine V Teixeira, Hugo Verli

Molecules· March 2014

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