Search Results - "Gront, Dominik"

Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters by Nkosi, Bridget Valeria Zinhle, Padayachee, Tiara, Gront, Dominik, Nelson, David R, Syed, Khajamohiddin

“…Species belonging to the bacterial phyla and represent over 90% of the gastrointestinal microbiota. Changes in the ratio of these two bacterial groups were…”
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SURPASS Low-Resolution Coarse-Grained Protein Modeling by Dawid, Aleksandra E, Gront, Dominik, Kolinski, Andrzej

“…Coarse-grained modeling of biomolecules has a very important role in molecular biology. In this work we present a novel SURPASS (Single United Residue per…”
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More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus , Cyanobacteria , and Mycobacterium by Mnguni, Fanele Cabangile, Padayachee, Tiara, Chen, Wanping, Gront, Dominik, Yu, Jae-Hyuk, Nelson, David R, Syed, Khajamohiddin

“…Unraveling the role of cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins present in living and non-living entities, in secondary metabolite…”
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Generalized fragment picking in Rosetta: design, protocols and applications by Gront, Dominik, Kulp, Daniel W, Vernon, Robert M, Strauss, Charlie E M, Baker, David

“…The Rosetta de novo structure prediction and loop modeling protocols begin with coarse grained Monte Carlo searches in which the moves are based on short…”
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In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles by Akapo, Olufunmilayo Olukemi, Macnar, Joanna M, Kryś, Justyna D, Syed, Puleng Rosinah, Syed, Khajamohiddin, Gront, Dominik

“…Cytochrome P450 monooxygenase CYP51 (sterol 14α-demethylase) is a well-known target of the azole drug fluconazole for treating cryptococcosis, a…”
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Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates by Gront, Dominik, Kmiecik, Sebastian, Kolinski, Andrzej

“…In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy…”
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Diversification of Ferredoxins across Living Organisms by Nzuza, Nomfundo, Padayachee, Tiara, Chen, Wanping, Gront, Dominik, Nelson, David R, Syed, Khajamohiddin

“…Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the…”
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In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria by Msomi, Ntombizethu Nokuphiwa, Padayachee, Tiara, Nzuza, Nomfundo, Syed, Puleng Rosinah, Kryś, Justyna Dorota, Chen, Wanping, Gront, Dominik, Nelson, David R, Syed, Khajamohiddin

“…The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate…”
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Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria by Msweli, Siphesihle, Chonco, Andiswa, Msweli, Lihle, Syed, Puleng Rosinah, Karpoormath, Rajshekhar, Chen, Wanping, Gront, Dominik, Nkosi, Bridget Valeria Zinhle, Nelson, David R, Syed, Khajamohiddin

“…For the last six decades, cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, have been under the spotlight due to their regio- and…”
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Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species by Nzuza, Nomfundo, Padayachee, Tiara, Syed, Puleng Rosinah, Kryś, Justyna Dorota, Chen, Wanping, Gront, Dominik, Nelson, David R., Syed, Khajamohiddin

“…Cytochrome P450 monooxygenases (CYPs/P450s), heme-thiolate proteins, are well-known players in the generation of chemicals valuable to humans and as a drug…”
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Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks by Saqib, Mohammad N., Kryś, Justyna D., Gront, Dominik

“…The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational…”
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An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species by Malinga, Nsikelelo Allison, Nzuza, Nomfundo, Padayachee, Tiara, Syed, Puleng Rosinah, Karpoormath, Rajshekhar, Gront, Dominik, Nelson, David R, Syed, Khajamohiddin

“…Cytochrome P450 monooxygenases (CYPs/P450s) are heme thiolate proteins present in species across the biological kingdoms. By virtue of their broad substrate…”
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Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics by Wabik, Jacek, Kmiecik, Sebastian, Gront, Dominik, Kouza, Maksim, Koliński, Andrzej

“…We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The…”
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BioShell 3.0: Library for Processing Structural Biology Data by Macnar, Joanna M, Szulc, Natalia A, Kryś, Justyna D, Badaczewska-Dawid, Aleksandra E, Gront, Dominik

“…BioShell is an open-source package for processing biological data, particularly focused on structural applications. The package provides parsers, data…”
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Comparison of α‑Helix and β‑Sheet Structure Adaptation to a Quantum Dot Geometry: Toward the Identification of an Optimal Motif for a Protein Nanoparticle Cover by Kopeć, Katarzyna, Pędziwiatr, Marta, Gront, Dominik, Sztatelman, Olga, Sławski, Jakub, Łazicka, Magdalena, Worch, Remigiusz, Zawada, Katarzyna, Makarova, Katerina, Nyk, Marcin, Grzyb, Joanna

“…While quantum dots (QDs) are useful as fluorescent labels, their application in biosciences is limited due to the stability and hydrophobicity of their…”
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Optimal Temperature Set for Replica Exchange Sampling by Gront, Dominik

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Coarse-Grained Protein Models and Their Applications by Kmiecik, Sebastian, Gront, Dominik, Kolinski, Michal, Wieteska, Lukasz, Dawid, Aleksandra Elzbieta, Kolinski, Andrzej

“…The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the…”
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Modular Platform for Biomolecular Modeling and Simulations by Gront, Dominik

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Analysis of protein structures containing HEPES and MES molecules by Macnar, Joanna Magdalena, Brzezinski, Dariusz, Chruszcz, Maksymilian, Gront, Dominik

“…X‐ray crystallography is the main experimental method behind ligand–macromolecule complexes found in the Protein Data Bank (PDB). Applying bioinformatics…”
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Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily by Ibryashkina, Elena M, Zakharova, Marina V, Baskunov, Vladimir B, Bogdanova, Ekaterina S, Nagornykh, Maxim O, Den'mukhamedov, Marat M, Melnik, Bogdan S, Kolinski, Andrzej, Gront, Dominik, Feder, Marcin, Solonin, Alexander S, Bujnicki, Janusz M

“…The majority of experimentally determined crystal structures of Type II restriction endonucleases (REases) exhibit a common PD-(D/E)XK fold. Crystal structures…”
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