Search Results - "Gajda, Michal"

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment by Rauscher, Sarah, Gapsys, Vytautas, Gajda, Michal J, Zweckstetter, Markus, de Groot, Bert L, Grubmüller, Helmut

“…Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be…”
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MetaMQAP: a meta-server for the quality assessment of protein models by Pawlowski, Marcin, Gajda, Michal J, Matlak, Ryszard, Bujnicki, Janusz M

“…Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on…”
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Mechanistic Basis of Phenothiazine-Driven Inhibition of Tau Aggregation by Akoury, Elias, Pickhardt, Marcus, Gajda, Michal, Biernat, Jacek, Mandelkow, Eckhard, Zweckstetter, Markus

“…Blues brothers: Aggregation of the Tau protein is a key event in Alzheimer's disease and Tau aggregation inhibitors are important as potential drugs…”
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The Influence of Copper Oxide Particle Size on the Properties of Epoxy Resin by Bazan, Patrycja, Gajda, Michał, Nosal, Przemysław, Bąk, Agnieszka, Setlak, Kinga, Łach, Michał

“…This study examines the relationship between the size of copper particles and the properties of epoxy resin. Epoxy resin is a type of thermosetting resin…”
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Structural Basis for Efficient Chromophore Communication and Energy Transfer in a Constructed Didomain Protein Scaffold by Arpino, James A. J, Czapinska, Honorata, Piasecka, Anna, Edwards, Wayne R, Barker, Paul, Gajda, Michal J, Bochtler, Matthias, Jones, D. Dafydd

“…The construction of useful functional biomolecular components not currently part of the natural repertoire is central to synthetic biology. A new…”
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Modeling the structure of RNA molecules with small-angle X-ray scattering data by Gajda, Michal Jan, Martinez Zapien, Denise, Uchikawa, Emiko, Dock-Bregeon, Anne-Catherine

“…We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering…”
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Solution structure of the natively assembled yeast ribosomal stalk determined by small-angle X-ray scattering by Grela, Przemysław, Gajda, Michal J, Armache, Jean-Paul, Beckmann, Roland, Krokowski, Dawid, Svergun, Dmitri I, Grankowski, Nikodem, Tchórzewski, Marek

“…The ribosomal stalk of the 60S subunit has been shown to play a crucial role in all steps of protein synthesis, but its structure and exact molecular function…”
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HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format by Gajda, Michał Jan

“…Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level…”
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FILTREST3D: discrimination of structural models using restraints from experimental data by Gajda, Michal J., Tuszynska, Irina, Kaczor, Marta, Bakulina, Anastasia Yu, Bujnicki, Janusz M.

“…Automatic methods for macromolecular structure prediction (fold recognition, de novo folding and docking programs) produce large sets of alternative models…”
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MODOMICS: a database of RNA modification pathways by Dunin-Horkawicz, Stanislaw, Czerwoniec, Anna, Gajda, Michal J, Feder, Marcin, Grosjean, Henri, Bujnicki, Janusz M

“…MODOMICS is the first comprehensive database resource for systems biology of RNA modification. It integrates information about the chemical structure of…”
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FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6 by Kosinski, Jan, Gajda, Michal J., Cymerman, Iwona A., Kurowski, Michal A., Pawlowski, Marcin, Boniecki, Michal, Obarska, Agnieszka, Papaj, Grzegorz, Sroczynska-Obuchowicz, Paulina, Tkaczuk, Karolina L., Sniezynska, Paulina, Sasin, Joanna M., Augustyn, Anna, Bujnicki, Janusz M., Feder, Marcin

“…In the course of CASP6, we generated models for all targets using a new version of the “FRankenstein's monster approach.” Previously (in CASP5) we were able to…”
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THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain by Gabant, Guillaume, Auxilien, Sylvie, Tuszynska, Irina, Locard, Marie, Gajda, Michal J., Chaussinand, Guylaine, Fernandez, Bernard, Dedieu, Alain, Grosjean, Henri, Golinelli-Pimpaneau, Béatrice, Bujnicki, Janusz M., Armengaud, Jean

“…The tRNA:m22G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA…”
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New developments in the ATSAS program package for small-angle scattering data analysis by Petoukhov, Maxim V., Franke, Daniel, Shkumatov, Alexander V., Tria, Giancarlo, Kikhney, Alexey G., Gajda, Michal, Gorba, Christian, Mertens, Haydyn D. T., Konarev, Petr V., Svergun, Dmitri I.

“…New developments in the program package ATSAS (version 2.4) for the processing and analysis of isotropic small‐angle X‐ray and neutron scattering data are…”
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Probabilistic cross‐link analysis and experiment planning for high‐throughput elucidation of protein structure by Ye, Xiaoduan, O'Neil, Patrick K., Foster, Adrienne N., Gajda, Michal J., Kosinski, Jan, Kurowski, Michal A., Bujnicki, Janusz M., Friedman, Alan M., Bailey‐Kellogg, Chris

“…Emerging high‐throughput techniques for the characterization of protein and protein‐complex structures yield noisy data with sparse information content,…”
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Predictive Atomic Resolution Descriptions of Intrinsically Disordered hTau40 and α-Synuclein in Solution from NMR and Small Angle Scattering by Schwalbe, Martin, Ozenne, Valéry, Bibow, Stefan, Jaremko, Mariusz, Jaremko, Lukasz, Gajda, Michal, Jensen, Malene Ringkjøbing, Biernat, Jacek, Becker, Stefan, Mandelkow, Eckhard, Zweckstetter, Markus, Blackledge, Martin

“…The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize…”
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Inhibition of Tau Filament Formation by Conformational Modulation by Akoury, Elias, Gajda, Michal, Pickhardt, Marcus, Biernat, Jacek, Soraya, Pornsuwan, Griesinger, Christian, Mandelkow, Eckhard, Zweckstetter, Markus

“…Antiaggregation drugs play an important role in therapeutic approaches for Alzheimer’s disease. Although a large number of small molecules that inhibit the…”
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Characterization of the effects of phosphorylation by CK2 on the structure and binding properties of human HP1β by Munari, Francesca, Gajda, Michal Jan, Hiragami-Hamada, Kyoko, Fischle, Wolfgang, Zweckstetter, Markus

“…•HP1β contains two primary sites for CK2 with distinct phosphorylation kinetics.•Localized conformational and dynamic changes occur at the sites of…”
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Structural insights into eRF3 and stop codon recognition by eRF1 by Cheng, Zhihong, Saito, Kazuki, Pisarev, Andrey V, Wada, Miki, Pisareva, Vera P, Pestova, Tatyana V, Gajda, Michal, Round, Adam, Kong, Chunguang, Lim, Mengkiat, Nakamura, Yoshikazu, Svergun, Dmitri I, Ito, Koichi, Song, Haiwei

“…Eukaryotic translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act cooperatively to ensure efficient stop codon…”
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Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment by Rauscher, Sarah, Gapsys, Vytautas, Zhou, Man, Van, Qui, Gajda, Michal, Zweckstetter, Markus, Enderlein, Joerg, de Groot, Bert L., Grubmüller, Helmut

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The FTIR and SAXS studies of influence of a morpholine derivatives on the DMPC-based biological membrane systems by Kozak, Maciej, Szpotkowski, Kamil, Kozak, Anna, Zieliński, Ryszard, Wieczorek, Daria, Gajda, Michał J., Domka, Ludwik

“…Fourier transformed infrared (FTIR) spectroscopy and small-angle scattering of synchrotron radiation have been used to analyze the influence of two…”
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