Search Results - "Mateusz, Banach"

Structural Outlier Detection and Zernike-Canterakis Moments for Molecular Surface Meshes-Fast Implementation in Python by Banach, Mateusz

“…Object retrieval systems measure the degree of similarity of the shape of 3D models. They search for the elements of the 3D model databases that resemble the…”
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Improved Assessment of Globularity of Protein Structures and the Ellipsoid Profile of the Biological Assemblies from the PDB by Banach, Mateusz

“…In this paper, we present an update to the ellipsoid profile algorithm (EP), a simple technique for the measurement of the globularity of protein structures…”
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Symmetrization in the Calculation Pipeline of Gauss Function-Based Modeling of Hydrophobicity in Protein Structures by Banach, Mateusz

“…In this paper, we show, discuss, and compare the effects of symmetrization in two calculation subroutines of the Fuzzy Oil Drop model, a coarse-grained model…”
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Assessment of Globularity of Protein Structures via Minimum Volume Ellipsoids and Voxel-Based Atom Representation by Banach, Mateusz

“…A computer algorithm for assessment of globularity of protein structures is presented. By enclosing the input protein in a minimum volume ellipsoid (MVEE) and…”
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Model of Environmental Membrane Field for Transmembrane Proteins by Roterman, Irena, Stapor, Katarzyna, Fabian, Piotr, Konieczny, Leszek, Banach, Mateusz

“…The water environment determines the activity of biological processes. The role of such an environment interpreted in the form of an external field expressed…”
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Downhill, Ultrafast and Fast Folding Proteins Revised by Banach, Mateusz, Stapor, Katarzyna, Konieczny, Leszek, Fabian, Piotr, Roterman, Irena

“…Research on the protein folding problem differentiates the protein folding process with respect to the duration of this process. The current structure encoded…”
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Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution by Ptak-Kaczor, Magdalena, Banach, Mateusz, Stapor, Katarzyna, Fabian, Piotr, Konieczny, Leszek, Roterman, Irena

“…Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the…”
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The Structure of Amyloid Versus the Structure of Globular Proteins by Fabian, Piotr, Banach, Mateusz, Stapor, Katarzyna, Konieczny, Leszek, Ptak-Kaczor, Magdalena, Roterman, Irena

“…The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are…”
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Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins by Barbara Kalinowska, Mateusz Banach, Leszek Konieczny, Irena Roterman

“…The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins…”
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Alternative Structures of α-Synuclein by Dułak, Dawid, Gadzała, Małgorzata, Banach, Mateusz, Konieczny, Leszek, Roterman, Irena

“…The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of…”
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Structure of the Hydrophobic Core Determines the 3D Protein Structure-Verification by Single Mutation Proteins by Banach, Mateusz, Fabian, Piotr, Stapor, Katarzyna, Konieczny, Leszek, Roterman, And Irena

“…Four de novo proteins differing in single mutation positions, with a chain length of 56 amino acids, represent diverse 3D structures: monomeric 3α and 4β + α…”
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Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes by Dygut, Jacek, Kalinowska, Barbara, Banach, Mateusz, Piwowar, Monika, Konieczny, Leszek, Roterman, Irena

“…The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the…”
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Contribution to the Understanding of Protein–Protein Interface and Ligand Binding Site Based on Hydrophobicity Distribution—Application to Ferredoxin I and II Cases by Banach, Mateusz, Chomilier, Jacques, Roterman, Irena

“…Ferredoxin I and II are proteins carrying a specific ligand—an iron-sulfur cluster—which allows transport of electrons. These two classes of ferredoxin in…”
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Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin by Banach, Mateusz, Stapor, Katarzyna, Fabian, Piotr, Konieczny, Leszek, Roterman, Irena

“…The two forms of transthyretin differing slightly in the tertiary structure, despite the presence of five mutations, show radically different properties in…”
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Is the hydrophobic core a universal structural element in proteins? by Kalinowska, Barbara, Banach, Mateusz, Wiśniowski, Zdzisław, Konieczny, Leszek, Roterman, Irena

“…The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of…”
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Filamentous Aggregates of Tau Proteins Fulfil Standard Amyloid Criteria Provided by the Fuzzy Oil Drop (FOD) Model by Dułak, Dawid, Gadzała, Małgorzata, Banach, Mateusz, Ptak, Magdalena, Wiśniowski, Zdzisław, Konieczny, Leszek, Roterman, Irena

“…Abnormal filamentous aggregates that are formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all the criteria defined under the fuzzy…”
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Different Synergy in Amyloids and Biologically Active Forms of Proteins by Fabian, Piotr, Stapor, Katarzyna, Banach, Mateusz, Ptak-Kaczor, Magdalena, Konieczny, Leszek, Roterman, Irena

“…Protein structure is the result of the high synergy of all amino acids present in the protein. This synergy is the result of an overall strategy for adapting a…”
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Influence of the Aqueous Environment on Protein Structure—A Plausible Hypothesis Concerning the Mechanism of Amyloidogenesis by Roterman, Irena, Banach, Mateusz, Kalinowska, Barbara, Konieczny, Leszek

“…The aqueous environment is a pervasive factor which, in many ways, determines the protein folding process and consequently the activity of proteins. Proteins…”
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Propagation of Fibrillar Structural Forms in Proteins Stopped by Naturally Occurring Short Polypeptide Chain Fragments by Roterman, Irena, Banach, Mateusz, Konieczny, Leszek

“…Amyloids characterized by unbounded growth of fibrillar structures cause many pathological processes. Such unbounded propagation is due to the presence of a…”
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Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity by Banach, Mateusz, Konieczny, Leszek, Roterman, Irena

“…The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid…”
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