Rafał Ślusarz
Zatrudnienie
- 2001 - present w Wydział Chemii
Publikacje
Filtry
wszystkich: 44
Katalog Publikacji
Rok 2022
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublikacjaIn this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...
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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide
Publikacja
Rok 2021
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublikacjaThe UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...
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Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
PublikacjaWe present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...
Rok 2020
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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
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Influence of Carbohydrate Residues on Antibacterial Activity of Vancomycin
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The Quaternization Reaction of 5-O-Sulfonates of Methyl 2,3-o-Isopropylidene-β-D-Ribofuranoside with Selected Heterocyclic and Aliphatic Amines
PublikacjaThe synthesis of N-((methyl 5-deoxy-2,3-O-isopropylidene-β-D-ribofuranoside)-5-yl) ammonium salts are presented. To determine the effect of the nucleophile type and outgoing group on the quaternization reaction, selected aliphatic and heterocyclic aromatic amines reacted with: methyl 2,3-O-isopropylidene-5-O-tosyl-β-D-ribofuranoside or methyl 2,3-O-isopropylidene-5-O-mesyl-β-D -ribofuranoside or methyl 2,3-O-isopropylidene-5-O-triflyl-β-D-ribofuranoside...
Rok 2019
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Efficient synthesis and antifungal investigation of nucleosides’ quaternary ammonium salt derivatives
PublikacjaQuaternary ammonium salts are a group of compounds with diverse biological properties, the most important of which are their antiviral, antibacterial, and antifungal activities. The quaternization reactions of 5'-O-tosyl derivatives of uridine and thymidine with triethylamine, trimethylamine, 4-(N ,N -dimethylamino)pyridine, 2-methylpyridine, and pyridine are described in this article. Two of the synthesized compounds are exceptional...
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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
Publikacja
Rok 2018
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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The Oxolane Ring Opening of Some Muramic Acid Derivatives Under Acidic Conditions
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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
Publikacja
Rok 2017
Rok 2016
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
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Solid phase synthesis of two muramyl pentapeptide derivatives
Publikacja
Rok 2015
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Conformational Studies of [11è12(CN4)]ScyII and [15è16(CN4)]ScyII? Two Scyliorhinin II Analogues by means of 2D NMR Spectroscopy and Theoretical Methods
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
Publikacja
Rok 2014
wyświetlono 99 razy