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Rafał Ślusarz
Employment
- 2001 - present at Wydział Chemii
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total: 44
Catalog Publications
Year 2022
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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
PublicationIn 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
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Year 2021
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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
PublicationThe 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
PublicationWe 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...
Year 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
PublicationThe 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...
Year 2019
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Efficient synthesis and antifungal investigation of nucleosides’ quaternary ammonium salt derivatives
PublicationQuaternary 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
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Year 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
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Year 2017
Year 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
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Year 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
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Year 2014
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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
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Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties
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Year 2013
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Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study
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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
Publication
Year 2011
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Conformational changes of peptidoglycan fragments during their interactions with vancomycin
Publication
Year 2010
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Conformational stability of the full-atom hexameric model of the ClpB chaperone fromEscherichia coli
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Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies
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Year 2009
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An Influence of the Aromatic Side Chains Conformations in Positions 2 and 3 of Vasopressin Analogs on Interactions with Vasopressin and Oxytocin Receptors
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Molecular Dynamics Study of the Internal Water Molecules in Vasopressin and Oxytocin Receptors
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Year 2008
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Conformational studies of highly potent 1-aminocyclohexane-1-carboxylic acid substituted V2 vasopressin agonists
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Theoretical Study on Interactions of Bicyclic Vasopressin Analogues with Human Neurohypophyseal Hormone Receptors
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Year 2006
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Analysis of interactions responsible for vasopressin binding to human neurohypophyseal hormone receptors—molecular dynamics study of the activated receptor–vasopressin–Gα systems
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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Investigation ofcis/trans ratios of peptide bonds in AVP analogues containingN-methylphenylalanine enantiomers
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Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors
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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin—modeling of an activated state
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Molecular Modeling of Meta II Rhodopsin
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Year 2005
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A hypothesis for GPCR activation
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Study of New Oxytocin Antagonist Barusiban (Fe200 440) Affinity Toward Human Oxytocin Receptor Versus Vasopressin V1a and V2 Receptors - Molecular Dynamics Simulation in POPC Bilayer
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Year 2004
Year 2003
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Molecular dynamics study of 4-OH-phenylacetyl- D -Y(Me)FQNRPR-NH 2 selectivity to V1a receptor
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Molecular Modeling of Interaction of the Vasopressin Analogs with Vasopressin and Oxytocin Receptors
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Molecular Modeling of the Neurohypophyseal Receptor/Atosiban Complexes
Publication
Year 2001
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Neurohypophyseal Receptors-Ligands: Where We Are After the Landmark Rhodopsin Structure Determination
Publication
Year 2000
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