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dr Krzysztof Bojarski
Employment
- Assistant professor at Department of Physical Chemistry
- 2022 - present at Chemistry
- 2019 - 2021 Principal Investigator at Chemistry
Keywords Help
- molecular dynamics
- alphafold, blind prediction, capri, casp, deep learning, protein assemblies, protein complexes, protein-protein interaction
- colloidal stability
- hyperbranched polyglycerol
- molecular docking
- molecular modeling
- nanodiamonds
- optical sensing
- procathepsin processing
- protein-ligand interactions
Publications
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total: 12
Catalog Publications
Year 2024
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublicationPre-treatment of diamond surface in low-temperature plasma for oxygenation and in acids for carboxylation was hypothesized to promote the branching density of the hyperbranched glycidol polymer. This was expected to increase the homogeneity of the branching level and suppress interactions with proteins. As a result, composite nanodiamonds with reduced hydrodynamic diameters that are maintained in physiological environments were...
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In silico approaches for better understanding cysteine cathepsin-glycosaminoglycan interactions
PublicationCysteine cathepsins constitute the largest cathepsin family, with 11 proteases in human that are present primarily within acidic endosomal and lysosomal compartments. They are involved in the turnover of intracellular and extracellular proteins. They are synthesized as inactive procathepsins that are converted to mature active forms. Cathepsins play important roles in physiological and pathological processes and, therefore, receive...
Year 2023
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublicationWe present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody–antigen complexes, and 7 large assemblies. On average 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups...
Year 2022
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublicationGlycosaminoglcyans (GAGs), linear anionic periodic polysaccharides, are crucial for many biologically relevant functions in the extracellular matrix. By interacting with proteins GAGs mediate processes such as cancer development, cell proliferation and the onset of neurodegenerative diseases. Despite this eminent importance of GAGs, they still represent a limited focus for the computational community in comparison to other classes...
Year 2021
Year 2020
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Rat cathepsin K: Enzymatic specificity and regulation of its collagenolytic activity
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Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
Publication
Year 2019
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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations
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Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
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Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans
Publication
Year 2018
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