Wyszukiwarka
dr Krzysztof Bojarski
Zatrudnienie
- Adiunkt w Katedra Chemii Fizycznej
- 2022 - present w Chemistry
- 2019 - 2021 Principal Investigator w Chemistry
Słowa kluczowe Pomoc
- 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
Publikacje
Filtry
wszystkich: 12
Katalog Publikacji
Rok 2024
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Enhancing colloidal stability of nanodiamond via surface modification with dendritic molecules for optical sensing in physiological environments
PublikacjaPre-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
PublikacjaCysteine 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...
Rok 2023
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment
PublikacjaWe 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...
Rok 2022
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Explicit solvent repulsive scaling replica exchange molecular dynamics ( RS‐REMD ) in molecular modeling of protein‐glycosaminoglycan complexes
PublikacjaGlycosaminoglcyans (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...
Rok 2021
Rok 2020
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Rat cathepsin K: Enzymatic specificity and regulation of its collagenolytic activity
Publikacja -
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
Publikacja
Rok 2019
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Local and long range potentials for heparin‐protein systems for coarse‐grained simulations
Publikacja -
Molecular dynamics insights into protein‐glycosaminoglycan systems from microsecond‐scale simulations
Publikacja -
Synthesis and in silico characterization of artificially phosphorylated glycosaminoglycans
Publikacja
Rok 2018
wyświetlono 745 razy