Agnieszka G. Lipska

Gdańsk University of Technology — Poland

Biochemistry, Genetics and Molecular Biology · Life Sciences

13h-index724citations31works4.52yr avg
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Research Topics

Protein Structure and Dynamics(26), Enzyme Structure and Function(20), RNA and protein synthesis mechanisms(5), Mass Spectrometry Techniques and Applications(5), DNA and Nucleic Acid Chemistry(2)

Publications31 total

Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
Computer Physics Communications·2024· 9 citedOpen Access
Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales
Biophysical Journal·2024Open Access
Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches
The Journal of Physical Chemistry Letters·2023· 5 citedOpen Access
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales
Bioinformatics·2023· 8 citedOpen Access
Long‐time scale simulations of virus‐like particles from three human‐norovirus strains
Journal of Computational Chemistry·2023· 3 citedOpen Access
Optimization of parallel implementation of<scp>UNRES</scp>package for coarse‐grained simulations to treat large proteins
Journal of Computational Chemistry·2022· 27 cited
The Influence of Multiple Classes on Learning Online Classifiers from Imbalanced and Concept Drifting Data Streams
arXiv (Cornell University)·2022Open Access
Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins
Journal of Molecular Modeling·2022· 7 cited
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
Methods in molecular biology·2021· 30 cited
Coarse-Grained Modeling of The Calcium, Sodium, Magnesium And Potassium Cations Interacting With Proteins
Research Square (Research Square)·2021Open Access
Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
Biomolecules·2021· 59 citedOpen Access
Prediction of protein assemblies, the next frontier: The <scp>CASP14‐CAPRI</scp> experiment
Proteins Structure Function and Bioinformatics·2021· 122 citedOpen Access
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
Journal of Molecular Graphics and Modelling·2021· 31 cited
Author response for "Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment"
2021Open Access
Further analyses of APRIL/APRIL-receptor/glycosaminoglycan interactions by biochemical assays linked to computational studies
Glycobiology·2021· 11 cited
Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
Biophysical Journal·2021· 8 citedOpen Access
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Journal of Chemical Information and Modeling·2020· 15 citedOpen Access
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
Progress in molecular biology and translational science·2020· 27 cited
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
Proteins Structure Function and Bioinformatics·2019· 138 citedOpen Access
Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction
International Journal of Molecular Sciences·2019· 21 citedOpen Access
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Frequent Co-authors

Adam K. Sieradzan(26), Adam Liwo(25), Cezary Czaplewski(21), Emilia A. Lubecka(13), Paweł Krupa(10), Agnieszka Karczyńska(9), Sergey A. Samsonov(9), Artur Giełdoń(9), Rafał Ślusarz(9), Magdalena A. Mozolewska(7), Anna Antoniak(6), Patryk A. Wesołowski(6), Karolina Zięba(5), Magdalena J. Ślusarz(5), Krzysztof M. Ocetkiewicz(5), Jerzy Proficz(5), Paweł Czarnul(5), Henryk Krawczyk(5), Łukasz Golon(4), Chaok Seok(4)