Agnieszka Karczynska
Agnieszka Karczynska
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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
P Krupa, MA Mozolewska, M Wi¶niewska, Y Yin, Y He, AK Sieradzan, ...
Bioinformatics 32 (21), 3270-3278, 2016
Blind prediction of homo‐and hetero‐protein complexes: The CASP13‐CAPRI experiment
MF Lensink, G Brysbaert, N Nadzirin, S Velankar, RAG Chaleil, T Gerguri, ...
Proteins: Structure, Function, and Bioinformatics 87 (12), 1200-1221, 2019
A maximum-likelihood approach to force-field calibration
B Zaborowski, D Jagieła, C Czaplewski, A Hałabis, A Lewandowska, ...
Journal of chemical information and modeling 55 (9), 2050-2070, 2015
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
C Czaplewski, A Karczyńska, AK Sieradzan, A Liwo
Nucleic acids research 46 (W1), W304-W309, 2018
Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information
AS Karczyńska, MA Mozolewska, P Krupa, A Giełdoń, A Liwo, ...
Proteins: Structure, Function, and Bioinformatics 86, 228-239, 2018
Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13
JE Fajardo, R Shrestha, N Gil, A Belsom, SN Crivelli, C Czaplewski, ...
Proteins: Structure, Function, and Bioinformatics 87 (12), 1283-1297, 2019
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
A Karczyńska, MA Mozolewska, P Krupa, A Giełdoń, KK Bojarski, ...
Journal of Molecular Graphics and Modelling 83, 92-99, 2018
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
EA Lubecka, AS Karczyńska, AG Lipska, AK Sieradzan, K Ziȩba, ...
Journal of Molecular Graphics and Modelling 92, 154-166, 2019
Disulfide-linked peptides for blocking BTLA/HVEM binding
M Spodzieja, K Kuncewicz, A Sieradzan, A Karczyńska, J Iwaszkiewicz, ...
International journal of molecular sciences 21 (2), 636, 2020
A structural model of the immune checkpoint CD160–HVEM complex derived from HDX-mass spectrometry and molecular modeling
K Kuncewicz, M Spodzieja, A Sieradzan, A Karczyńska, K D±browska, ...
Oncotarget 10 (4), 536, 2019
Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins
AS Karczyńska, C Czaplewski, P Krupa, MA Mozolewska, K Joo, J Lee, ...
Journal of computational chemistry 38 (31), 2730-2746, 2017
UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations
P Krupa, AS Karczyńska, MA Mozolewska, A Liwo, C Czaplewski
Bioinformatics, 2020
Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study
KK Bojarski, AS Karczyńska, SA Samsonov
Journal of chemical information and modeling 60 (4), 2247-2256, 2020
Truncation of Huia versabilis Bowman-Birk inhibitor increases its selectivity, matriptase-1 inhibitory activity and proteolytic stability
A Gitlin-Domagalska, D Dębowski, K Gucwa, D Starego, N Ptaszyńska, ...
Biochimie 171, 178-186, 2020
Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems
AK Sieradzan, CR Czaplewski, EA Lubecka, AG Lipska, AS Karczynska, ...
Biophysical Journal 120 (3), 83a-84a, 2021
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
AS Karczyńska, K Ziȩba, U Uciechowska, MA Mozolewska, P Krupa, ...
Journal of chemical information and modeling 60 (3), 1844-1864, 2020
Fragments of gD Protein as Inhibitors of BTLA/HVEM Complex Formation-Design, Synthesis, and Cellular Studies
K Kuncewicz, C Battin, A Sieradzan, A Karczyńska, M Orlikowska, ...
International journal of molecular sciences 21 (22), 8876, 2020
Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
A Liwo, C Czaplewski, AK Sieradzan, EA Lubecka, AG Lipska, Ł Golon, ...
Progress in molecular biology and translational science 170, 73-122, 2020
Modeling of protein structure and dynamics with the UNRES force field assisted by limited experimental data and knowledge-based information
C Czplewski, A Karczynska, MA Mozolewska, P Krupa, A Gieldon, ...
Acta Biochimica Polonica 65 (S2), 2018
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