Aleksandra E. Badaczewska-Dawid
Aleksandra E. Badaczewska-Dawid
Research Scientist IV, Genome Informatics Facility, Iowa State University
Verified email at - Homepage
Cited by
Cited by
Coarse-grained protein models and their applications
S Kmiecik, D Gront, M Kolinski, L Wieteska, AE Dawid, A Kolinski
Chemical reviews 116 (14), 7898-7936, 2016
Flexible docking of peptides to proteins using CABS‐dock
M Kurcinski, A Badaczewska‐Dawid, M Kolinski, A Kolinski, S Kmiecik
Protein Science 29 (1), 211-222, 2020
CABS-dock standalone: a toolbox for flexible protein–peptide docking
M Kurcinski, M Pawel Ciemny, T Oleniecki, A Kuriata, ...
Bioinformatics 35 (20), 4170-4172, 2019
Modeling of protein structural flexibility and large-scale dynamics: Coarse-grained simulations and elastic network models
S Kmiecik, M Kouza, AE Badaczewska-Dawid, A Kloczkowski, A Kolinski
International journal of molecular sciences 19 (11), 3496, 2018
Computational reconstruction of atomistic protein structures from coarse-grained models
AE Badaczewska-Dawid, A Kolinski, S Kmiecik
Computational and structural biotechnology journal 18, 162-176, 2020
Modeling of disordered protein structures using monte carlo simulations and knowledge-based statistical force fields
MP Ciemny, AE Badaczewska-Dawid, M Pikuzinska, A Kolinski, ...
International journal of molecular sciences 20 (3), 606, 2019
SURPASS low-resolution coarse-grained protein modeling
AE Dawid, D Gront, A Kolinski
Journal of chemical theory and computation 13 (11), 5766-5779, 2017
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes
AE Badaczewska-Dawid, C Nithin, K Wroblewski, M Kurcinski, S Kmiecik
Nucleic Acids Research 50 (W1), W474-W482, 2022
HaDeX: an R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments
W Puchała, M Burdukiewicz, M Kistowski, KA Dąbrowska, ...
Bioinformatics 36 (16), 4516-4518, 2020
Protocols for fast simulations of protein structure flexibility using CABS-flex and SURPASS
A Badaczewska-Dawid, A Kolinski, S Kmiecik
Protein Structure Prediction. Methods in Molecular Biology 2165, 337-353, 2020
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement
A Badaczewska-Dawid, S Kmiecik, M Kolinski
Briefings in Bioinformatics, 1-9, 2020
BioShell 3.0: library for processing structural biology data
JM Macnar, NA Szulc, JD Kryś, AE Badaczewska-Dawid, D Gront
Biomolecules 10 (3), 461, 2020
Coarse-grained modeling of the interplay between secondary structure propensities and protein fold assembly
AE Dawid, D Gront, A Kolinski
Journal of Chemical Theory and Computation 14 (4), 2277-2287, 2018
BIAPSS: a comprehensive physicochemical Analyzer of proteins undergoing liquid–liquid phase separation
AE Badaczewska-Dawid, VN Uversky, DA Potoyan
International Journal of Molecular Sciences 23 (11), 6204, 2022
Protocols for all-atom reconstruction and high-resolution refinement of protein-peptide complex structures
A Badaczewska-Dawid, A Khramushin, A Kolinski, O Schueler-Furman, ...
Protein Structure Prediction. Methods in Molecular Biology 2165, 273-287, 2020
A3D database: structure-based predictions of protein aggregation for the human proteome
AE Badaczewska-Dawid, J Garcia-Pardo, A Kuriata, J Pujols, S Ventura, ...
Bioinformatics 38 (11), 3121-3123, 2022
A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms
AE Badaczewska-Dawid, A Kuriata, C Pintado-Grima, J Garcia-Pardo, ...
Nucleic Acids Research 52 (D1), D360-D367, 2024
A3DyDB: exploring structural aggregation propensities in the yeast proteome
J Garcia-Pardo, AE Badaczewska-Dawid, C Pintado-Grima, V Iglesias, ...
Microbial cell factories 22 (1), 186, 2023
Structure prediction of linear and cyclic peptides using CABS-flex
A Badaczewska-Dawid, K Wróblewski, M Kurcinski, S Kmiecik
Briefings in Bioinformatics 25 (2), bbae003, 2024
Protocols for rational design of protein solubility and aggregation properties using Aggrescan3D standalone
A Kuriata, AE Badaczewska-Dawid, J Pujols, S Ventura, S Kmiecik
Computer Simulations of Aggregation of Proteins and Peptides, 17-40, 2022
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