A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
Liwo, Adam, Baranowski, Maciej, Czaplewski, Cezary, Gołaś, Ewa, He, Yi, Jagieła, Dawid, Krupa, Paweł, Maciejczyk, Maciej, Makowski, Mariusz, Mozolewska, Magdalena A., Niadzvedtski, Andrei, Ołdziej, Stanisław, Scheraga, Harold A., Sieradzan, Adam K., Ślusarz, Rafał, Wirecki, Tomasz, Yin, Yanping, Zaborowski, Bartłomiej
Published in Journal of molecular modeling (01.08.2014)
Published in Journal of molecular modeling (01.08.2014)
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Journal Article
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
He, Yi, Mozolewska, Magdalena A., Krupa, Paweł, Sieradzan, Adam K., Wirecki, Tomasz K., Liwo, Adam, Kachlishvili, Khatuna, Rackovsky, Shalom, Jagieła, Dawid, Ślusarz, Rafał, Czaplewski, Cezary R., Ołdziej, Stanisław, Scheraga, Harold A.
Published in Proceedings of the National Academy of Sciences - PNAS (10.09.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (10.09.2013)
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Journal Article
Preventing fibril formation of a protein by selective mutation
Maisuradze, Gia G., Medina, Jordi, Kachlishvili, Khatuna, Krupa, Pawel, Mozolewska, Magdalena A., Martin-Malpartida, Pau, Maisuradze, Luka, Macias, Maria J., Scheraga, Harold A.
Published in Proceedings of the National Academy of Sciences - PNAS (03.11.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (03.11.2015)
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Journal Article
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
Lubecka, Emilia A., Karczyńska, Agnieszka S., Lipska, Agnieszka G., Sieradzan, Adam K., Ziȩba, Karolina, Sikorska, Celina, Uciechowska, Urszula, Samsonov, Sergey A., Krupa, Paweł, Mozolewska, Magdalena A., Golon, Łukasz, Giełdoń, Artur, Czaplewski, Cezary, Ślusarz, Rafał, Ślusarz, Magdalena, Crivelli, Silvia N., Liwo, Adam
Published in Journal of molecular graphics & modelling (01.11.2019)
Published in Journal of molecular graphics & modelling (01.11.2019)
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Journal Article
Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information
Karczyńska, Agnieszka S., Mozolewska, Magdalena A., Krupa, Paweł, Giełdoń, Artur, Liwo, Adam, Czaplewski, Cezary
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
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Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches
Mozolewska, Magdalena A., Krupa, Paweł, Scheraga, Harold A., Liwo, Adam
Published in Proteins, structure, function, and bioinformatics (01.08.2015)
Published in Proteins, structure, function, and bioinformatics (01.08.2015)
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Journal Article
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
Sieradzan, Adam K, Czaplewski, Cezary, Krupa, Paweł, Mozolewska, Magdalena A, Karczyńska, Agnieszka S, Lipska, Agnieszka G, Lubecka, Emilia A, Gołaś, Ewa, Wirecki, Tomasz, Makowski, Mariusz, Ołdziej, Stanisław, Liwo, Adam
Published in Methods in molecular biology (Clifton, N.J.) (2022)
Published in Methods in molecular biology (Clifton, N.J.) (2022)
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Journal Article
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
Krupa, Paweł, Mozolewska, Magdalena A, Wiśniewska, Marta, Yin, Yanping, He, Yi, Sieradzan, Adam K, Ganzynkowicz, Robert, Lipska, Agnieszka G, Karczyńska, Agnieszka, Ślusarz, Magdalena, Ślusarz, Rafał, Giełdoń, Artur, Czaplewski, Cezary, Jagieła, Dawid, Zaborowski, Bartłomiej, Scheraga, Harold A, Liwo, Adam
Published in Bioinformatics (Oxford, England) (01.11.2016)
Published in Bioinformatics (Oxford, England) (01.11.2016)
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Journal Article
Extension of coarse-grained UNRES force field to treat carbon nanotubes
Sieradzan, Adam K., Mozolewska, Magdalena A.
Published in Journal of molecular modeling (01.05.2018)
Published in Journal of molecular modeling (01.05.2018)
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Journal Article
Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
Mozolewska, Magdalena A, Krupa, Paweł, Zaborowski, Bartłomiej, Liwo, Adam, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary
Published in Journal of chemical information and modeling (28.11.2016)
Published in Journal of chemical information and modeling (28.11.2016)
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Journal Article
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
Karczyńska, Agnieszka S, Ziȩba, Karolina, Uciechowska, Urszula, Mozolewska, Magdalena A, Krupa, Paweł, Lubecka, Emilia A, Lipska, Agnieszka G, Sikorska, Celina, Samsonov, Sergey A, Sieradzan, Adam K, Giełdoń, Artur, Liwo, Adam, Ślusarz, Rafał, Ślusarz, Magdalena, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary
Published in Journal of chemical information and modeling (23.03.2020)
Published in Journal of chemical information and modeling (23.03.2020)
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Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival
Dabrowski, Michal J., Draminski, Michal, Diamanti, Klev, Stepniak, Karolina, Mozolewska, Magdalena A., Teisseyre, Paweł, Koronacki, Jacek, Komorowski, Jan, Kaminska, Bozena, Wojtas, Bartosz
Published in Scientific reports (13.03.2018)
Published in Scientific reports (13.03.2018)
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Journal Article
Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins
Karczyńska, Agnieszka S, Czaplewski, Cezary, Krupa, Paweł, Mozolewska, Magdalena A, Joo, Keehyoung, Lee, Jooyoung, Liwo, Adam
Published in Journal of computational chemistry (05.12.2017)
Published in Journal of computational chemistry (05.12.2017)
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Journal Article
WeFold: A coopetition for protein structure prediction
Khoury, George A., Liwo, Adam, Khatib, Firas, Zhou, Hongyi, Chopra, Gaurav, Bacardit, Jaume, Bortot, Leandro O., Faccioli, Rodrigo A., Deng, Xin, He, Yi, Krupa, Pawel, Li, Jilong, Mozolewska, Magdalena A., Sieradzan, Adam K., Smadbeck, James, Wirecki, Tomasz, Cooper, Seth, Flatten, Jeff, Xu, Kefan, Baker, David, Cheng, Jianlin, Delbem, Alexandre C. B., Floudas, Christodoulos A., Keasar, Chen, Levitt, Michael, Popović, Zoran, Scheraga, Harold A., Skolnick, Jeffrey, Crivelli, Silvia N., Players, Foldit
Published in Proteins, structure, function, and bioinformatics (01.09.2014)
Published in Proteins, structure, function, and bioinformatics (01.09.2014)
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Journal Article
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets
Karczyńska, Agnieszka, Mozolewska, Magdalena A., Krupa, Paweł, Giełdoń, Artur, Bojarski, Krzysztof K., Zaborowski, Bartłomiej, Liwo, Adam, Ślusarz, Rafał, Ślusarz, Magdalena, Lee, Jooyoung, Joo, Keehyoung, Czaplewski, Cezary
Published in Journal of molecular graphics & modelling (01.08.2018)
Published in Journal of molecular graphics & modelling (01.08.2018)
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