Projects search

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins

Authors:

Agnieszka S. Karczyńska, Cezary Czaplewski, Paweł Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, and Adam Liwo

Academic press:

Journal of Computational Chemistry (year: 2017, volume: 38, pages: 2730-2746), Publisher: Wiley

Status:

Published

DOI:

10.1002/jcc.25070 – link to the publication

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Authors:

Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B.K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergei Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players, Silvia N. Crivelli

Academic press:

Scientific Reports (year: 2018, volume: 8, pages: 9939-1 - 9939-18), Publisher: Nature Publishing Group

Status:

Published

DOI:

10.1038/s41598-018-26812-8 – link to the publication

Reoptimized UNRES Potential for Protein Model Quality Assessment

Authors:

Eshel Faraggi, Pawel Krupa, Magdalena A. Mozolewska, Adam Liwo, Andrzej Kloczkowski

Academic press:

Genes (year: 2018, volume: 9, pages: 601-1 - 601-17), Publisher: MDPI

Status:

Published

DOI:

10.3390/genes9120601 – link to the publication

Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics

Authors:

Paweł Krupa, Anna Hałabis, Wioletta Żmudzińska, Stanisław Ołdziej, Harold A. Scheraga, Adam Liwo

Academic press:

Journal of Chemical Information and Modeling (year: 2017, volume: 57, pages: 2364-2377), Publisher: American Chemical Society

Status:

Published

DOI:

10.1021/acs.jcim.7b00254 – link to the publication

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information

Authors:

Agnieszka S. Karczyńnska, Magdalena A. Mozolewska, Paweł Krupa, Artur Giełdoń, Adam Liwo, Cezary Czaplewski

Academic press:

Proteins: Structure Function and Bioinformatics (year: 2018, volume: 86, pages: 228-239), Publisher: Wiley

Status:

Published

DOI:

10.1002/prot.25421 – link to the publication

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Authors:

Magdalena A. Mozolewska, Paweł Krupa, Bartłomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski

Academic press:

Journal of Chemical Iinformation and Modeling (year: 2016, volume: 56, pages: 2263-2279), Publisher: American Chemical Society

Status:

Published

DOI:

10.1021/acs.jcim.6b00189 – link to the publication

Prediction of protein structure by template-based modeling combined with the UNRES force field

Authors:

Paweł Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo

Academic press:

Journal of Chemical Information and Modeling (year: 2015, volume: 55, pages: 1271-1281), Publisher: American Chemical Society

Status:

Published

DOI:

10.1021/acs.jcim.5b00117 – link to the publication

Use of the UNRES force field in template-assisted prediction of proteins structures and the refinement of server models: test with CASP12 targets

Authors:

Agnieszka Karczyńska, Magdalena A. Mozolewska, Paweł Krupa, Artur Giełdoń, Krzysztof K. Bojarski, Bartłomiej Zaborowski, Adam Liwo, Rafał Ślusarz, Magdalena Ślusarz, Jooyoung Lee, Keehyoung Joo and Cezary Czaplewski

Academic press:

J. Mol. Graph. Model. (year: 2018, volume: 83, pages: 92-99), Publisher: Elsevier

Status:

Published

DOI:

10.1016/j.jmgm.2018.05.008 – link to the publication

In situ data analytics and indexing of protein trajectories

Authors:

Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer

Academic press:

Journal of Computational Chemistry (year: 2017, volume: 38, pages: 1419-1430), Publisher: Wiley

Status:

Published

DOI:

10.1002/jcc.24729 – link to the publication

Chemoinformatics Methods for Studying Biomolecules

Authors:

Adam Liwo, Cezary Czaplewski, Stanisław Ołdziej, Bartłomiej Zaborowski, Dawid Jagieła, Jooyoung Lee

Book:

Handbook of Computational Chemistry (year: 2017, volume: 5, pages: 2183-2199), Publisher: Springer International Publishing Switzerland

Status:

Published

DOI:

link to the publication