Enhancing resolution and predictive power of the UNRES force field for protein folding simulations by revision of the potentials of interactions involving protein main chain
2011/01/N/ST4/01772
Keywords
Descriptors
- ST4_15: Chemia teoretyczna i obliczeniowa
- ST4_13: Chemia fizyczna układów biologicznych
Panel
ST4 – Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development
Host institution
Uniwersytet Gdański, Wydział Chemii
Voivodeship: pomorskie
Principal investigator (from the host institution)
Number of co-investigators in the project: 2
Call
PRELUDIUM 1 – announced on 2011-03-15
- Amount awarded
- 150 000 PLN
- Project start date
- 2011-12-13
- Project end date
- 2014-12-12
- Project duration
- 36 months (the same as in the proposal)
- Project status
- Project settled
Equipment purchased [PL]
- Komputery. Cost: 18 040 PLN
- Switch. Cost: 9 537 PLN
- UPS. Cost: 50 400 PLN
- Zestawy komputerowe do klastra obliczeniowego wraz z monitorami do obsługi klastra (8 pcs). Cost: 32 000 PLN
- tablet.
Information in the final report
Publication in academic press/journals (6)
-
Extension of UNRES Force Field to Treat Polypeptide Chains with d-Amino Acid Residues
- Authors:
- Adam K. Sieradzan, Ulrich H. E. Hansmann, Harold A. Scheraga, and Adam Liwo
- Academic press:
- J. Chem. Theory Comput. (year: 2012, volume: 8(11), pages: 4746-4757), Publisher: ACS Publications
- Status:
- Published
- DOI:
- 10.1021/ct3005563 – link to the publication
-
Folding and Self-Assembly of a Small Protein Complex
- Authors:
- Adam K. Sieradzan, Adam Liwo, and Ulrich H. E. Hansmann
- Academic press:
- J. Chem. Theory Comput. (year: 2012, volume: 8(9), pages: 3416-3422), Publisher: ACS Publications
- Status:
- Published
- DOI:
- 10.1021/ct300528r – link to the publication
-
WeFold:Acoopetitionforprotein structureprediction
- Authors:
- George A. Khoury, Adam Liwo, Firas Khatib, Hongyi Zhou, Gaurav Chopra, Jaume Bacardit, Leandro O. Bortot, Rodrigo A. Faccioli, Xin Deng, Yi He, Pawel Krupa, Jilong Li, Magdalena A. Mozolewska, Adam K. Sieradzan, James Smadbeck, Tomasz Wirecki, Seth Cooper, Jeff Flatten, Kefan Xu, David Baker, Jianlin Cheng, Alexandre C. B. Delbem, Christodoulos A. Floudas, Chen Keasar, Michael Levitt, Zoran Popovic, Harold A. Scheraga, Jeffrey Skolnick, Silvia N. Crivelli , and Foldit Players
- Academic press:
- Proteins: Structure, Function, and Bioinformatics (year: 2014, volume: 82, pages: 1850-1868), Publisher: Wiley
- Status:
- Published
- DOI:
- 10.1002/prot.24538 – link to the publication
-
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
- Authors:
- Yi He, Magdalena A. Mozolewska, Paweł Krupa, Adam K. Sieradzan, Tomasz K. Wirecki, Adam Liwo, Khatuna Kachlishvili, Shalom Rackovsky, Dawid Jagieła, Rafał Ślusarz, Cezary R. Czaplewski, Stanisław Ołdziej, and Harold A. Scheraga
- Academic press:
- Proceedings of the National Academy of Sciences of the United States of America PNAS (year: 2013, volume: 110, pages: 14936–14941), Publisher: National Academy of Sciences
- Status:
- Published
- DOI:
- 10.1073/pnas.1313316110 – link to the publication
-
Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
- Authors:
- Paweł Krupa, Adam K. Sieradzan, S. Rackovsky, Maciej Baranowski, Stanisław Ołdziej, Harold A. Scheraga, Adam Liwo, and Cezary Czaplewski
- Academic press:
- J. Chem. Theory Comput. (year: 2013, volume: 9, pages: 4620–4632), Publisher: ACS Publications
- Status:
- Published
- DOI:
- 10.1021/ct4004977 – link to the publication
-
Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations
- Authors:
- Adam K. Sieradzan , Pawel Krupa , Harold A.Scheraga , Adam Liwo , and Cezary Czaplewski
- Status:
- Accepted for publication