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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.
Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium; Crivelli SN. Keasar C, et al. Among authors: krupa p. Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8. Sci Rep. 2018. PMID: 29967418 Free PMC article.
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.
He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Ślusarz R, Czaplewski CR, Ołdziej S, Scheraga HA. He Y, et al. Among authors: krupa p. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14936-41. doi: 10.1073/pnas.1313316110. Epub 2013 Aug 26. Proc Natl Acad Sci U S A. 2013. PMID: 23980156 Free PMC article.
WeFold: a coopetition for protein structure prediction.
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem AC, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN; Foldit Players. Khoury GA, et al. Among authors: krupa p. Proteins. 2014 Sep;82(9):1850-68. doi: 10.1002/prot.24538. Epub 2014 Jul 8. Proteins. 2014. PMID: 24677212 Free PMC article.
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.
Liwo A, Baranowski M, Czaplewski C, Gołaś E, He Y, Jagieła D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Ołdziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B. Liwo A, et al. Among authors: krupa p. J Mol Model. 2014 Aug;20(8):2306. doi: 10.1007/s00894-014-2306-5. Epub 2014 Jul 15. J Mol Model. 2014. PMID: 25024008 Free PMC article.
Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations.
Sieradzan AK, Krupa P, Scheraga HA, Liwo A, Czaplewski C. Sieradzan AK, et al. Among authors: krupa p. J Chem Theory Comput. 2015 Feb 10;11(2):817-31. doi: 10.1021/ct500736a. J Chem Theory Comput. 2015. PMID: 25691834 Free PMC article.
The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely, a united peptide group (p) located halfway between the two neighboring alpha-carbon atoms (Calphas), which serve o …
The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interact …
Preventing fibril formation of a protein by selective mutation.
Maisuradze GG, Medina J, Kachlishvili K, Krupa P, Mozolewska MA, Martin-Malpartida P, Maisuradze L, Macias MJ, Scheraga HA. Maisuradze GG, et al. Among authors: krupa p. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13549-54. doi: 10.1073/pnas.1518298112. Epub 2015 Oct 19. Proc Natl Acad Sci U S A. 2015. PMID: 26483482 Free PMC article.
123 results