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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.
Ołdziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kaźmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, Kang YK, Gibson KD, Scheraga HA. Ołdziej S, et al. Among authors: makowski m. Proc Natl Acad Sci U S A. 2005 May 24;102(21):7547-52. doi: 10.1073/pnas.0502655102. Epub 2005 May 13. Proc Natl Acad Sci U S A. 2005. PMID: 15894609 Free PMC article.
Further evidence for the absence of polyproline II stretch in the XAO peptide.
Makowska J, Rodziewicz-Motowidlo S, Baginska K, Makowski M, Vila JA, Liwo A, Chmurzynski L, Scheraga HA. Makowska J, et al. Among authors: makowski m. Biophys J. 2007 Apr 15;92(8):2904-17. doi: 10.1529/biophysj.106.097550. Epub 2007 Feb 2. Biophys J. 2007. PMID: 17277185 Free PMC article.
Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 3. Calculation and parameterization of the potentials of mean force of pairs of identical hydrophobic side chains.
Makowski M, Sobolewski E, Czaplewski C, Liwo A, Ołdziej S, No JH, Scheraga HA. Makowski M, et al. J Phys Chem B. 2007 Mar 22;111(11):2925-31. doi: 10.1021/jp065918c. Epub 2007 Feb 27. J Phys Chem B. 2007. PMID: 17388418
Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.
Sobolewski E, Makowski M, Oldziej S, Czaplewski C, Liwo A, Scheraga HA. Sobolewski E, et al. Among authors: makowski m. Protein Eng Des Sel. 2009 Sep;22(9):547-52. doi: 10.1093/protein/gzp028. Epub 2009 Jun 25. Protein Eng Des Sel. 2009. PMID: 19556395 Free PMC article.
633 results