Oldziej S - Search Results

1

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: oldziej s. 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.

2

A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.

Liwo A, Arłukowicz P, Czaplewski C, Ołdziej S, Pillardy J, Scheraga HA. Liwo A, et al. Among authors: oldziej s. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1937-42. doi: 10.1073/pnas.032675399. Proc Natl Acad Sci U S A. 2002. PMID: 11854494 Free PMC article.

3

Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: negative evidence for the involvement of peroxa and endoperoxide intermediates.

Bobrowski M, Liwo A, Ołdziej S, Jeziorek D, Ossowski T. Bobrowski M, et al. Among authors: oldziej s. J Comput Chem. 2002 Aug;23(11):1076-89. doi: 10.1002/jcc.10102. J Comput Chem. 2002. PMID: 12116394

4

Use of NMR and fluorescence spectroscopy as well as theoretical conformational analysis in conformation-activity studies of cyclic enkephalin analogues.

Malicka J, Czaplewski C, Groth M, Wiczk W, Oldziej S, Lankiewicz L, Ciarkowski J, Liwo A. Malicka J, et al. Among authors: oldziej s. Curr Top Med Chem. 2004;4(1):123-33. doi: 10.2174/1568026043451591. Curr Top Med Chem. 2004. PMID: 14754380 Review.

5

Prediction of the structures of proteins with the UNRES force field, including dynamic formation and breaking of disulfide bonds.

Czaplewski C, Oldziej S, Liwo A, Scheraga HA. Czaplewski C, et al. Among authors: oldziej s. Protein Eng Des Sel. 2004 Jan;17(1):29-36. doi: 10.1093/protein/gzh003. Protein Eng Des Sel. 2004. PMID: 14985535

6

A united residue force-field for calcium-protein interactions.

Khalili M, Saunders JA, Liwo A, Ołdziej S, Scheraga HA. Khalili M, et al. Among authors: oldziej s. Protein Sci. 2004 Oct;13(10):2725-35. doi: 10.1110/ps.04878904. Protein Sci. 2004. PMID: 15388862 Free PMC article.

7

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.

Nanias M, Chinchio M, Ołdziej S, Czaplewski C, Scheraga HA. Nanias M, et al. Among authors: oldziej s. J Comput Chem. 2005 Nov 15;26(14):1472-86. doi: 10.1002/jcc.20286. J Comput Chem. 2005. PMID: 16088925

8

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. Among authors: oldziej s. 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

9

Potential of mean force of hydrophobic association: dependence on solute size.

Sobolewski E, Makowski M, Czaplewski C, Liwo A, Ołdziej S, Scheraga HA. Sobolewski E, et al. Among authors: oldziej s. J Phys Chem B. 2007 Sep 13;111(36):10765-74. doi: 10.1021/jp070594t. Epub 2007 Aug 22. J Phys Chem B. 2007. PMID: 17713937

10

Computational techniques for efficient conformational sampling of proteins.

Liwo A, Czaplewski C, Ołdziej S, Scheraga HA. Liwo A, et al. Among authors: oldziej s. Curr Opin Struct Biol. 2008 Apr;18(2):134-9. doi: 10.1016/j.sbi.2007.12.001. Epub 2008 Jan 22. Curr Opin Struct Biol. 2008. PMID: 18215513 Free PMC article. Review.

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