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Journal Abstract Search

221 related items for PubMed ID: 20073062

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  • 4. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.
    Sieradzan AK, Niadzvedtski A, Scheraga HA, Liwo A.
    J Chem Theory Comput; 2014 May 13; 10(5):2194-2203. PubMed ID: 24839411
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  • 5. Determination of effective potentials for the stretching of C(α) ⋯ C(α) virtual bonds in polypeptide chains for coarse-grained simulations of proteins from ab initio energy surfaces of N-methylacetamide and N-acetylpyrrolidine.
    Sieradzan AK, Scheraga HA, Liwo A.
    J Chem Theory Comput; 2012 Apr 10; 8(4):1334-1343. PubMed ID: 23087598
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  • 7. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.
    Maisuradze GG, Senet P, Czaplewski C, Liwo A, Scheraga HA.
    J Phys Chem A; 2010 Apr 08; 114(13):4471-85. PubMed ID: 20166738
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  • 8. Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.
    Sieradzan AK, Hansmann UH, Scheraga HA, Liwo A.
    J Chem Theory Comput; 2012 Nov 13; 8(11):4746-4757. PubMed ID: 24729761
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  • 9. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains.
    Lubecka EA, Liwo A.
    J Chem Phys; 2017 Sep 21; 147(11):115101. PubMed ID: 28938819
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  • 10. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation.
    Liwo A, Sieradzan AK, Lipska AG, Czaplewski C, Joung I, Żmudzińska W, Hałabis A, Ołdziej S.
    J Chem Phys; 2019 Apr 21; 150(15):155104. PubMed ID: 31005069
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  • 11. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains.
    Sieradzan AK, Makowski M, Augustynowicz A, Liwo A.
    J Chem Phys; 2017 Mar 28; 146(12):124106. PubMed ID: 28388107
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  • 12. Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method.
    Kaźmierkiewicz R, Liwo A, Scheraga HA.
    J Comput Chem; 2002 May 28; 23(7):715-23. PubMed ID: 11948589
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  • 13. Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
    He Y, Xiao Y, Liwo A, Scheraga HA.
    J Comput Chem; 2009 Oct 28; 30(13):2127-35. PubMed ID: 19242966
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  • 14. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins.
    Schrauber H, Eisenhaber F, Argos P.
    J Mol Biol; 1993 Mar 20; 230(2):592-612. PubMed ID: 8464066
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  • 15. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
    Arnautova YA, Jagielska A, Scheraga HA.
    J Phys Chem B; 2006 Mar 16; 110(10):5025-44. PubMed ID: 16526746
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  • 16. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
    Murarka RK, Liwo A, Scheraga HA.
    J Chem Phys; 2007 Oct 21; 127(15):155103. PubMed ID: 17949219
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  • 18. Intrinsic energy landscapes of amino acid side-chains.
    Zhu X, Lopes PE, Shim J, MacKerell AD.
    J Chem Inf Model; 2012 Jun 25; 52(6):1559-72. PubMed ID: 22582825
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  • 19. Rotamer strain energy in protein helices - quantification of a major force opposing protein folding.
    Penel S, Doig AJ.
    J Mol Biol; 2001 Jan 26; 305(4):961-8. PubMed ID: 11162106
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