These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

182 related articles for article (PubMed ID: 28388107)

  • 1. 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; 146(12):124106. PubMed ID: 28388107
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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; 147(11):115101. PubMed ID: 28938819
    [TBL] [Abstract][Full Text] [Related]  

  • 3. 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; 127(15):155103. PubMed ID: 17949219
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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; 150(15):155104. PubMed ID: 31005069
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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
    J Chem Theory Comput; 2015 Feb; 11(2):817-31. PubMed ID: 25691834
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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; 10(5):2194-2203. PubMed ID: 24839411
    [TBL] [Abstract][Full Text] [Related]  

  • 7. 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; 8(11):4746-4757. PubMed ID: 24729761
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers.
    Liwo A; Czaplewski C; Sieradzan AK; Lubecka EA; Lipska AG; Golon Ł; Karczyńska A; Krupa P; Mozolewska MA; Makowski M; Ganzynkowicz R; Giełdoń A; Maciejczyk M
    Prog Mol Biol Transl Sci; 2020; 170():73-122. PubMed ID: 32145953
    [TBL] [Abstract][Full Text] [Related]  

  • 9. An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics.
    Shen H; Liwo A; Scheraga HA
    J Phys Chem B; 2009 Jun; 113(25):8738-44. PubMed ID: 19480420
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.
    Kozłowska U; Maisuradze GG; Liwo A; Scheraga HA
    J Comput Chem; 2010 Apr; 31(6):1154-67. PubMed ID: 20017135
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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; 114(13):4471-85. PubMed ID: 20166738
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method.
    Kozłowska U; Liwo A; Scheraga HA
    J Comput Chem; 2010 Apr; 31(6):1143-53. PubMed ID: 20073062
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A united residue force-field for calcium-protein interactions.
    Khalili M; Saunders JA; Liwo A; Ołdziej S; Scheraga HA
    Protein Sci; 2004 Oct; 13(10):2725-35. PubMed ID: 15388862
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
    Arnautova YA; Jagielska A; Scheraga HA
    J Phys Chem B; 2006 Mar; 110(10):5025-44. PubMed ID: 16526746
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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; 8(4):1334-1343. PubMed ID: 23087598
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.
    Liwo A; Czaplewski C
    J Chem Phys; 2020 Feb; 152(5):054902. PubMed ID: 32035448
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Improvement of the treatment of loop structures in the UNRES force field by inclusion of coupling between backbone- and side-chain-local conformational states.
    Krupa P; Sieradzan AK; Rackovsky S; Baranowski M; Ołldziej S; Scheraga HA; Liwo A; Czaplewski C
    J Chem Theory Comput; 2013 Oct; 9(10):. PubMed ID: 24273465
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Coarse-grained protein model with residue orientation energies derived from atomic force fields.
    Betancourt MR
    J Phys Chem B; 2009 Nov; 113(44):14824-30. PubMed ID: 19817469
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery.
    Sikorska C; Liwo A
    J Phys Chem B; 2022 Nov; 126(46):9493-9505. PubMed ID: 36367920
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers.
    Salerno KM; Bernstein N
    J Chem Theory Comput; 2018 Apr; 14(4):2219-2229. PubMed ID: 29529375
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.