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.


PUBMED FOR HANDHELDS

Journal Abstract Search


321 related items for PubMed ID: 21598285

  • 1. Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry.
    Fu Z, Li X, Merz KM.
    J Comput Chem; 2011 Sep; 32(12):2587-97. PubMed ID: 21598285
    [Abstract] [Full Text] [Related]

  • 2. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD, Feig M, Brooks CL.
    J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
    [Abstract] [Full Text] [Related]

  • 3. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H, Lu Z, Parks JM, Burger SK, Yang W.
    J Chem Phys; 2008 Jan 21; 128(3):034105. PubMed ID: 18205486
    [Abstract] [Full Text] [Related]

  • 4. Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field.
    Jagielska A, Skolnick J.
    J Comput Chem; 2007 Jul 30; 28(10):1648-57. PubMed ID: 17342701
    [Abstract] [Full Text] [Related]

  • 5. Conformational Analysis of Free and Bound Retinoic Acid.
    Fu Z, Li X, Merz KM.
    J Chem Theory Comput; 2012 Apr 10; 8(4):1436-1448. PubMed ID: 22844234
    [Abstract] [Full Text] [Related]

  • 6. 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
    [Abstract] [Full Text] [Related]

  • 7. Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
    Yu N, Yennawar HP, Merz KM.
    Acta Crystallogr D Biol Crystallogr; 2005 Mar 16; 61(Pt 3):322-32. PubMed ID: 15735343
    [Abstract] [Full Text] [Related]

  • 8. A robust force field based method for calculating conformational energies of charged drug-like molecules.
    Poehlsgaard J, Harpsøe K, Jørgensen FS, Olsen L.
    J Chem Inf Model; 2012 Feb 27; 52(2):409-19. PubMed ID: 21985436
    [Abstract] [Full Text] [Related]

  • 9. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding.
    Perola E, Charifson PS.
    J Med Chem; 2004 May 06; 47(10):2499-510. PubMed ID: 15115393
    [Abstract] [Full Text] [Related]

  • 10. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
    [Abstract] [Full Text] [Related]

  • 11. Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.
    Hsiao YW, Sanchez-Garcia E, Doerr M, Thiel W.
    J Phys Chem B; 2010 Nov 25; 114(46):15413-23. PubMed ID: 20977248
    [Abstract] [Full Text] [Related]

  • 12. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions.
    Morgado CA, Jurecka P, Svozil D, Hobza P, Sponer J.
    Phys Chem Chem Phys; 2010 Apr 14; 12(14):3522-34. PubMed ID: 20336251
    [Abstract] [Full Text] [Related]

  • 13. Fluorine bonding--how does it work in protein-ligand interactions?
    Zhou P, Zou J, Tian F, Shang Z.
    J Chem Inf Model; 2009 Oct 14; 49(10):2344-55. PubMed ID: 19788294
    [Abstract] [Full Text] [Related]

  • 14. Computational modeling of carbohydrate-recognition process in E-selectin complex: structural mapping of sialyl Lewis X onto ab initio QM/MM free energy surface.
    Ishida T.
    J Phys Chem B; 2010 Mar 25; 114(11):3950-64. PubMed ID: 20078087
    [Abstract] [Full Text] [Related]

  • 15. Fragment quantum mechanical calculation of proteins and its applications.
    He X, Zhu T, Wang X, Liu J, Zhang JZ.
    Acc Chem Res; 2014 Sep 16; 47(9):2748-57. PubMed ID: 24851673
    [Abstract] [Full Text] [Related]

  • 16. Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.
    Fu Z, Li X, Miao Y, Merz KM.
    J Chem Theory Comput; 2013 Dec 03; 9(3):1686-1693. PubMed ID: 23526889
    [Abstract] [Full Text] [Related]

  • 17. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
    Rosta E, Klähn M, Warshel A.
    J Phys Chem B; 2006 Feb 16; 110(6):2934-41. PubMed ID: 16471904
    [Abstract] [Full Text] [Related]

  • 18. QM methods in structure based design: utility in probing protein-ligand interactions.
    Gleeson MP, Hannongbua S, Gleeson D.
    J Mol Graph Model; 2010 Dec 16; 29(4):507-17. PubMed ID: 21075029
    [Abstract] [Full Text] [Related]

  • 19. Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.
    Nagy PI, Erhardt PW.
    J Phys Chem A; 2008 May 08; 112(18):4342-54. PubMed ID: 18373368
    [Abstract] [Full Text] [Related]

  • 20. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
    Lu Z, Yang W.
    J Chem Phys; 2004 Jul 01; 121(1):89-100. PubMed ID: 15260525
    [Abstract] [Full Text] [Related]


    Page: [Next] [New Search]
    of 17.