BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

816 related articles for article (PubMed ID: 11746709)

  • 1. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
    Liu Y; Beveridge DL
    Proteins; 2002 Jan; 46(1):128-46. PubMed ID: 11746709
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Free energy determinants of secondary structure formation: I. alpha-Helices.
    Yang AS; Honig B
    J Mol Biol; 1995 Sep; 252(3):351-65. PubMed ID: 7563056
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA; Mehler EL; Zhang D; Weinstein H
    Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Conformational analysis of endothelin-1: effects of solvation free energy.
    Hempel JC; Fine RM; Hassan M; Ghoul W; Guaragna A; Koerber SC; Li Z; Hagler AT
    Biopolymers; 1995 Sep; 36(3):283-301. PubMed ID: 7669916
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins.
    Avbelj F
    J Mol Biol; 2000 Jul; 300(5):1335-59. PubMed ID: 10903873
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Prediction of polyelectrolyte polypeptide structures using Monte Carlo conformational search methods with implicit solvation modeling.
    Evans JS; Chan SI; Goddard WA
    Protein Sci; 1995 Oct; 4(10):2019-31. PubMed ID: 8535238
    [TBL] [Abstract][Full Text] [Related]  

  • 7. The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.
    Iwaoka M; Tomoda S
    J Comput Chem; 2003 Jul; 24(10):1192-200. PubMed ID: 12820126
    [TBL] [Abstract][Full Text] [Related]  

  • 8. New-generation amber united-atom force field.
    Yang L; Tan CH; Hsieh MJ; Wang J; Duan Y; Cieplak P; Caldwell J; Kollman PA; Luo R
    J Phys Chem B; 2006 Jul; 110(26):13166-76. PubMed ID: 16805629
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model.
    de Bakker PI; DePristo MA; Burke DF; Blundell TL
    Proteins; 2003 Apr; 51(1):21-40. PubMed ID: 12596261
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.
    Khalili M; Liwo A; Jagielska A; Scheraga HA
    J Phys Chem B; 2005 Jul; 109(28):13798-810. PubMed ID: 16852728
    [TBL] [Abstract][Full Text] [Related]  

  • 11. 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]  

  • 12. Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures.
    Brasseur R
    J Mol Graph; 1995 Oct; 13(5):312-22. PubMed ID: 8603060
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.
    Steinbach PJ
    J Phys Chem B; 2018 Dec; 122(49):11355-11362. PubMed ID: 30230838
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators.
    Fogolari F; Tosatto SC; Colombo G
    BMC Bioinformatics; 2005 Dec; 6():301. PubMed ID: 16354298
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Energetics of the native and non-native states of the glycophorin transmembrane helix dimer.
    Mottamal M; Zhang J; Lazaridis T
    Proteins; 2006 Mar; 62(4):996-1009. PubMed ID: 16395713
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.
    Moulinier L; Case DA; Simonson T
    Acta Crystallogr D Biol Crystallogr; 2003 Dec; 59(Pt 12):2094-103. PubMed ID: 14646067
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem.
    Jackson RM; Gabb HA; Sternberg MJ
    J Mol Biol; 1998 Feb; 276(1):265-85. PubMed ID: 9514726
    [TBL] [Abstract][Full Text] [Related]  

  • 19. TOUCHSTONE II: a new approach to ab initio protein structure prediction.
    Zhang Y; Kolinski A; Skolnick J
    Biophys J; 2003 Aug; 85(2):1145-64. PubMed ID: 12885659
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Conformational structure, dynamics, and solvation energies of small alanine peptides in water and carbon tetrachloride.
    Xiang TX; Anderson BD
    J Pharm Sci; 2006 Jun; 95(6):1269-87. PubMed ID: 16625657
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 41.