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 *

165 related articles for article (PubMed ID: 19717427)

  • 21. All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.
    Arnautova YA; Abagyan R; Totrov M
    J Chem Theory Comput; 2015 May; 11(5):2167-2186. PubMed ID: 25999804
    [TBL] [Abstract][Full Text] [Related]  

  • 22. 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]  

  • 23. 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]  

  • 24. Protein dynamics derived from clusters of crystal structures.
    van Aalten DM; Conn DA; de Groot BL; Berendsen HJ; Findlay JB; Amadei A
    Biophys J; 1997 Dec; 73(6):2891-6. PubMed ID: 9414203
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
    Kim YC; Hummer G
    J Mol Biol; 2008 Feb; 375(5):1416-33. PubMed ID: 18083189
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.
    Kumari I; Sandhu P; Ahmed M; Akhter Y
    Curr Protein Pept Sci; 2017 Aug; 18(11):1163-1179. PubMed ID: 28637405
    [TBL] [Abstract][Full Text] [Related]  

  • 27. High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.
    Kuster DJ; Liu C; Fang Z; Ponder JW; Marshall GR
    PLoS One; 2015; 10(4):e0123146. PubMed ID: 25894612
    [TBL] [Abstract][Full Text] [Related]  

  • 28. An evaluation of force-field treatments of aromatic interactions.
    Chessari G; Hunter CA; Low CM; Packer MJ; Vinter JG; Zonta C
    Chemistry; 2002 Jul; 8(13):2860-7. PubMed ID: 12489214
    [TBL] [Abstract][Full Text] [Related]  

  • 29. The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors.
    Na H; Song G
    Proteins; 2015 Jul; 83(7):1273-83. PubMed ID: 25917684
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry.
    van Vlijmen HW; Karplus M
    J Mol Biol; 2005 Jul; 350(3):528-42. PubMed ID: 15922356
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Force-induced remodelling of proteins and their complexes.
    Chen Y; Radford SE; Brockwell DJ
    Curr Opin Struct Biol; 2015 Feb; 30():89-99. PubMed ID: 25710390
    [TBL] [Abstract][Full Text] [Related]  

  • 32. 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]  

  • 33. 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]  

  • 34. Determination of atomic desolvation energies from the structures of crystallized proteins.
    Zhang C; Vasmatzis G; Cornette JL; DeLisi C
    J Mol Biol; 1997 Apr; 267(3):707-26. PubMed ID: 9126848
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.
    Bahar I; Atilgan AR; Erman B
    Fold Des; 1997; 2(3):173-81. PubMed ID: 9218955
    [TBL] [Abstract][Full Text] [Related]  

  • 36. REACH coarse-grained simulation of a cellulose fiber.
    Glass DC; Moritsugu K; Cheng X; Smith JC
    Biomacromolecules; 2012 Sep; 13(9):2634-44. PubMed ID: 22937726
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Development and testing of a general amber force field.
    Wang J; Wolf RM; Caldwell JW; Kollman PA; Case DA
    J Comput Chem; 2004 Jul; 25(9):1157-74. PubMed ID: 15116359
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
    Liwo A; Khalili M; Czaplewski C; Kalinowski S; Ołdziej S; Wachucik K; Scheraga HA
    J Phys Chem B; 2007 Jan; 111(1):260-85. PubMed ID: 17201450
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
    Dauber-Osguthorpe P; Hagler AT
    J Comput Aided Mol Des; 2019 Feb; 33(2):133-203. PubMed ID: 30506158
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes.
    Piana S; Robustelli P; Tan D; Chen S; Shaw DE
    J Chem Theory Comput; 2020 Apr; 16(4):2494-2507. PubMed ID: 31914313
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 9.