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 *

204 related articles for article (PubMed ID: 16493626)

  • 1. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules.
    Myers J; Grothaus G; Narayanan S; Onufriev A
    Proteins; 2006 Jun; 63(4):928-38. PubMed ID: 16493626
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A fast and simple method to calculate protonation states in proteins.
    Sandberg L; Edholm O
    Proteins; 1999 Sep; 36(4):474-83. PubMed ID: 10450090
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Dynamic docking and electron-transfer between cytochrome b5 and a suite of myoglobin surface-charge mutants. Introduction of a functional-docking algorithm for protein-protein complexes.
    Liang ZX; Kurnikov IV; Nocek JM; Mauk AG; Beratan DN; Hoffman BM
    J Am Chem Soc; 2004 Mar; 126(9):2785-98. PubMed ID: 14995196
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.
    Bürgi R; Kollman PA; Van Gunsteren WF
    Proteins; 2002 Jun; 47(4):469-80. PubMed ID: 12001225
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins.
    Gilson MK
    Proteins; 1993 Mar; 15(3):266-82. PubMed ID: 8456096
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins.
    Liang J; Edelsbrunner H; Fu P; Sudhakar PV; Subramaniam S
    Proteins; 1998 Oct; 33(1):18-29. PubMed ID: 9741841
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Constant pH molecular dynamics in generalized Born implicit solvent.
    Mongan J; Case DA; McCammon JA
    J Comput Chem; 2004 Dec; 25(16):2038-48. PubMed ID: 15481090
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping.
    Bombarda E; Becker T; Ullmann GM
    J Am Chem Soc; 2006 Sep; 128(37):12129-39. PubMed ID: 16967962
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Empirical parametrization of pK values for carboxylic acids in proteins using a genetic algorithm.
    Godoy-Ruiz R; Perez-Jimenez R; Garcia-Mira MM; Plaza del Pino IM; Sanchez-Ruiz JM
    Biophys Chem; 2005 Apr; 115(2-3):263-6. PubMed ID: 15752616
    [TBL] [Abstract][Full Text] [Related]  

  • 10. On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data.
    Huang L; Makarov DE
    J Chem Phys; 2006 Feb; 124(6):64108. PubMed ID: 16483197
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Monte Carlo and modified Tanford-Kirkwood results for macromolecular electrostatics calculations.
    de Carvalho SJ; Ghiotto RC; da Silva FL
    J Phys Chem B; 2006 May; 110(17):8832-9. PubMed ID: 16640442
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Grand canonical free-energy calculations of protein-ligand binding.
    Clark M; Meshkat S; Wiseman JS
    J Chem Inf Model; 2009 Apr; 49(4):934-43. PubMed ID: 19309088
    [TBL] [Abstract][Full Text] [Related]  

  • 13. H++: a server for estimating pKas and adding missing hydrogens to macromolecules.
    Gordon JC; Myers JB; Folta T; Shoja V; Heath LS; Onufriev A
    Nucleic Acids Res; 2005 Jul; 33(Web Server issue):W368-71. PubMed ID: 15980491
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles.
    Whitelam S; Geissler PL
    J Chem Phys; 2007 Oct; 127(15):154101. PubMed ID: 17949126
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Efficient implementation of three-dimensional reference interaction site model self-consistent-field method: application to solvatochromic shift calculations.
    Minezawa N; Kato S
    J Chem Phys; 2007 Feb; 126(5):054511. PubMed ID: 17302489
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Very fast prediction and rationalization of pKa values for protein-ligand complexes.
    Bas DC; Rogers DM; Jensen JH
    Proteins; 2008 Nov; 73(3):765-83. PubMed ID: 18498103
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method.
    Lu B; Zhang D; McCammon JA
    J Chem Phys; 2005 Jun; 122(21):214102. PubMed ID: 15974723
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach.
    Pihur V; Datta S; Datta S
    Bioinformatics; 2007 Jul; 23(13):1607-15. PubMed ID: 17483500
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules.
    Anandakrishnan R; Onufriev A
    J Comput Biol; 2008 Mar; 15(2):165-84. PubMed ID: 18312148
    [TBL] [Abstract][Full Text] [Related]  

  • 20. MUMBO: a protein-design approach to crystallographic model building and refinement.
    Stiebritz MT; Muller YA
    Acta Crystallogr D Biol Crystallogr; 2006 Jun; 62(Pt 6):648-58. PubMed ID: 16699192
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.