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: 16581373)

  • 1. Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results.
    Friesner RA
    Adv Protein Chem; 2005; 72():79-104. PubMed ID: 16581373
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties.
    Li X; Hassan SA; Mehler EL
    Proteins; 2005 Aug; 60(3):464-84. PubMed ID: 15959866
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.
    Duan LL; Feng GQ; Zhang QG
    Sci Rep; 2016 Aug; 6():31488. PubMed ID: 27507430
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Estimates of ligand-binding affinities supported by quantum mechanical methods.
    Söderhjelm P; Kongsted J; Genheden S; Ryde U
    Interdiscip Sci; 2010 Mar; 2(1):21-37. PubMed ID: 20640794
    [TBL] [Abstract][Full Text] [Related]  

  • 5. High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.
    Borbulevych O; Martin RI; Westerhoff LM
    Acta Crystallogr D Struct Biol; 2018 Nov; 74(Pt 11):1063-1077. PubMed ID: 30387765
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water.
    Manzoni V; Lyra ML; Coutinho K; Canuto S
    J Chem Phys; 2011 Oct; 135(14):144103. PubMed ID: 22010694
    [TBL] [Abstract][Full Text] [Related]  

  • 7. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S; Mackerell AD; Brooks CL
    J Comput Chem; 2004 Sep; 25(12):1504-14. PubMed ID: 15224394
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Some practical approaches to treating electrostatic polarization of proteins.
    Ji C; Mei Y
    Acc Chem Res; 2014 Sep; 47(9):2795-803. PubMed ID: 24883956
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Quantum mechanics/molecular mechanics strategies for docking pose refinement: distinguishing between binders and decoys in cytochrome C peroxidase.
    Burger SK; Thompson DC; Ayers PW
    J Chem Inf Model; 2011 Jan; 51(1):93-101. PubMed ID: 21133348
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.
    Monari A; Rivail JL; Assfeld X
    Acc Chem Res; 2013 Feb; 46(2):596-603. PubMed ID: 23249409
    [TBL] [Abstract][Full Text] [Related]  

  • 11. How accurate is the description of ligand-protein interactions by a hybrid QM/MM approach?
    Kollar J; Frecer V
    J Mol Model; 2017 Dec; 24(1):11. PubMed ID: 29234892
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Quantum-Mechanics Methodologies in Drug Discovery: Applications of Docking and Scoring in Lead Optimization.
    Crespo A; Rodriguez-Granillo A; Lim VT
    Curr Top Med Chem; 2017; 17(23):2663-2680. PubMed ID: 28685695
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions.
    Arcon JP; Defelipe LA; Modenutti CP; López ED; Alvarez-Garcia D; Barril X; Turjanski AG; Martí MA
    J Chem Inf Model; 2017 Apr; 57(4):846-863. PubMed ID: 28318252
    [TBL] [Abstract][Full Text] [Related]  

  • 14. A quantum mechanical computational method for modeling electrostatic and solvation effects of protein.
    Wang X; Li Y; Gao Y; Yang Z; Lu C; Zhu T
    Sci Rep; 2018 Apr; 8(1):5475. PubMed ID: 29615707
    [TBL] [Abstract][Full Text] [Related]  

  • 15. On the polarization of ligands by proteins.
    Willow SY; Xie B; Lawrence J; Eisenberg RS; Minh DDL
    Phys Chem Chem Phys; 2020 Jun; 22(21):12044-12057. PubMed ID: 32421120
    [TBL] [Abstract][Full Text] [Related]  

  • 16. On-the-Fly QM/MM Docking with Attracting Cavities.
    Chaskar P; Zoete V; Röhrig UF
    J Chem Inf Model; 2017 Jan; 57(1):73-84. PubMed ID: 27983849
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization.
    Liu J; He X; Zhang JZ
    J Chem Inf Model; 2013 Jun; 53(6):1306-14. PubMed ID: 23651068
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model.
    Jiang N; Ma J
    J Phys Chem A; 2008 Oct; 112(40):9854-67. PubMed ID: 18788721
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Halothane solvation in water and organic solvents from molecular simulations with new polarizable potential function.
    Subbotina JO; Johannes J; Lev B; Noskov SY
    J Phys Chem B; 2010 May; 114(19):6401-8. PubMed ID: 20411978
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.
    Misini Ignjatović M; Caldararu O; Dong G; Muñoz-Gutierrez C; Adasme-Carreño F; Ryde U
    J Comput Aided Mol Des; 2016 Sep; 30(9):707-730. PubMed ID: 27565797
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.