BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

286 related articles for article (PubMed ID: 16240095)

  • 1. AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine.
    Homeyer N; Horn AH; Lanig H; Sticht H
    J Mol Model; 2006 Feb; 12(3):281-9. PubMed ID: 16240095
    [TBL] [Abstract][Full Text] [Related]  

  • 2. An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
    Craft JW; Legge GB
    J Biomol NMR; 2005 Sep; 33(1):15-24. PubMed ID: 16222554
    [TBL] [Abstract][Full Text] [Related]  

  • 3. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
    Duan Y; Wu C; Chowdhury S; Lee MC; Xiong G; Zhang W; Yang R; Cieplak P; Luo R; Lee T; Caldwell J; Wang J; Kollman P
    J Comput Chem; 2003 Dec; 24(16):1999-2012. PubMed ID: 14531054
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. Development of the force field parameters for phosphoimidazole and phosphohistidine.
    Kosinsky YA; Volynsky PE; Lagant P; Vergoten G; Suzuki E; Arseniev AS; Efremov RG
    J Comput Chem; 2004 Aug; 25(11):1313-21. PubMed ID: 15185324
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Phosphoamino acid analysis.
    Sefton BM
    Curr Protoc Protein Sci; 2001 May; Chapter 13():Unit13.3. PubMed ID: 18429115
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Rapid separation of phosphoamino acids including the phosphohistidines by isocratic high-performance liquid chromatography of the orthophthalaldehyde derivatives.
    Carlomagno L; Huebner VD; Matthews HR
    Anal Biochem; 1985 Sep; 149(2):344-8. PubMed ID: 2416240
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems.
    Lin F; Wang R
    J Chem Theory Comput; 2010 Jun; 6(6):1852-70. PubMed ID: 26615845
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
    Pérez A; Marchán I; Svozil D; Sponer J; Cheatham TE; Laughton CA; Orozco M
    Biophys J; 2007 Jun; 92(11):3817-29. PubMed ID: 17351000
    [TBL] [Abstract][Full Text] [Related]  

  • 10. A fast and high-quality charge model for the next generation general AMBER force field.
    He X; Man VH; Yang W; Lee TS; Wang J
    J Chem Phys; 2020 Sep; 153(11):114502. PubMed ID: 32962378
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
    Hu H; Elstner M; Hermans J
    Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187
    [TBL] [Abstract][Full Text] [Related]  

  • 12. General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions.
    Werneck AS; Filho TM; Dardenne LE
    J Phys Chem A; 2008 Jan; 112(2):268-80. PubMed ID: 18095663
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Development and benchmark to obtain AMBER parameters dataset for non-standard amino acids modified with 4-hydroxy-2-nonenal.
    Alviz-Amador A; Galindo-Murillo R; Pineda-Alemán R; Pérez-González H; Rodríguez-Cavallo E; Vivas-Reyes R; Méndez-Cuadro D
    Data Brief; 2018 Dec; 21():2581-2589. PubMed ID: 30761340
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids.
    Stoppelman JP; Ng TT; Nerenberg PS; Wang LP
    J Phys Chem B; 2021 Nov; 125(43):11927-11942. PubMed ID: 34668708
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
    Katagiri D; Fuji H; Neya S; Hoshino T
    J Comput Chem; 2008 Sep; 29(12):1930-44. PubMed ID: 18366016
    [TBL] [Abstract][Full Text] [Related]  

  • 16. VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems.
    Zheng S; Tang Q; He J; Du S; Xu S; Wang C; Xu Y; Lin F
    J Chem Inf Model; 2016 Apr; 56(4):811-8. PubMed ID: 26998926
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Phosphoamino acid analysis.
    Sefton BM
    Curr Protoc Cell Biol; 2001 May; Chapter 14():Unit 14.5. PubMed ID: 18228327
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Genetic Encoding of Phosphorylated Amino Acids into Proteins.
    Allen MC; Karplus PA; Mehl RA; Cooley RB
    Chem Rev; 2024 May; 124(10):6592-6642. PubMed ID: 38691379
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates.
    Woods RJ; Chappelle R
    Theochem; 2000 Aug; 527(1-3):149-156. PubMed ID: 25309012
    [TBL] [Abstract][Full Text] [Related]  

  • 20. The general AMBER force field (GAFF) can accurately predict thermodynamic and transport properties of many ionic liquids.
    Sprenger KG; Jaeger VW; Pfaendtner J
    J Phys Chem B; 2015 May; 119(18):5882-95. PubMed ID: 25853313
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 15.