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323 related items for PubMed ID: 30387765

  • 1. 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 01; 74(Pt 11):1063-1077. PubMed ID: 30387765
    [Abstract] [Full Text] [Related]

  • 2. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.
    Borbulevych OY, Plumley JA, Martin RI, Merz KM, Westerhoff LM.
    Acta Crystallogr D Biol Crystallogr; 2014 May 01; 70(Pt 5):1233-47. PubMed ID: 24816093
    [Abstract] [Full Text] [Related]

  • 3. The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design.
    Borbulevych OY, Martin RI, Westerhoff LM.
    J Comput Aided Mol Des; 2021 Apr 01; 35(4):433-451. PubMed ID: 33108589
    [Abstract] [Full Text] [Related]

  • 4. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.
    Borbulevych O, Martin RI, Tickle IJ, Westerhoff LM.
    Acta Crystallogr D Struct Biol; 2016 Apr 01; 72(Pt 4):586-98. PubMed ID: 27050137
    [Abstract] [Full Text] [Related]

  • 5. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.
    Janowski PA, Moriarty NW, Kelley BP, Case DA, York DM, Adams PD, Warren GL.
    Acta Crystallogr D Struct Biol; 2016 Sep 01; 72(Pt 9):1062-72. PubMed ID: 27599738
    [Abstract] [Full Text] [Related]

  • 6. Using quantum mechanical approaches to study biological systems.
    Merz KM.
    Acc Chem Res; 2014 Sep 16; 47(9):2804-11. PubMed ID: 25099338
    [Abstract] [Full Text] [Related]

  • 7. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
    Moriarty NW, Janowski PA, Swails JM, Nguyen H, Richardson JS, Case DA, Adams PD.
    Acta Crystallogr D Struct Biol; 2020 Jan 01; 76(Pt 1):51-62. PubMed ID: 31909743
    [Abstract] [Full Text] [Related]

  • 8. Multiscale Quantum Refinement Approaches for Metalloproteins.
    Yan Z, Li X, Chung LW.
    J Chem Theory Comput; 2021 Jun 08; 17(6):3783-3796. PubMed ID: 34032440
    [Abstract] [Full Text] [Related]

  • 9. Combining crystallography with quantum mechanics.
    Bergmann J, Oksanen E, Ryde U.
    Curr Opin Struct Biol; 2022 Feb 08; 72():18-26. PubMed ID: 34392061
    [Abstract] [Full Text] [Related]

  • 10. In situ ligand restraints from quantum-mechanical methods.
    Liebschner D, Moriarty NW, Poon BK, Adams PD.
    Acta Crystallogr D Struct Biol; 2023 Feb 01; 79(Pt 2):100-110. PubMed ID: 36762856
    [Abstract] [Full Text] [Related]

  • 11. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery.
    Kulkarni PU, Shah H, Vyas VK.
    Mini Rev Med Chem; 2022 Feb 01; 22(8):1096-1107. PubMed ID: 34620049
    [Abstract] [Full Text] [Related]

  • 12. Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.
    Hsiao YW, Sanchez-Garcia E, Doerr M, Thiel W.
    J Phys Chem B; 2010 Nov 25; 114(46):15413-23. PubMed ID: 20977248
    [Abstract] [Full Text] [Related]

  • 13. Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.
    Yu N, Yennawar HP, Merz KM.
    Acta Crystallogr D Biol Crystallogr; 2005 Mar 25; 61(Pt 3):322-32. PubMed ID: 15735343
    [Abstract] [Full Text] [Related]

  • 14. Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes.
    Steiner RA, Tucker JA.
    Acta Crystallogr D Struct Biol; 2017 Feb 01; 73(Pt 2):93-102. PubMed ID: 28177305
    [Abstract] [Full Text] [Related]

  • 15. MolProbity: More and better reference data for improved all-atom structure validation.
    Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC.
    Protein Sci; 2018 Jan 01; 27(1):293-315. PubMed ID: 29067766
    [Abstract] [Full Text] [Related]

  • 16. Fluorine bonding--how does it work in protein-ligand interactions?
    Zhou P, Zou J, Tian F, Shang Z.
    J Chem Inf Model; 2009 Oct 01; 49(10):2344-55. PubMed ID: 19788294
    [Abstract] [Full Text] [Related]

  • 17. The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.
    Askerka M, Brudvig GW, Batista VS.
    Acc Chem Res; 2017 Jan 17; 50(1):41-48. PubMed ID: 28001034
    [Abstract] [Full Text] [Related]

  • 18. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
    Headd JJ, Echols N, Afonine PV, Grosse-Kunstleve RW, Chen VB, Moriarty NW, Richardson DC, Richardson JS, Adams PD.
    Acta Crystallogr D Biol Crystallogr; 2012 Apr 17; 68(Pt 4):381-90. PubMed ID: 22505258
    [Abstract] [Full Text] [Related]

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