226 related articles for article (PubMed ID: 27599738)
1. 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; 72(Pt 9):1062-72. PubMed ID: 27599738
[TBL] [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; 70(Pt 5):1233-47. PubMed ID: 24816093
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. 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; 35(4):433-451. PubMed ID: 33108589
[TBL] [Abstract][Full Text] [Related]
5. 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; 76(Pt 1):51-62. PubMed ID: 31909743
[TBL] [Abstract][Full Text] [Related]
6. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.
Moriarty NW; Tronrud DE; Adams PD; Karplus PA
FEBS J; 2014 Sep; 281(18):4061-71. PubMed ID: 24890778
[TBL] [Abstract][Full Text] [Related]
7. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.
Moriarty NW; Tronrud DE; Adams PD; Karplus PA
Acta Crystallogr D Struct Biol; 2016 Jan; 72(Pt 1):176-9. PubMed ID: 26894545
[TBL] [Abstract][Full Text] [Related]
8. An editor for the generation and customization of geometry restraints.
Moriarty NW; Draizen EJ; Adams PD
Acta Crystallogr D Struct Biol; 2017 Feb; 73(Pt 2):123-130. PubMed ID: 28177308
[TBL] [Abstract][Full Text] [Related]
9. In situ ligand restraints from quantum-mechanical methods.
Liebschner D; Moriarty NW; Poon BK; Adams PD
Acta Crystallogr D Struct Biol; 2023 Feb; 79(Pt 2):100-110. PubMed ID: 36762856
[TBL] [Abstract][Full Text] [Related]
10. Towards automated crystallographic structure refinement with phenix.refine.
Afonine PV; Grosse-Kunstleve RW; Echols N; Headd JJ; Moriarty NW; Mustyakimov M; Terwilliger TC; Urzhumtsev A; Zwart PH; Adams PD
Acta Crystallogr D Biol Crystallogr; 2012 Apr; 68(Pt 4):352-67. PubMed ID: 22505256
[TBL] [Abstract][Full Text] [Related]
11. Real-space refinement in PHENIX for cryo-EM and crystallography.
Afonine PV; Poon BK; Read RJ; Sobolev OV; Terwilliger TC; Urzhumtsev A; Adams PD
Acta Crystallogr D Struct Biol; 2018 Jun; 74(Pt 6):531-544. PubMed ID: 29872004
[TBL] [Abstract][Full Text] [Related]
12. RNA Structure Refinement Using the ERRASER-Phenix Pipeline.
Chou FC; Echols N; Terwilliger TC; Das R
Methods Mol Biol; 2016; 1320():269-82. PubMed ID: 26227049
[TBL] [Abstract][Full Text] [Related]
13. Using more than 801 296 small-molecule crystal structures to aid in protein structure refinement and analysis.
Cole JC; Giangreco I; Groom CR
Acta Crystallogr D Struct Biol; 2017 Mar; 73(Pt 3):234-239. PubMed ID: 28291758
[TBL] [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; 73(Pt 2):93-102. PubMed ID: 28177305
[TBL] [Abstract][Full Text] [Related]
15. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles.
Singharoy A; Venkatakrishnan B; Liu Y; Mayne CG; Lee S; Chen CH; Zlotnick A; Schulten K; Flood AH
J Am Chem Soc; 2015 Jul; 137(27):8810-8. PubMed ID: 26121416
[TBL] [Abstract][Full Text] [Related]
16. Automated structure solution with the PHENIX suite.
Zwart PH; Afonine PV; Grosse-Kunstleve RW; Hung LW; Ioerger TR; McCoy AJ; McKee E; Moriarty NW; Read RJ; Sacchettini JC; Sauter NK; Storoni LC; Terwilliger TC; Adams PD
Methods Mol Biol; 2008; 426():419-35. PubMed ID: 18542881
[TBL] [Abstract][Full Text] [Related]
17. Conformational variability of benzamidinium-based inhibitors.
Li X; He X; Wang B; Merz K
J Am Chem Soc; 2009 Jun; 131(22):7742-54. PubMed ID: 19435349
[TBL] [Abstract][Full Text] [Related]
18. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.
van Zundert GCP; Moriarty NW; Sobolev OV; Adams PD; Borrelli KW
Structure; 2021 Aug; 29(8):913-921.e4. PubMed ID: 33823127
[TBL] [Abstract][Full Text] [Related]
19. Automated refinement of macromolecular structures at low resolution using prior information.
Kovalevskiy O; Nicholls RA; Murshudov GN
Acta Crystallogr D Struct Biol; 2016 Oct; 72(Pt 10):1149-1161. PubMed ID: 27710936
[TBL] [Abstract][Full Text] [Related]
20. 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; 68(Pt 4):381-90. PubMed ID: 22505258
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]