209 related articles for article (PubMed ID: 31909743)
1. 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]
2. 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]
3. 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]
4. 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]
5. Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform
Mikhailovskii O; Xue Y; Skrynnikov NR
IUCrJ; 2022 Jan; 9(Pt 1):114-133. PubMed ID: 35059216
[TBL] [Abstract][Full Text] [Related]
6. 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]
7. 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]
8. Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases.
Kuszewski J; Gronenborn AM; Clore GM
Protein Sci; 1996 Jun; 5(6):1067-80. PubMed ID: 8762138
[TBL] [Abstract][Full Text] [Related]
9. Real-space quantum-based refinement for cryo-EM: Q|R#3.
Wang L; Kruse H; Sobolev OV; Moriarty NW; Waller MP; Afonine PV; Biczysko M
Acta Crystallogr D Struct Biol; 2020 Dec; 76(Pt 12):1184-1191. PubMed ID: 33263324
[TBL] [Abstract][Full Text] [Related]
10. 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]
11. Improving NMR protein structure quality by Rosetta refinement: a molecular replacement study.
Ramelot TA; Raman S; Kuzin AP; Xiao R; Ma LC; Acton TB; Hunt JF; Montelione GT; Baker D; Kennedy MA
Proteins; 2009 Apr; 75(1):147-67. PubMed ID: 18816799
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement.
Headd JJ; Echols N; Afonine PV; Moriarty NW; Gildea RJ; Adams PD
Acta Crystallogr D Biol Crystallogr; 2014 May; 70(Pt 5):1346-56. PubMed ID: 24816103
[TBL] [Abstract][Full Text] [Related]
14. In some cases more complicated approaches to refinement of macromolecular structures are not necessary.
Dauter Z; Wlodawer A
IUCrJ; 2024 Jul; 11(Pt 4):643-644. PubMed ID: 38958017
[TBL] [Abstract][Full Text] [Related]
15. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.
Schnieders MJ; Fenn TD; Pande VS
J Chem Theory Comput; 2011 Apr; 7(4):1141-56. PubMed ID: 26606362
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. Arginine off-kilter: guanidinium is not as planar as restraints denote.
Moriarty NW; Liebschner D; Tronrud DE; Adams PD
Acta Crystallogr D Struct Biol; 2020 Dec; 76(Pt 12):1159-1166. PubMed ID: 33263321
[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. 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]
20. Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.
Koepke J; Scharff EI; Lücke C; Rüterjans H; Fritzsch G
Acta Crystallogr D Biol Crystallogr; 2003 Oct; 59(Pt 10):1744-54. PubMed ID: 14501113
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
