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.
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. 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]
4. 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]
5. 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]
6. 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]
7. 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]
8. 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]
9. 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; 61(Pt 3):322-32. PubMed ID: 15735343 [TBL] [Abstract][Full Text] [Related]
12. 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]
13. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Moriarty NW; Grosse-Kunstleve RW; Adams PD Acta Crystallogr D Biol Crystallogr; 2009 Oct; 65(Pt 10):1074-80. PubMed ID: 19770504 [TBL] [Abstract][Full Text] [Related]
14. 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]
15. 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]
16. 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]
17. A radical approach to radicals. Liu Y; Biczysko M; Moriarty NW Acta Crystallogr D Struct Biol; 2022 Jan; 78(Pt 1):43-51. PubMed ID: 34981760 [TBL] [Abstract][Full Text] [Related]
18. Evaluation of site-directed spin labeling for characterizing protein-ligand complexes using simulated restraints. Constantine KL Biophys J; 2001 Sep; 81(3):1275-84. PubMed ID: 11509344 [TBL] [Abstract][Full Text] [Related]
19. 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; 72(Pt 4):586-98. PubMed ID: 27050137 [TBL] [Abstract][Full Text] [Related]
20. 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] [Next] [New Search]