During the first five years of the PHENIX project we have developed a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that we have built and made available to the community. The algorithms are tightly linked and made easily accessible to the user through the PHENIX Wizards and the PHENIX GUI. These crystallographic libraries, algorithms, and automation form a framework that we will use during the next five years to develop a system that can begin with reduced X-ray diffraction data from any experimental source (anomalous diffraction, isomorphous replacement, molecular replacement), automatically solve and complete the structure, generate a model or set of models most consistent with the data, and prepare the models and data for deposition. Ultimately we plan to produce minimally biased atomic coordinates with little or no human intervention. The impact of our system will extend beyond the realm of structural genomics, allowing all crystallographers to solve challenging biological problems.
| Richardson, Jane S; Williams, Christopher J; Hintze, Bradley J et al. (2018) Model validation: local diagnosis, correction and when to quit. Acta Crystallogr D Struct Biol 74:132-142 |
| Herzik Jr, Mark A; Fraser, James S; Lander, Gabriel C (2018) A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Structure : |
| Kryshtafovych, Andriy; Monastyrskyy, Bohdan; Adams, Paul D et al. (2018) Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. Data Brief 20:1629-1638 |
| Moriarty, Nigel W; Liebschner, Dorothee; Klei, Herbert E et al. (2018) Interactive comparison and remediation of collections of macromolecular structures. Protein Sci 27:182-194 |
| Kryshtafovych, Andriy; Adams, Paul D; Lawson, Catherine L et al. (2018) Evaluation system and web infrastructure for the second cryo-EM model challenge. J Struct Biol 204:96-108 |
| Terwilliger, Thomas C; Adams, Paul D; Afonine, Pavel V et al. (2018) Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J Struct Biol 204:338-343 |
| Williams, Christopher J; Headd, Jeffrey J; Moriarty, Nigel W et al. (2018) MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci 27:293-315 |
| Terwilliger, Thomas C; Adams, Paul D; Afonine, Pavel V et al. (2018) A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nat Methods 15:905-908 |
| Richardson, Jane S; Williams, Christopher J; Videau, Lizbeth L et al. (2018) Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale. J Struct Biol 204:301-312 |
| Hintze, Bradley J; Richardson, Jane S; Richardson, David C (2017) Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol 73:852-859 |
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