Publications

List of Phenix references.

Detection of translational noncrystallographic symmetry in patterson functions. I. Caballero, M. D. Sammito, P. V. Afonine, I. Usón, R. J. Read, A. J. McCoy. Acta Crystallogr D Struct Biol 77, 131–141 (2021). doi:10.1107/S2059798320016836.

Improving SARS-CoV-2 structures: peer review by early coordinate release. T. I. Croll, C. J. Williams, V. B. Chen, D. C. Richardson, J. S. Richardson. Biophys J 120, 1085–1096 (2021). doi:10.1016/j.bpj.2020.12.029.

Phasertng: directed acyclic graphs for crystallographic phasing. A. J. McCoy, D. H. Stockwell, M. D. Sammito, R. D. Oeffner, K. S. Hatti, T. I. Croll, R. J. Read. Acta Crystallogr D Struct Biol 77, 1–10 (2021). doi:10.1107/S2059798320014746.

Accurate prediction of protein structures and interactions using a three-track neural network. M. Baek, F. DiMaio, I. Anishchenko, J. Dauparas, S. Ovchinnikov, G. R. Lee, J. Wang, Q. Cong, L. N. Kinch, R. D. Schaeffer, C. Millán, H. Park, C. Adams, C. R. Glassman, A. DeGiovanni, J. H. Pereira, A. V. Rodrigues, A. A. van Dijk, A. C. Ebrecht, D. J. Opperman, T. Sagmeister, C. Buhlheller, T. Pavkov-Keller, M. K. Rathinaswamy, U. Dalwadi, C. K. Yip, J. E. Burke, K. C. Garcia, N. V. Grishin, P. D. Adams, R. J. Read, D. Baker. Science (2021). doi:10.1126/science.abj8754.

Macromolecular refinement of x-ray and cryoelectron microscopy structures with phenix/OPLS3e for improved structure and ligand quality. G. C. P. van Zundert, N. W. Moriarty, O. V. Sobolev, P. D. Adams, K. W. Borrelli. Structure (2021). doi:10.1016/j.str.2021.03.011.

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. C. L. Lawson, A. Kryshtafovych, P. D. Adams, P. V. Afonine, M. L. Baker, B. A. Barad, P. Bond, T. Burnley, R. Cao, J. Cheng, G. Chojnowski, K. Cowtan, K. A. Dill, F. DiMaio, D. P. Farrell, J. S. Fraser, M. A. Herzik, S. W. Hoh, J. Hou, L.-W. Hung, M. Igaev, A. P. Joseph, D. Kihara, D. Kumar, S. Mittal, B. Monastyrskyy, M. Olek, C. M. Palmer, A. Patwardhan, A. Perez, J. Pfab, G. D. Pintilie, J. S. Richardson, P. B. Rosenthal, D. Sarkar, L. U. Schäfer, M. F. Schmid, G. F. Schröder, M. Shekhar, D. Si, A. Singharoy, G. Terashi, T. C. Terwilliger, A. Vaiana, L. Wang, Z. Wang, S. A. Wankowicz, C. J. Williams, M. Winn, T. Wu, X. Yu, K. Zhang, H. M. Berman, W. Chiu. Nat Methods 18, 156–164 (2021). doi:10.1038/s41592-020-01051-w.

CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. D. Liebschner, P. V. Afonine, N. W. Moriarty, B. K. Poon, V. B. Chen, P. D. Adams. Acta Crystallogr D Struct Biol 77, 48–61 (2021). doi:10.1107/S2059798320015879.

Making the invisible enemy visible. T. Croll, K. Diederichs, F. Fischer, C. Fyfe, Y. Gao, S. Horrell, A. P. Joseph, L. Kandler, O. Kippes, F. Kirsten, K. Müller, K. Nolte, A. Payne, M. G. Reeves, J. Richardson, G. Santoni, S. Stäb, D. Tronrud, L. von Soosten, C. Williams, A. Thorn. BioRxiv (2020). doi:10.1101/2020.10.07.307546.

Improved chemistry restraints for crystallographic refinement by integrating the amber force field into phenix. N. W. Moriarty, P. A. Janowski, J. M. Swails, H. Nguyen, J. S. Richardson, D. A. Case, P. D. Adams. Acta Crystallogr D Struct Biol 76, 51–62 (2020). doi:10.1107/S2059798319015134.

A global ramachandran score identifies protein structures with unlikely stereochemistry. O. V. Sobolev, P. V. Afonine, N. W. Moriarty, M. L. Hekkelman, R. P. Joosten, A. Perrakis, P. D. Adams. Structure 28, 1249–1258.e2 (2020). doi:10.1016/j.str.2020.08.005.

A new way to see rnas. J. S. Richardson. Nat Methods 17, 663–664 (2020). doi:10.1038/s41592-020-0888-7.

Implementation of the riding hydrogen model in CCTBX to support the next generation of x-ray and neutron joint refinement in phenix. D. Liebschner, P. V. Afonine, A. G. Urzhumtsev, P. D. Adams. Meth Enzymol 634, 177–199 (2020). doi:10.1016/bs.mie.2020.01.007.

Cryo-EM map interpretation and protein model-building using iterative map segmentation. T. C. Terwilliger, P. D. Adams, P. V. Afonine, O. V. Sobolev. Protein Sci 29, 87–99 (2020). doi:10.1002/pro.3740.

What are the current limits on determination of protonation state using neutron macromolecular crystallography? D. Liebschner, P. V. Afonine, N. W. Moriarty, P. D. Adams. Meth Enzymol 634, 225–255 (2020). doi:10.1016/bs.mie.2020.01.008.

Measuring and using information gained by observing diffraction data. R. J. Read, R. D. Oeffner, A. J. McCoy. Acta Crystallogr D Struct Biol 76, 238–247 (2020). doi:10.1107/S2059798320001588.

Untangling the sequence of events during the s2 → s3 transition in photosystem II and implications for the water oxidation mechanism. M. Ibrahim, T. Fransson, R. Chatterjee, M. H. Cheah, R. Hussein, L. Lassalle, K. D. Sutherlin, I. D. Young, F. D. Fuller, S. Gul, I.-S. Kim, P. S. Simon, C. de Lichtenberg, P. Chernev, I. Bogacz, C. C. Pham, A. M. Orville, N. Saichek, T. Northen, A. Batyuk, S. Carbajo, R. Alonso-Mori, K. Tono, S. Owada, A. Bhowmick, R. Bolotovsky, D. Mendez, N. W. Moriarty, J. M. Holton, H. Dobbek, A. S. Brewster, P. D. Adams, N. K. Sauter, U. Bergmann, A. Zouni, J. Messinger, J. Kern, V. K. Yachandra, J. Yano. Proc Natl Acad Sci USA 117, 12624–12635 (2020). doi:10.1073/pnas.2000529117.

Improvement of cryo-EM maps by density modification. T. C. Terwilliger, S. J. Ludtke, R. J. Read, P. D. Adams, P. V. Afonine. Nat Methods 17, 923–927 (2020). doi:10.1038/s41592-020-0914-9.

Density modification of cryo-EM maps. T. C. Terwilliger, O. V. Sobolev, P. V. Afonine, P. D. Adams, R. J. Read. Acta Crystallogr D Struct Biol 76, 912–925 (2020). doi:10.1107/{S205979832001061X}.

Arginine off-kilter: guanidinium is not as planar as restraints denote. N. W. Moriarty, D. Liebschner, D. E. Tronrud, P. D. Adams. Acta Crystallogr D Struct Biol 76, 1159–1166 (2020). doi:10.1107/S2059798320013534.

Macromolecular structure determination using x-rays, neutrons and electrons: recent developments in phenix. D. Liebschner, P. V. Afonine, M. L. Baker, G. Bunkóczi, V. B. Chen, T. I. Croll, B. Hintze, L. W. Hung, S. Jain, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, B. K. Poon, M. G. Prisant, R. J. Read, J. S. Richardson, D. C. Richardson, M. D. Sammito, O. V. Sobolev, D. H. Stockwell, T. C. Terwilliger, A. G. Urzhumtsev, L. L. Videau, C. J. Williams, P. D. Adams. Acta Crystallogr D Struct Biol 75, 861–877 (2019). doi:10.1107/S2059798319011471.

A multi-model approach to assessing local and global cryo-EM map quality. M. A. Herzik, J. S. Fraser, G. C. Lander. Structure 27, 344–358.e3 (2019). doi:10.1016/j.str.2018.10.003.

Federating structural models and data: outcomes from a workshop on archiving integrative structures. H. M. Berman, P. D. Adams, A. A. Bonvin, S. K. Burley, B. Carragher, W. Chiu, F. DiMaio, T. E. Ferrin, M. J. Gabanyi, T. D. Goddard, P. R. Griffin, J. Haas, C. A. Hanke, J. C. Hoch, G. Hummer, G. Kurisu, C. L. Lawson, A. Leitner, J. L. Markley, J. Meiler, G. T. Montelione, G. N. Phillips, T. Prisner, J. Rappsilber, D. C. Schriemer, T. Schwede, C. A. M. Seidel, T. S. Strutzenberg, D. I. Svergun, E. Tajkhorshid, J. Trewhella, B. Vallat, S. Velankar, G. W. Vuister, B. Webb, J. D. Westbrook, K. L. White, A. Sali. Structure 27, 1745–1759 (2019). doi:10.1016/j.str.2019.11.002.

Iron-sulfur clusters have no right angles. N. W. Moriarty and P. D. Adams. Acta Crystallogr D Struct Biol 75, 16–20 (2019). doi:10.1107/{S205979831801519X}.

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the protein data bank (PDB). P. D. Adams, P. V. Afonine, K. Baskaran, H. M. Berman, J. Berrisford, G. Bricogne, D. G. Brown, S. K. Burley, M. Chen, Z. Feng, C. Flensburg, A. Gutmanas, J. C. Hoch, Y. Ikegawa, Y. Kengaku, E. Krissinel, G. Kurisu, Y. Liang, D. Liebschner, L. Mak, J. L. Markley, N. W. Moriarty, G. N. Murshudov, M. Noble, E. Peisach, I. Persikova, B. K. Poon, O. V. Sobolev, E. L. Ulrich, S. Velankar, C. Vonrhein, J. Westbrook, M. Wojdyr, M. Yokochi, J. Y. Young. Acta Crystallogr D Struct Biol 75, 451–454 (2019). doi:10.1107/S2059798319004522.

Cryo_fit: democratization of flexible fitting for cryo-EM. D. N. Kim, N. W. Moriarty, S. Kirmizialtin, P. V. Afonine, B. Poon, O. V. Sobolev, P. D. Adams, K. Sanbonmatsu. J Struct Biol 208, 1–6 (2019). doi:10.1016/j.jsb.2019.05.012.

Evaluation system and web infrastructure for the second cryo-EM model challenge. A. Kryshtafovych, P. D. Adams, C. L. Lawson, W. Chiu. J Struct Biol 204, 96–108 (2018). doi:10.1016/j.jsb.2018.07.006.

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. S. Richardson, C. J. Williams, L. L. Videau, V. B. Chen, D. C. Richardson. J Struct Biol 204, 301–312 (2018). doi:10.1016/j.jsb.2018.08.007.

Real-space refinement in PHENIX for cryo-EM and crystallography. P. V. Afonine, B. K. Poon, R. J. Read, O. V. Sobolev, T. C. Terwilliger, A. Urzhumtsev, P. D. Adams. Acta Crystallogr D Struct Biol 74, 531–544 (2018). doi:10.1107/S2059798318006551.

Structures of the intermediates of kok's photosynthetic water oxidation clock. J. Kern, R. Chatterjee, I. D. Young, F. D. Fuller, L. Lassalle, M. Ibrahim, S. Gul, T. Fransson, A. S. Brewster, R. Alonso-Mori, R. Hussein, M. Zhang, L. Douthit, C. de Lichtenberg, M. H. Cheah, D. Shevela, J. Wersig, I. Seuffert, D. Sokaras, E. Pastor, C. Weninger, T. Kroll, R. G. Sierra, P. Aller, A. Butryn, A. M. Orville, M. Liang, A. Batyuk, J. E. Koglin, S. Carbajo, S. Boutet, N. W. Moriarty, J. M. Holton, H. Dobbek, P. D. Adams, U. Bergmann, N. K. Sauter, A. Zouni, J. Messinger, J. Yano, V. K. Yachandra. Nature 563, 421–425 (2018). doi:10.1038/s41586-018-0681-2.

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination. C. Millán, M. D. Sammito, A. J. McCoy, A. F. Z. Nascimento, G. Petrillo, R. D. Oeffner, T. Domínguez-Gil, J. A. Hermoso, R. J. Read, I. Usón. Acta Crystallogr D Struct Biol 74, 290–304 (2018). doi:10.1107/S2059798318001365.

Evaluation of models determined by neutron diffraction and proposed improvements to their validation and deposition. D. Liebschner, P. V. Afonine, N. W. Moriarty, P. Langan, P. D. Adams. Acta Crystallogr D Struct Biol 74, 800–813 (2018). doi:10.1107/S2059798318004588.

Interactive comparison and remediation of collections of macromolecular structures. N. W. Moriarty, D. Liebschner, H. E. Klei, N. Echols, P. V. Afonine, J. J. Headd, B. K. Poon, P. D. Adams. Protein Sci 27, 182–194 (2018). doi:10.1002/pro.3296.

On the application of the expected log-likelihood gain to decision making in molecular replacement. R. D. Oeffner, P. V. Afonine, C. Millán, M. Sammito, I. Usón, R. J. Read, A. J. McCoy. Acta Crystallogr D Struct Biol 74, 245–255 (2018). doi:10.1107/S2059798318004357.

Automated map sharpening by maximization of detail and connectivity. T. C. Terwilliger, O. V. Sobolev, P. V. Afonine, P. D. Adams. Acta Crystallogr D Struct Biol 74, 545–559 (2018). doi:10.1107/S2059798318004655.

From deep TLS validation to ensembles of atomic models built from elemental motions. II. analysis of TLS refinement results by explicit interpretation. P. V. Afonine, P. D. Adams, A. Urzhumtsev. Acta Crystallogr D Struct Biol 74, 621–631 (2018). doi:10.1107/S2059798318005764.

Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. A. Kryshtafovych, B. Monastyrskyy, P. D. Adams, C. L. Lawson, W. Chiu. Data Brief 20, 1629–1638 (2018). doi:10.1016/j.dib.2018.08.214.

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. W. Wang, C. Walmacq, J. Chong, M. Kashlev, D. Wang. Proc Natl Acad Sci USA 115, E2538–E2545 (2018). doi:10.1073/pnas.1722050115.

Gyre and gimble: a maximum-likelihood replacement for patterson correlation refinement. A. J. McCoy, R. D. Oeffner, C. Millán, M. Sammito, I. Usón, R. J. Read. Acta Crystallogr D Struct Biol 74, 279–289 (2018). doi:10.1107/S2059798318001353.

MolProbity: more and better reference data for improved all-atom structure validation. C. J. Williams, J. J. Headd, N. W. Moriarty, M. G. Prisant, L. L. Videau, L. N. Deis, V. Verma, D. A. Keedy, B. J. Hintze, V. B. Chen, S. Jain, S. M. Lewis, W. B. Arendall, J. Snoeyink, P. D. Adams, S. C. Lovell, J. S. Richardson, D. C. Richardson. Protein Sci 27, 293–315 (2018). doi:10.1002/pro.3330.

New tools for the analysis and validation of cryo-EM maps and atomic models. P. V. Afonine, B. P. Klaholz, N. W. Moriarty, B. K. Poon, O. V. Sobolev, T. C. Terwilliger, P. D. Adams, A. Urzhumtsev. Acta Crystallogr D Struct Biol 74, 814–840 (2018). doi:10.1107/S2059798318009324.

Model validation: local diagnosis, correction and when to quit. J. S. Richardson, C. J. Williams, B. J. Hintze, V. B. Chen, M. G. Prisant, L. L. Videau, D. C. Richardson. Acta Crystallogr D Struct Biol 74, 132–142 (2018). doi:10.1107/S2059798317009834.

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. T. C. Terwilliger, P. D. Adams, P. V. Afonine, O. V. Sobolev. Nat Methods 15, 905–908 (2018). doi:10.1038/s41592-018-0173-1.

Map segmentation, automated model-building and their application to the cryo-EM model challenge. T. C. Terwilliger, P. D. Adams, P. V. Afonine, O. V. Sobolev. J Struct Biol 204, 338–343 (2018). doi:10.1016/j.jsb.2018.07.016.

Solving the scalability issue in quantum-based refinement: Q\textbarR \#1. M. Zheng, N. W. Moriarty, Y. Xu, J. R. Reimers, P. V. Afonine, M. P. Waller. Acta Crystallogr D Struct Biol 73, 1020–1028 (2017). doi:10.1107/S2059798317016746.

Insights into hunter syndrome from the structure of iduronate-2-sulfatase. M. Demydchuk, C. H. Hill, A. Zhou, G. Bunkóczi, P. E. Stein, D. Marchesan, J. E. Deane, R. J. Read. Nat Commun 8, 15786 (2017). doi:10.1038/ncomms15786.

Broad analysis of vicinal disulfides: occurrences, conformations with cis or with trans peptides, and functional roles including sugar binding. J. S. Richardson, L. L. Videau, C. J. Williams, D. C. Richardson. J Mol Biol 429, 1321–1335 (2017). doi:10.1016/j.jmb.2017.03.017.

Polder maps: improving OMIT maps by excluding bulk solvent. D. Liebschner, P. V. Afonine, N. W. Moriarty, B. K. Poon, O. V. Sobolev, T. C. Terwilliger, P. D. Adams. Acta Crystallogr D Struct Biol 73, 148–157 (2017). doi:10.1107/S2059798316018210.

The cryo-electron microscopy structure of human transcription factor IIH. B. J. Greber, T. H. D. Nguyen, J. Fang, P. V. Afonine, P. D. Adams, E. Nogales. Nature 549, 414–417 (2017). doi:10.1038/nature23903.

Accurate model annotation of a near-atomic resolution cryo-EM map. C. F. Hryc, D.-H. Chen, P. V. Afonine, J. Jakana, Z. Wang, C. Haase-Pettingell, W. Jiang, P. D. Adams, J. A. King, M. F. Schmid, W. Chiu. Proc Natl Acad Sci USA 114, 3103–3108 (2017). doi:10.1073/pnas.1621152114.

An editor for the generation and customization of geometry restraints. N. W. Moriarty, E. J. Draizen, P. D. Adams. Acta Crystallogr D Struct Biol 73, 123–130 (2017). doi:10.1107/S2059798316016570.

Q\textbarR : quantum-based refinement. M. Zheng, J. R. Reimers, M. P. Waller, P. V. Afonine. Acta Crystallogr D Struct Biol 73, 45–52 (2017). doi:10.1107/S2059798316019847.

Mismodeled purines: implicit alternates and hidden hoogsteens. B. J. Hintze, J. S. Richardson, D. C. Richardson. Acta Crystallogr D Struct Biol 73, 852–859 (2017). doi:10.1107/S2059798317013729.

Ab initio solution of macromolecular crystal structures without direct methods. A. J. McCoy, R. D. Oeffner, A. G. Wrobel, J. R. M. Ojala, K. Tryggvason, B. Lohkamp, R. J. Read. Proc Natl Acad Sci USA 114, 3637–3641 (2017). doi:10.1073/pnas.1701640114.

Improved ligand geometries in crystallographic refinement using AFITT in PHENIX. P. A. Janowski, N. W. Moriarty, B. P. Kelley, D. A. Case, D. M. York, P. D. Adams, G. L. Warren. Acta Crystallogr D Struct Biol 72, 1062–1072 (2016). doi:10.1107/S2059798316012225.

Structure of photosystem II and substrate binding at room temperature. I. D. Young, M. Ibrahim, R. Chatterjee, S. Gul, F. Fuller, S. Koroidov, A. S. Brewster, R. Tran, R. Alonso-Mori, T. Kroll, T. Michels-Clark, H. Laksmono, R. G. Sierra, C. A. Stan, R. Hussein, M. Zhang, L. Douthit, M. Kubin, C. de Lichtenberg, P. Long Vo, H\aakan Nilsson, M. H. Cheah, D. Shevela, C. Saracini, M. A. Bean, I. Seuffert, D. Sokaras, T.-C. Weng, E. Pastor, C. Weninger, T. Fransson, L. Lassalle, P. Bräuer, P. Aller, P. T. Docker, B. Andi, A. M. Orville, J. M. Glownia, S. Nelson, M. Sikorski, D. Zhu, M. S. Hunter, T. J. Lane, A. Aquila, J. E. Koglin, J. Robinson, M. Liang, S. Boutet, A. Y. Lyubimov, M. Uervirojnangkoorn, N. W. Moriarty, D. Liebschner, P. V. Afonine, D. G. Waterman, G. Evans, P. Wernet, H. Dobbek, W. I. Weis, A. T. Brunger, P. H. Zwart, P. D. Adams, A. Zouni, J. Messinger, U. Bergmann, N. K. Sauter, J. Kern, V. K. Yachandra, J. Yano. Nature 540, 453–457 (2016). doi:10.1038/nature20161.

Efficient merging of data from multiple samples for determination of anomalous substructure. D. L. Akey, T. C. Terwilliger, J. L. Smith. Acta Crystallogr D Struct Biol 72, 296–302 (2016). doi:10.1107/S2059798315021920.

Can i solve my structure by SAD phasing? anomalous signal in SAD phasing. T. C. Terwilliger, G. Bunkóczi, L. W. Hung, P. H. Zwart, J. L. Smith, D. L. Akey, P. D. Adams. Acta Crystallogr D Struct Biol 72, 346–358 (2016). doi:10.1107/S2059798315019269.

RNA structure refinement using the ERRASER-phenix pipeline. F.-C. Chou, N. Echols, T. C. Terwilliger, R. Das. Methods Mol Biol 1320, 269–282 (2016). doi:10.1007/978-1-4939-2763-0\_17.

From deep TLS validation to ensembles of atomic models built from elemental motions. addenda and corrigendum. A. Urzhumtsev, P. V. Afonine, A. H. Van Benschoten, J. S. Fraser, P. D. Adams. Acta Crystallogr D Struct Biol 72, 1073–1075 (2016). doi:10.1107/S2059798316013048.

Molprobity's ultimate rotamer-library distributions for model validation. B. J. Hintze, S. M. Lewis, J. S. Richardson, D. C. Richardson. Proteins 84, 1177–1189 (2016). doi:10.1002/prot.25039.

Can i solve my structure by SAD phasing? planning an experiment, scaling data and evaluating the useful anomalous correlation and anomalous signal. T. C. Terwilliger, G. Bunkóczi, L. W. Hung, P. H. Zwart, J. L. Smith, D. L. Akey, P. D. Adams. Acta Crystallogr D Struct Biol 72, 359–374 (2016). doi:10.1107/S2059798315019403.

Outcome of the first wwPDB/CCDC/D3R ligand validation workshop. P. D. Adams, K. Aertgeerts, C. Bauer, J. A. Bell, H. M. Berman, T. N. Bhat, J. M. Blaney, E. Bolton, G. Bricogne, D. Brown, S. K. Burley, D. A. Case, K. L. Clark, T. Darden, P. Emsley, V. A. Feher, Z. Feng, C. R. Groom, S. F. Harris, J. Hendle, T. Holder, A. Joachimiak, G. J. Kleywegt, T. Krojer, J. Marcotrigiano, A. E. Mark, J. L. Markley, M. Miller, W. Minor, G. T. Montelione, G. Murshudov, A. Nakagawa, H. Nakamura, A. Nicholls, M. Nicklaus, R. T. Nolte, A. K. Padyana, C. E. Peishoff, S. Pieniazek, R. J. Read, C. Shao, S. Sheriff, O. Smart, S. Soisson, J. Spurlino, T. Stouch, R. Svobodova, W. Tempel, T. C. Terwilliger, D. Tronrud, S. Velankar, S. C. Ward, G. L. Warren, J. D. Westbrook, P. Williams, H. Yang, J. Young. Structure 24, 502–508 (2016). doi:10.1016/j.str.2016.02.017.

A new default restraint library for the protein backbone in phenix: a conformation-dependent geometry goes mainstream. N. W. Moriarty, D. E. Tronrud, P. D. Adams, P. A. Karplus. Acta Crystallogr D Struct Biol 72, 176–179 (2016). doi:10.1107/S2059798315022408.

The solvent component of macromolecular crystals. C. X. Weichenberger, P. V. Afonine, K. Kantardjieff, B. Rupp. Acta Crystallogr D Biol Crystallogr 71, 1023–1038 (2015). doi:10.1107/S1399004715006045.

Macromolecular crystallographic estructure refinement. P. V. Afonine, A. Urzhumtsev, P. D. Adams. Arbor 191, a219 (2015). doi:10.3989/arbor.2015.772n2005.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures. N. Morshed, N. Echols, P. D. Adams. Acta Crystallogr D Biol Crystallogr 71, 1147–1158 (2015). doi:10.1107/S1399004715004241.

FEM: feature-enhanced map. P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C. Terwilliger, D. Turk, A. Urzhumtsev, P. D. Adams. Acta Crystallogr D Biol Crystallogr 71, 646–666 (2015). doi:10.1107/S1399004714028132.

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns. A. S. Brewster, M. R. Sawaya, J. Rodriguez, J. Hattne, N. Echols, H. T. McFarlane, D. Cascio, P. D. Adams, D. S. Eisenberg, N. K. Sauter. Acta Crystallogr D Biol Crystallogr 71, 357–366 (2015). doi:10.1107/S1399004714026145.

EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. B. A. Barad, N. Echols, R. Y.-R. Wang, Y. Cheng, F. DiMaio, P. D. Adams, J. S. Fraser. Nat Methods 12, 943–946 (2015). doi:10.1038/nmeth.3541.

Programming new geometry restraints: parallelity of atomic groups. O. V. Sobolev, P. V. Afonine, P. D. Adams, A. Urzhumtsev. J Appl Crystallogr 48, 1130–1141 (2015). doi:10.1107/S1600576715010432.

Local error estimates dramatically improve the utility of homology models for solving crystal structures by molecular replacement. G. Bunkóczi, B. Wallner, R. J. Read. Structure 23, 397–406 (2015). doi:10.1016/j.str.2014.11.020.

Macromolecular x-ray structure determination using weak, single-wavelength anomalous data. G. Bunkóczi, A. J. McCoy, N. Echols, R. W. Grosse-Kunstleve, P. D. Adams, J. M. Holton, R. J. Read, T. C. Terwilliger. Nat Methods 12, 127–130 (2015). doi:10.1038/nmeth.3212.

From deep TLS validation to ensembles of atomic models built from elemental motions. A. Urzhumtsev, P. V. Afonine, A. H. Van Benschoten, J. S. Fraser, P. D. Adams. Acta Crystallogr D Biol Crystallogr 71, 1668–1683 (2015). doi:10.1107/S1399004715011426.

X-ray structure determination using low-resolution electron microscopy maps for molecular replacement. R. N. Jackson, A. J. McCoy, T. C. Terwilliger, R. J. Read, B. Wiedenheft. Nat Protoc 10, 1275–1284 (2015). doi:10.1038/nprot.2015.069.

Protein crystallography from the perspective of technology developments. X.-D. Su, H. Zhang, T. C. Terwilliger, A. Liljas, J. Xiao, Y. Dong. Crystallogr Rev 21, 122–153 (2015). doi:10.1080/{0889311X}.2014.973868.

New insights into hoogsteen base pairs in DNA duplexes from a structure-based survey. H. Zhou, B. J. Hintze, I. J. Kimsey, B. Sathyamoorthy, S. Yang, J. S. Richardson, H. M. Al-Hashimi. Nucleic Acids Res 43, 3420–3433 (2015). doi:10.1093/nar/gkv241.

NMR exchange format: a unified and open standard for representation of NMR restraint data. A. Gutmanas, P. D. Adams, B. Bardiaux, H. M. Berman, D. A. Case, R. H. Fogh, P. Güntert, P. M. S. Hendrickx, T. Herrmann, G. J. Kleywegt, N. Kobayashi, O. F. Lange, J. L. Markley, G. T. Montelione, M. Nilges, T. J. Ragan, C. D. Schwieters, R. Tejero, E. L. Ulrich, S. Velankar, W. F. Vranken, J. R. Wedell, J. Westbrook, D. S. Wishart, G. W. Vuister. Nat Struct Mol Biol 22, 433–434 (2015). doi:10.1038/nsmb.3041.

Structure and membrane remodeling activity of ESCRT-III helical polymers. J. McCullough, A. K. Clippinger, N. Talledge, M. L. Skowyra, M. G. Saunders, T. V. Naismith, L. A. Colf, P. Afonine, C. Arthur, W. I. Sundquist, P. I. Hanson, A. Frost. Science 350, 1548–1551 (2015). doi:10.1126/science.aad8305.

Computational methods for RNA structure validation and improvement. S. Jain, D. C. Richardson, J. S. Richardson. Meth Enzymol 558, 181–212 (2015). doi:10.1016/bs.mie.2015.01.007.

Outcome of the first wwPDB hybrid/integrative methods task force workshop. A. Sali, H. M. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S. K. Burley, J. Markley, H. Nakamura, P. Adams, A. M. J. J. Bonvin, W. Chiu, M. D. Peraro, F. Di Maio, T. E. Ferrin, K. Grünewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. L. Lawson, J. Meiler, M. A. Marti-Renom, G. T. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. J. Read, H. Saibil, G. F. Schröder, C. D. Schwieters, C. A. M. Seidel, D. Svergun, M. Topf, E. L. Ulrich, S. Velankar, J. D. Westbrook. Structure 23, 1156–1167 (2015). doi:10.1016/j.str.2015.05.013.

Predicting x-ray diffuse scattering from translation-libration-screw structural ensembles. A. H. Van Benschoten, P. V. Afonine, T. C. Terwilliger, M. E. Wall, C. J. Jackson, N. K. Sauter, P. D. Adams, A. Urzhumtsev, J. S. Fraser. Acta Crystallogr D Biol Crystallogr 71, 1657–1667 (2015). doi:10.1107/S1399004715007415.

An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Z. Wang, C. F. Hryc, B. Bammes, P. V. Afonine, J. Jakana, D.-H. Chen, X. Liu, M. L. Baker, C. Kao, S. J. Ludtke, M. F. Schmid, P. D. Adams, W. Chiu. Nat Commun 5, 4808 (2014). doi:10.1038/ncomms5808.

Diffuse x-ray scattering to model protein motions. M. E. Wall, P. D. Adams, J. S. Fraser, N. K. Sauter. Structure 22, 182–184 (2014). doi:10.1016/j.str.2014.01.002.

New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. G. J. Kapral, S. Jain, J. Noeske, J. A. Doudna, D. C. Richardson, J. S. Richardson. Nucleic Acids Res 42, 12833–12846 (2014). doi:10.1093/nar/gku992.

Taking snapshots of photosynthetic water oxidation using femtosecond x-ray diffraction and spectroscopy. J. Kern, R. Tran, R. Alonso-Mori, S. Koroidov, N. Echols, J. Hattne, M. Ibrahim, S. Gul, H. Laksmono, R. G. Sierra, R. J. Gildea, G. Han, J. Hellmich, B. Lassalle-Kaiser, R. Chatterjee, A. S. Brewster, C. A. Stan, C. Glöckner, A. Lampe, D. DiFiore, D. Milathianaki, A. R. Fry, M. M. Seibert, J. E. Koglin, E. Gallo, J. Uhlig, D. Sokaras, T.-C. Weng, P. H. Zwart, D. E. Skinner, M. J. Bogan, M. Messerschmidt, P. Glatzel, G. J. Williams, S. Boutet, P. D. Adams, A. Zouni, J. Messinger, N. K. Sauter, U. Bergmann, J. Yano, V. K. Yachandra. Nat Commun 5, 4371 (2014). doi:10.1038/ncomms5371.

Accurate macromolecular structures using minimal measurements from x-ray free-electron lasers. J. Hattne, N. Echols, R. Tran, J. Kern, R. J. Gildea, A. S. Brewster, R. Alonso-Mori, C. Glöckner, J. Hellmich, H. Laksmono, R. G. Sierra, B. Lassalle-Kaiser, A. Lampe, G. Han, S. Gul, D. DiFiore, D. Milathianaki, A. R. Fry, A. Miahnahri, W. E. White, D. W. Schafer, M. M. Seibert, J. E. Koglin, D. Sokaras, T.-C. Weng, J. Sellberg, M. J. Latimer, P. Glatzel, P. H. Zwart, R. W. Grosse-Kunstleve, M. J. Bogan, M. Messerschmidt, G. J. Williams, S. Boutet, J. Messinger, A. Zouni, J. Yano, U. Bergmann, V. K. Yachandra, P. D. Adams, N. K. Sauter. Nat Methods 11, 545–548 (2014). doi:10.1038/nmeth.2887.

Metrics for comparison of crystallographic maps. A. Urzhumtsev, P. V. Afonine, V. Y. Lunin, T. C. Terwilliger, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 2593–2606 (2014). doi:10.1107/S1399004714016289.

Dxtbx: the diffraction experiment toolbox. J. M. Parkhurst, A. S. Brewster, L. Fuentes-Montero, D. G. Waterman, J. Hattne, A. W. Ashton, N. Echols, G. Evans, N. K. Sauter, G. Winter. J Appl Crystallogr 47, 1459–1465 (2014). doi:10.1107/S1600576714011996.

Archiving raw crystallographic data. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 70, 2500–2501 (2014). doi:10.1107/{S139900471402118X}.

Continuous mutual improvement of macromolecular structure models in the PDB and of x-ray crystallographic software: the dual role of deposited experimental data. T. C. Terwilliger and G. Bricogne. Acta Crystallogr D Biol Crystallogr 70, 2533–2543 (2014). doi:10.1107/S1399004714017040.

Improved crystal orientation and physical properties from single-shot XFEL stills. N. K. Sauter, J. Hattne, A. S. Brewster, N. Echols, P. H. Zwart, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 3299–3309 (2014). doi:10.1107/S1399004714024134.

Automated identification of elemental ions in macromolecular crystal structures. N. Echols, N. Morshed, P. V. Afonine, A. J. McCoy, M. D. Miller, R. J. Read, J. S. Richardson, T. C. Terwilliger, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 1104–1114 (2014). doi:10.1107/S1399004714001308.

Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse x-ray scattering. M. E. Wall, A. H. Van Benschoten, N. K. Sauter, P. D. Adams, J. S. Fraser, T. C. Terwilliger. Proc Natl Acad Sci USA 111, 17887–17892 (2014). doi:10.1073/pnas.1416744111.

Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. L. N. Deis, C. W. Pemble, Y. Qi, A. Hagarman, D. C. Richardson, J. S. Richardson, T. G. Oas. Structure 22, 1467–1477 (2014). doi:10.1016/j.str.2014.08.014.

Structural biology. crystal structure of the CRISPR RNA-guided surveillance complex from escherichia coli. R. N. Jackson, S. M. Golden, P. B. G. van Erp, J. Carter, E. R. Westra, S. J. J. Brouns, J. van der Oost, T. C. Terwilliger, R. J. Read, B. Wiedenheft. Science 345, 1473–1479 (2014). doi:10.1126/science.1256328.

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. J. J. Headd, N. Echols, P. V. Afonine, N. W. Moriarty, R. J. Gildea, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 1346–1356 (2014). doi:10.1107/S1399004714003277.

Biophysical highlights from 54 years of macromolecular crystallography. J. S. Richardson and D. C. Richardson. Biophys J 106, 510–525 (2014). doi:10.1016/j.bpj.2014.01.001.

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. N. W. Moriarty, D. E. Tronrud, P. D. Adams, P. A. Karplus. FEBS J 281, 4061–4071 (2014). doi:10.1111/febs.12860.

Ligand placement based on prior structures: the guided ligand-replacement method. H. E. Klei, N. W. Moriarty, N. Echols, T. C. Terwilliger, E. T. Baldwin, M. Pokross, S. Posy, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 134–143 (2014). doi:10.1107/S1399004713030071.

Automating crystallographic structure solution and refinement of protein-ligand complexes. N. Echols, N. W. Moriarty, H. E. Klei, P. V. Afonine, G. Bunkóczi, J. J. Headd, A. J. McCoy, R. D. Oeffner, R. J. Read, T. C. Terwilliger, P. D. Adams. Acta Crystallogr D Biol Crystallogr 70, 144–154 (2014). doi:10.1107/{S139900471302748X}.

The zen of model anomalies – correct most of them. treasure the meaningful valid few. live serenely with the rest! J. S. Richardson and D. C. Richardson. In R. Read, A. G. Urzhumtsev, V. Y. Lunin, editors, Advancing methods for biomolecular crystallography, NATO science for peace and security series A: chemistry and biology, pages 1–10. Springer Netherlands, Dordrecht (2013). doi:10.1007/978-94-007-6232-9\_1.

Advances, interactions, and future developments in the CNS, phenix, and rosetta structural biology software systems. P. D. Adams, D. Baker, A. T. Brunger, R. Das, F. DiMaio, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger. Annu Rev Biophys 42, 265–287 (2013). doi:10.1146/annurev-biophys-083012-130253.

Improved low-resolution crystallographic refinement with phenix and rosetta. F. DiMaio, N. Echols, J. J. Headd, T. C. Terwilliger, P. D. Adams, D. Baker. Nat Methods 10, 1102–1104 (2013). doi:10.1038/nmeth.2648.

Doing molecular biophysics: finding, naming, and picturing signal within complexity. J. S. Richardson and D. C. Richardson. Annu Rev Biophys 42, 1–28 (2013). doi:10.1146/annurev-biophys-083012-130353.

Improved crystallographic structures using extensive combinatorial refinement. J. C. Nwachukwu, M. R. Southern, J. R. Kiefer, P. V. Afonine, P. D. Adams, T. C. Terwilliger, K. W. Nettles. Structure 21, 1923–1930 (2013). doi:10.1016/j.str.2013.07.025.

Simultaneous femtosecond x-ray spectroscopy and diffraction of photosystem II at room temperature. J. Kern, R. Alonso-Mori, R. Tran, J. Hattne, R. J. Gildea, N. Echols, C. Glöckner, J. Hellmich, H. Laksmono, R. G. Sierra, B. Lassalle-Kaiser, S. Koroidov, A. Lampe, G. Han, S. Gul, D. Difiore, D. Milathianaki, A. R. Fry, A. Miahnahri, D. W. Schafer, M. Messerschmidt, M. M. Seibert, J. E. Koglin, D. Sokaras, T.-C. Weng, J. Sellberg, M. J. Latimer, R. W. Grosse-Kunstleve, P. H. Zwart, W. E. White, P. Glatzel, P. D. Adams, M. J. Bogan, G. J. Williams, S. Boutet, J. Messinger, A. Zouni, N. K. Sauter, V. K. Yachandra, U. Bergmann, J. Yano. Science 340, 491–495 (2013). doi:10.1126/science.1234273.

Improving experimental phases for strong reflections prior to density modification. M. Uervirojnangkoorn, R. Hilgenfeld, T. C. Terwilliger, R. J. Read. Acta Crystallogr D Biol Crystallogr 69, 2039–2049 (2013). doi:10.1107/S0907444913018167.

Intensity statistics in the presence of translational noncrystallographic symmetry. R. J. Read, P. D. Adams, A. J. McCoy. Acta Crystallogr D Biol Crystallogr 69, 176–183 (2013). doi:10.1107/S0907444912045374.

Bulk-solvent and overall scaling revisited: faster calculations, improved results. P. V. Afonine, R. W. Grosse-Kunstleve, P. D. Adams, A. Urzhumtsev. Acta Crystallogr D Biol Crystallogr 69, 625–634 (2013). doi:10.1107/S0907444913000462.

Phaser.MRage: automated molecular replacement. G. Bunkóczi, N. Echols, A. J. McCoy, R. D. Oeffner, P. D. Adams, R. J. Read. Acta Crystallogr D Biol Crystallogr 69, 2276–2286 (2013). doi:10.1107/S0907444913022750.

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. M. L. Baker, C. F. Hryc, Q. Zhang, W. Wu, J. Jakana, C. Haase-Pettingell, P. V. Afonine, P. D. Adams, J. A. King, W. Jiang, W. Chiu. Proc Natl Acad Sci USA 110, 12301–12306 (2013). doi:10.1073/pnas.1309947110.

Model morphing and sequence assignment after molecular replacement. T. C. Terwilliger, R. J. Read, P. D. Adams, A. T. Brunger, P. V. Afonine, L.-W. Hung. Acta Crystallogr D Biol Crystallogr 69, 2244–2250 (2013). doi:10.1107/S0907444913017770.

Crystal structure of bacillus subtilis GabR, an autorepressor and transcriptional activator of gabT. R. Edayathumangalam, R. Wu, R. Garcia, Y. Wang, W. Wang, C. A. Kreinbring, A. Bach, J. Liao, T. A. Stone, T. C. Terwilliger, Q. Q. Hoang, B. R. Belitsky, G. A. Petsko, D. Ringe, D. Liu. Proc Natl Acad Sci USA 110, 17820–17825 (2013). doi:10.1073/pnas.1315887110.

New python-based methods for data processing. N. K. Sauter, J. Hattne, R. W. Grosse-Kunstleve, N. Echols. Acta Crystallogr D Biol Crystallogr 69, 1274–1282 (2013). doi:10.1107/S0907444913000863.

Finding non-crystallographic symmetry in density maps of macromolecular structures. T. C. Terwilliger. J Struct Funct Genomics 14, 91–95 (2013). doi:10.1007/s10969-013-9157-7.

Crystallographic structure refinement in a nutshell. P. V. Afonine and P. D. Adams. In R. Read, A. G. Urzhumtsev, V. Y. Lunin, editors, Advancing methods for biomolecular crystallography, NATO science for peace and security series A: chemistry and biology, pages 211–219. Springer Netherlands, Dordrecht (2013). doi:10.1007/978-94-007-6232-9\_20.

Model-building and reduction of model bias in electron density maps. T. C. Terwilliger. In R. Read, A. G. Urzhumtsev, V. Y. Lunin, editors, Advancing methods for biomolecular crystallography, NATO science for peace and security series A: chemistry and biology, pages 193–203. Springer Netherlands, Dordrecht (2013). doi:10.1007/978-94-007-6232-9\_18.

Extending the reach of molecular replacement. R. J. Read, A. J. McCoy, R. D. Oeffner, G. Bunkóczi. In R. Read, A. G. Urzhumtsev, V. Y. Lunin, editors, Advancing methods for biomolecular crystallography, NATO science for peace and security series A: chemistry and biology, pages 113–122. Springer Netherlands, Dordrecht (2013). doi:10.1007/978-94-007-6232-9\_11.

TLS from fundamentals to practice. A. Urzhumtsev, P. V. Afonine, P. D. Adams. Crystallogr Rev 19, 230–270 (2013). doi:10.1080/{0889311X}.2013.835806.

Improved estimates of coordinate error for molecular replacement. R. D. Oeffner, G. Bunkóczi, A. J. McCoy, R. J. Read. Acta Crystallogr D Biol Crystallogr 69, 2209–2215 (2013). doi:10.1107/S0907444913023512.

Modelling dynamics in protein crystal structures by ensemble refinement. B. T. Burnley, P. V. Afonine, P. D. Adams, P. Gros. elife 1, e00311 (2012). doi:10.7554/{eLife}.00311.

MolProbity : all-atom structure validation for macromolecular crystallography. V. B. Chen, W. B. Arendall, J. J. Headd, D. A. Keedy, R. M. Immormino, G. J. Kapral, L. W. Murray, J. S. Richardson, D. C. Richardson. In E. Arnold, D. M. Himmel, M. G. Rossmann, C. P. Brock, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, E. Arnold, D. M. Himmel, M. G. Rossmann, S. Hall, B. McMahon, editors, International Tables for Crystallography: Crystallography of biological macromolecules, volume F of International tables for crystallography: international tables online, pages 694–701. International Union of Crystallography, Chester, England (2012). doi:10.1107/97809553602060000884.

Automatic fortran to c++ conversion with FABLE. R. W. Grosse-Kunstleve, T. C. Terwilliger, N. K. Sauter, P. D. Adams. Source Code Biol Med 7, 5 (2012). doi:10.1186/1751-0473-7-5.

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. J. J. Headd, N. Echols, P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, N. W. Moriarty, D. C. Richardson, J. S. Richardson, P. D. Adams. Acta Crystallogr D Biol Crystallogr 68, 381–390 (2012). doi:10.1107/S0907444911047834.

Room temperature femtosecond x-ray diffraction of photosystem II microcrystals. J. Kern, R. Alonso-Mori, J. Hellmich, R. Tran, J. Hattne, H. Laksmono, C. Glöckner, N. Echols, R. G. Sierra, J. Sellberg, B. Lassalle-Kaiser, R. J. Gildea, P. Glatzel, R. W. Grosse-Kunstleve, M. J. Latimer, T. A. McQueen, D. DiFiore, A. R. Fry, M. Messerschmidt, A. Miahnahri, D. W. Schafer, M. M. Seibert, D. Sokaras, T.-C. Weng, P. H. Zwart, W. E. White, P. D. Adams, M. J. Bogan, S. Boutet, G. J. Williams, J. Messinger, N. K. Sauter, A. Zouni, U. Bergmann, J. Yano, V. K. Yachandra. Proc Natl Acad Sci USA 109, 9721–9726 (2012). doi:10.1073/pnas.1204598109.

PHENIX : a comprehensive python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. H. Zwart. In E. Arnold, D. M. Himmel, M. G. Rossmann, C. P. Brock, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, E. Arnold, D. M. Himmel, M. G. Rossmann, S. Hall, B. McMahon, editors, International Tables for Crystallography: Crystallography of biological macromolecules, volume F of International tables for crystallography: international tables online, pages 539–547. International Union of Crystallography, Chester, England (2012). doi:10.1107/97809553602060000865.

Energy-dispersive x-ray emission spectroscopy using an x-ray free-electron laser in a shot-by-shot mode. R. Alonso-Mori, J. Kern, R. J. Gildea, D. Sokaras, T.-C. Weng, B. Lassalle-Kaiser, R. Tran, J. Hattne, H. Laksmono, J. Hellmich, C. Glöckner, N. Echols, R. G. Sierra, D. W. Schafer, J. Sellberg, C. Kenney, R. Herbst, J. Pines, P. Hart, S. Herrmann, R. W. Grosse-Kunstleve, M. J. Latimer, A. R. Fry, M. M. Messerschmidt, A. Miahnahri, M. M. Seibert, P. H. Zwart, W. E. White, P. D. Adams, M. J. Bogan, S. Boutet, G. J. Williams, A. Zouni, J. Messinger, P. Glatzel, N. K. Sauter, V. K. Yachandra, J. Yano, U. Bergmann. Proc Natl Acad Sci USA 109, 19103–19107 (2012). doi:10.1073/pnas.1211384109.

Research priorities. shining light into black boxes. A. Morin, J. Urban, P. D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz. Science 336, 159–160 (2012). doi:10.1126/science.1218263.

1.7 refinement of x-ray crystal structures. A.T. Brunger and P.D. Adams. In Comprehensive Biophysics, pages 105–115. Elsevier (2012). doi:10.1016/B978-0-12-374920-8.00108-9.

Phenix.mr_rosetta: molecular replacement and model rebuilding with phenix and rosetta. T. C. Terwilliger, F. Dimaio, R. J. Read, D. Baker, G. Bunkóczi, P. D. Adams, R. W. Grosse-Kunstleve, P. V. Afonine, N. Echols. J Struct Funct Genomics 13, 81–90 (2012). doi:10.1007/s10969-012-9129-3.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution. A. T. Brunger, P. D. Adams, P. Fromme, R. Fromme, M. Levitt, G. F. Schröder. Structure 20, 957–966 (2012). doi:10.1016/j.str.2012.04.020.

KiNG and kinemages. V. B. Chen, J. S. Richardson, D. C. Richardson. In E. Arnold, D. M. Himmel, M. G. Rossmann, C. P. Brock, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, E. Arnold, D. M. Himmel, M. G. Rossmann, S. Hall, B. McMahon, editors, International Tables for Crystallography: Crystallography of biological macromolecules, volume F of International tables for crystallography: international tables online, pages 688–693. International Union of Crystallography, Chester, England (2012). doi:10.1107/97809553602060000883.

Graphical tools for macromolecular crystallography in PHENIX. N. Echols, R. W. Grosse-Kunstleve, P. V. Afonine, G. Bunkóczi, V. B. Chen, J. J. Headd, A. J. McCoy, N. W. Moriarty, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. D. Adams. J Appl Crystallogr 45, 581–586 (2012). doi:10.1107/S0021889812017293.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from corynebacterium glutamicum. A. T. Brunger, D. Das, A. M. Deacon, J. Grant, T. C. Terwilliger, R. J. Read, P. D. Adams, M. Levitt, G. F. Schröder. Acta Crystallogr D Biol Crystallogr 68, 391–403 (2012). doi:10.1107/{S090744491104978X}.

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement. T. C. Terwilliger, R. J. Read, P. D. Adams, A. T. Brunger, P. V. Afonine, R. W. Grosse-Kunstleve, L.-W. Hung. Acta Crystallogr D Biol Crystallogr 68, 861–870 (2012). doi:10.1107/S0907444912015636.

Nanoflow electrospinning serial femtosecond crystallography. R. G. Sierra, H. Laksmono, J. Kern, R. Tran, J. Hattne, R. Alonso-Mori, B. Lassalle-Kaiser, C. Glöckner, J. Hellmich, D. W. Schafer, N. Echols, R. J. Gildea, R. W. Grosse-Kunstleve, J. Sellberg, T. A. McQueen, A. R. Fry, M. M. Messerschmidt, A. Miahnahri, M. M. Seibert, C. Y. Hampton, D. Starodub, N. D. Loh, D. Sokaras, T.-C. Weng, P. H. Zwart, P. Glatzel, D. Milathianaki, W. E. White, P. D. Adams, G. J. Williams, S. Boutet, A. Zouni, J. Messinger, N. K. Sauter, U. Bergmann, J. Yano, V. K. Yachandra, M. J. Bogan. Acta Crystallogr D Biol Crystallogr 68, 1584–1587 (2012). doi:10.1107/S0907444912038152.

Towards automated crystallographic structure refinement with phenix.refine. P. V. Afonine, R. W. Grosse-Kunstleve, N. Echols, J. J. Headd, N. W. Moriarty, M. Mustyakimov, T. C. Terwilliger, A. Urzhumtsev, P. H. Zwart, P. D. Adams. Acta Crystallogr D Biol Crystallogr 68, 352–367 (2012). doi:10.1107/S0907444912001308.

Enhanced macromolecular refinement by simulated annealing. A. T. Brunger, P. D. Adams, L. M. Rice. In E. Arnold, D. M. Himmel, M. G. Rossmann, C. P. Brock, Th. Hahn, H. Wondratschek, U. Müller, U. Shmueli, E. Prince, A. Authier, V. Kopský, D. B. Litvin, E. Arnold, D. M. Himmel, M. G. Rossmann, S. Hall, B. McMahon, editors, International Tables for Crystallography: Crystallography of biological macromolecules, volume F of International tables for crystallography: international tables online, pages 466–473. International Union of Crystallography, Chester, England (2012). doi:10.1107/97809553602060000856.

The phenix software for automated determination of macromolecular structures. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, N. Echols, J. J. Headd, L.-W. Hung, S. Jain, G. J. Kapral, R. W. Grosse Kunstleve, A. J. McCoy, N. W. Moriarty, R. D. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. H. Zwart. Methods 55, 94–106 (2011). doi:10.1016/j.ymeth.2011.07.005.

Improved molecular replacement by density- and energy-guided protein structure optimization. F. DiMaio, T. C. Terwilliger, R. J. Read, A. Wlodawer, G. Oberdorfer, U. Wagner, E. Valkov, A. Alon, D. Fass, H. L. Axelrod, D. Das, S. M. Vorobiev, H. Iwaï, P. R. Pokkuluri, D. Baker. Nature 473, 540–543 (2011). doi:10.1038/nature09964.

Using SAD data in phaser. R. J. Read and A. J. McCoy. Acta Crystallogr D Biol Crystallogr 67, 338–344 (2011). doi:10.1107/S0907444910051371.

Improvement of molecular-replacement models with sculptor. G. Bunkóczi and R. J. Read. Acta Crystallogr D Biol Crystallogr 67, 303–312 (2011). doi:10.1107/S0907444910051218.

Iotbx.cif: a comprehensive CIF toolbox. R. J. Gildea, L. J. Bourhis, O. V. Dolomanov, R. W. Grosse-Kunstleve, H. Puschmann, P. D. Adams, J. A. K. Howard. J Appl Crystallogr 44, 1259–1263 (2011). doi:10.1107/S0021889811041161.

Exact direct-space asymmetric units for the 230 crystallographic space groups. R. W. Grosse-Kunstleve, B. Wong, M. Mustyakimov, P. D. Adams. Acta Crystallogr, A, Found Crystallogr 67, 269–275 (2011). doi:10.1107/S0108767311007008.

A new generation of crystallographic validation tools for the protein data bank. R. J. Read, P. D. Adams, W. B. Arendall, A. T. Brunger, P. Emsley, R. P. Joosten, G. J. Kleywegt, E. B. Krissinel, T. Lütteke, Z. Otwinowski, A. Perrakis, J. S. Richardson, W. H. Sheffler, J. L. Smith, I. J. Tickle, G. Vriend, P. H. Zwart. Structure 19, 1395–1412 (2011). doi:10.1016/j.str.2011.08.006.

Evidence of functional protein dynamics from x-ray crystallographic ensembles. J. E. Kohn, P. V. Afonine, J. Z. Ruscio, P. D. Adams, T. Head-Gordon. PLoS Comput Biol (2010). doi:10.1371/journal.pcbi.1000911.

Joint x-ray and neutron refinement with phenix.refine. P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W. Moriarty, P. Langan, P. D. Adams. Acta Crystallogr D Biol Crystallogr 66, 1153–1163 (2010). doi:10.1107/S0907444910026582.

Rapid model building of alpha-helices in electron-density maps. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 268–275 (2010). doi:10.1107/S0907444910000314.

PHENIX: a comprehensive python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger, P. H. Zwart. Acta Crystallogr D Biol Crystallogr 66, 213–221 (2010). doi:10.1107/S0907444909052925.

Phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P. V. Afonine, R. W. Grosse-Kunstleve, V. B. Chen, J. J. Headd, N. W. Moriarty, J. S. Richardson, D. C. Richardson, A. Urzhumtsev, P. H. Zwart, P. D. Adams. J Appl Crystallogr 43, 669–676 (2010). doi:10.1107/S0021889810015608.

Experimental phasing: best practice and pitfalls. A. J. McCoy and R. J. Read. Acta Crystallogr D Biol Crystallogr 66, 458–469 (2010). doi:10.1107/S0907444910006335.

Rapid model building of beta-sheets in electron-density maps. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 276–284 (2010). doi:10.1107/S0907444910000302.

Rapid chain tracing of polypeptide backbones in electron-density maps. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 66, 285–294 (2010). doi:10.1107/S0907444910000272.

Generalized x-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromolecules. P. D. Adams, M. Mustyakimov, P. V. Afonine, P. Langan. Acta Crystallogr D Biol Crystallogr 65, 567–573 (2009). doi:10.1107/S0907444909011548.

Crystallographic model quality at a glance. L. Urzhumtseva, P. V. Afonine, P. D. Adams, A. Urzhumtsev. Acta Crystallogr D Biol Crystallogr 65, 297–300 (2009). doi:10.1107/S0907444908044296.

Decision-making in structure solution using bayesian estimates of map quality: the PHENIX AutoSol wizard. T. C. Terwilliger, P. D. Adams, R. J. Read, A. J. McCoy, N. W. Moriarty, R. W. Grosse-Kunstleve, P. V. Afonine, P. H. Zwart, L. W. Hung. Acta Crystallogr D Biol Crystallogr 65, 582–601 (2009). doi:10.1107/S0907444909012098.

R. W. Grosse-Kunstleve, N. W. Moriarty, P. D. Adams. Torsion angle refinement and dynamics as a tool to aid crystallographic structure determination. In Volume 4: 7th International Conference on Multibody Systems, Nonlinear Dynamics, and Control, Parts A, B and C, 1477–1485. ASMEDC, (2009). doi:10.1115/{DETC2009}-87737.

On the use of logarithmic scales for analysis of diffraction data. A. Urzhumtsev, P. V. Afonine, P. D. Adams. Acta Crystallogr D Biol Crystallogr 65, 1283–1291 (2009). doi:10.1107/S0907444909039638.

Averaged kick maps: less noise, more signal... and probably less bias. J. Pražnikar, P. V. Afonine, G. Guncar, P. D. Adams, D. Turk. Acta Crystallogr D Biol Crystallogr 65, 921–931 (2009). doi:10.1107/S0907444909021933.

Electronic ligand builder and optimization workbench (eLBOW): a tool for ligand coordinate and restraint generation. N. W. Moriarty, R. W. Grosse-Kunstleve, P. D. Adams. Acta Crystallogr D Biol Crystallogr 65, 1074–1080 (2009). doi:10.1107/S0907444909029436.

Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place. J. J. Headd, R. M. Immormino, D. A. Keedy, P. Emsley, D. C. Richardson, J. S. Richardson. J Struct Funct Genomics 10, 83–93 (2009). doi:10.1007/s10969-008-9045-8.

Experience converting a large fortran-77 program to c++. R.W. Grosse-Kunstleve, T.C. Terwilliger, P.D. Adams. Newsletter of the IUCr Commission on Crystallographic Computing 10, 74–83 (2009). URL: https://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/10.

Automatic multiple-zone rigid-body refinement with a large convergence radius. P. V. Afonine, R. W. Grosse-Kunstleve, A. Urzhumtsev, P. D. Adams. J Appl Crystallogr 42, 607–615 (2009). doi:10.1107/S0021889809023528.

Recent developments in phasing and structure refinement for macromolecular crystallography. P. D. Adams, P. V. Afonine, R. W. Grosse-Kunstleve, R. J. Read, J. S. Richardson, D. C. Richardson, T. C. Terwilliger. Curr Opin Struct Biol 19, 566–572 (2009). doi:10.1016/j.sbi.2009.07.014.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. H. Zwart, L. W. Hung, R. J. Read, P. D. Adams. Acta Crystallogr D Biol Crystallogr 64, 61–69 (2008). doi:10.1107/{S090744490705024X}.

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, N. W. Moriarty, P. D. Adams, R. J. Read, P. H. Zwart, L.-W. Hung. Acta Crystallogr D Biol Crystallogr 64, 515–524 (2008). doi:10.1107/S0907444908004319.

Surprises and pitfalls arising from (pseudo)symmetry. P. H. Zwart, R. W. Grosse-Kunstleve, A. A. Lebedev, G. N. Murshudov, P. D. Adams. Acta Crystallogr D Biol Crystallogr 64, 99–107 (2008). doi:10.1107/{S090744490705531X}.

Protein structures by spallation neutron crystallography. P. Langan, Z. Fisher, A. Kovalevsky, M. Mustyakimov, A. Sutcliffe Valone, C. Unkefer, M. J. Waltman, L. Coates, P. D. Adams, P. V. Afonine, B. Bennett, C. Dealwis, B. P. Schoenborn. J Synchrotron Radiat 15, 215–218 (2008). doi:10.1107/S0909049508000824.

Automated structure solution with the PHENIX suite. P. H. Zwart, P. V. Afonine, R. W. Grosse-Kunstleve, L.-W. Hung, T. R. Ioerger, A. J. McCoy, E. McKee, N. W. Moriarty, R. J. Read, J. C. Sacchettini, N. K. Sauter, L. C. Storoni, T. C. Terwilliger, P. D. Adams. Methods Mol Biol 426, 419–435 (2008). doi:10.1007/978-1-60327-058-8\_28.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. T. C. Terwilliger, R. W. Grosse-Kunstleve, P. V. Afonine, P. D. Adams, N. W. Moriarty, P. Zwart, R. J. Read, D. Turk, L. W. Hung. Acta Crystallogr D Biol Crystallogr 63, 597–610 (2007). doi:10.1107/S0907444907009791.

On macromolecular refinement at subatomic resolution with interatomic scatterers. P. V. Afonine, R. W. Grosse-Kunstleve, P. D. Adams, V. Y. Lunin, A. Urzhumtsev. Acta Crystallogr D Biol Crystallogr 63, 1194–1197 (2007). doi:10.1107/S0907444907046148.

Substructure determination in isomorphous replacement and anomalous diffraction experiments. R. W. Grosse-Kunstleve and T. R. Schneider. Methods Mol Biol 364, 197–214 (2007). doi:10.1385/1-59745-266-1:197.

Crystallographic protein model-building on the web. K. Gopal, E. McKee, T. Romo, R. Pai, J. Smith, J. Sacchettini, T. Ioerger. Bioinformatics 23, 375–377 (2007). doi:10.1093/bioinformatics/btl584.

Automated structure determination with phenix. T. D. Romo, J. C. Sacchettini, T. C. Terwilliger, P. D. Adams, P. V. Afonine, R. W. Grosse-Kunstleve, N. W. Moriarty, N. K. Sauter, P. H. Zwart, K. Gopal, T. R. Ioerger, L. Kanbi, E. McKee, R. K. Pai, L.-W. Hung, T. Radhakannan, A. J. McCoy, R. J. Read, L. C. Storoni. In R. J. Read and J. L. Sussman, editors, Evolving methods for macromolecular crystallography, volume 245 of NATO science series II: mathematics, physics and chemistry, pages 101–109. Springer Netherlands, Dordrecht (2007). doi:10.1007/978-1-4020-6316-9\_9.

Phaser crystallographic software. A. J. McCoy, R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni, R. J. Read. J Appl Crystallogr 40, 658–674 (2007). doi:10.1107/S0021889807021206.

Ligand identification using electron-density map correlations. T. C. Terwilliger, P. D. Adams, N. W. Moriarty, J. D. Cohn. Acta Crystallogr D Biol Crystallogr 63, 101–107 (2007). doi:10.1107/S0907444906046233.

Exploring metric symmetry. P.H. Zwart, R.W. Grosse-Kunstleve, P.D. Adams. CCP4 newsletter (2006). URL: https://cci.lbl.gov/~phzwart/EHMS/really_final/explore_metric_symmetry.html.

Improving amino-acid identification, fit and c(alpha) prediction using the simplex method in automated model building. T. D. Romo, J. C. Sacchettini, T. R. Ioerger. Acta Crystallogr D Biol Crystallogr 62, 1401–1406 (2006). doi:10.1107/S0907444906034019.

Identifying non-crystallographic symmetry in protein electron-density maps: a feature-based approach. R. Pai, J. Sacchettini, T. Ioerger. Acta Crystallogr D Biol Crystallogr 62, 1012–1021 (2006). doi:10.1107/S0907444906023158.

Automated ligand fitting by core-fragment fitting and extension into density. T. C. Terwilliger, H. Klei, P. D. Adams, N. W. Moriarty, J. D. Cohn. Acta Crystallogr D Biol Crystallogr 62, 915–922 (2006). doi:10.1107/S0907444906017161.

Automated detection of disulfide bridges in electron density maps using linear discriminant analysis. T. R. Ioerger. J Appl Crystallogr 38, 121–125 (2005). doi:10.1107/S0021889804030250.

The phenix refinement framework. P.V. Afonine, R.W. Grosse-Kunstleve, P.D. Adams. CCP4 Newsletter (2005). URL: http://legacy.ccp4.ac.uk/newsletters/newsletter42/articles/Afonine_GrosseKunstleve_Adams_18JUL2005.doc.

Xtriage and fest: automatic assessment of x-ray data and substructure structure factor estimation. P.H. Zwart, R.W. Grosse-Kunstleve, P.D. Adams. CCP4 Newsletter (2005). URL: http://legacy.ccp4.ac.uk/newsletters/newsletter43/articles/PHZ_RWGK_PDA.pdf.

A robust bulk-solvent correction and anisotropic scaling procedure. P. V. Afonine, R. W. Grosse-Kunstleve, P. D. Adams. Acta Crystallogr D Biol Crystallogr 61, 850–855 (2005). doi:10.1107/S0907444905007894.

Determining relevant features to recognize electron density patterns in x-ray protein crystallography. K. Gopal, T. D. Romo, J. C. Sacchettini, T. R. Ioerger. J Bioinform Comput Biol 3, 645–676 (2005). doi:10.1142/s0219720005001272.

Characterisation of x-ray data sets. P. Zwart, R. Grosse-Kunstleve, P. Adams. CCP4 Newsletter (2005). URL: http://legacy.ccp4.ac.uk/newsletters/newsletter42/articles/CCP4_2005_PHZ_RWGK_PDA.doc.

FINDMOL: automated identification of macromolecules in electron-density maps. E. W. McKee, L. D. Kanbi, K. L. Childs, R. W. Grosse-Kunstleve, P. D. Adams, J. C. Sacchettini, T. R. Ioerger. Acta Crystallogr D Biol Crystallogr 61, 1514–1520 (2005). doi:10.1107/S0907444905027332.

Cctbx news. R. Grosse-Kunstleve, P. Afonine, N. Sauter, P. Adams. IUCr Computing Commission Newsletter 5, 69–91 (2005). URL: https://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/5.

Likelihood-enhanced fast translation functions. A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni, R. J. Read. Acta Crystallogr D Biol Crystallogr 61, 458–464 (2005). doi:10.1107/S0907444905001617.

Likelihood-enhanced fast rotation functions. L. C. Storoni, A. J. McCoy, R. J. Read. Acta Crystallogr D Biol Crystallogr 60, 432–438 (2004). doi:10.1107/S0907444903028956.

Numerically stable algorithms for the computation of reduced unit cells. R. W. Grosse-Kunstleve, N. K. Sauter, P. D. Adams. Acta Crystallogr A Found Crystallogr 60, 1–6 (2004). doi:10.1107/{S010876730302186X}.

Evaluation of geometric and probabilistic distance measures to retrieve electron density patterns for protein structure determination. K. Gopal, T. Romo, J. Sacchettini, T. Ioerger. Proceedings of the International Conference on Artificial Intelligence (2004).

Cctbx news. R. Grosse-Kunstleve, N. Sauter, P. Adams. IUCr Computing Commission Newsletter 3, 22–31 (2004). URL: https://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/3.

Cctbx news. R. Grosse-Kunstleve and P. Adams. IUCr Computing Commission Newsletter 4, 19–36 (2004). URL: http://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/4.

Recent developments in the PHENIX software for automated crystallographic structure determination. P. D. Adams, K. Gopal, R. W. Grosse-Kunstleve, L.-W. Hung, T. R. Ioerger, A. J. McCoy, N. W. Moriarty, R. K. Pai, R. J. Read, T. D. Romo, J. C. Sacchettini, N. K. Sauter, L. C. Storoni, T. C. Terwilliger. J Synchrotron Radiat 11, 53–55 (2004). doi:10.1107/s0909049503024130.

Simple algorithm for a maximum-likelihood SAD function. A. J. McCoy, L. C. Storoni, R. J. Read. Acta Crystallogr D Biol Crystallogr 60, 1220–1228 (2004). doi:10.1107/S0907444904009990.

Using prime-and-switch phasing to reduce model bias in molecular replacement. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 60, 2144–2149 (2004). doi:10.1107/S0907444904019535.

SOLVE and RESOLVE: automated structure solution, density modification and model building. T. Terwilliger. J Synchrotron Radiat 11, 49–52 (2004). doi:10.1107/s0909049503023938.

Statistical density modification using local pattern matching. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 1688–1701 (2003). doi:10.1107/s0907444903015142.

On symmetries of substructures. R. W. Grosse-Kunstleve and P. D. Adams. Acta Crystallogr D Biol Crystallogr 59, 1974–1977 (2003). doi:10.1107/s0907444903021206.

New ways of looking at experimental phasing. R. J. Read. Acta Crystallogr D Biol Crystallogr 59, 1891–1902 (2003). doi:10.1107/s0907444903017918.

Cctbx news: fast triplet generator for direct methods, gallery of direct-space asymmetric units, et. al. R. Grosse-Kunstleve, B. Wong, P. Adams. IUCr Computing Commission Newsletter (2003). URL: https://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/2.

State of the toolbox: an overview of the crystallography toolbox (CCTBX). R. Grosse-Kunstleve and P. Adams. IUCr Computing Commission Newsletter (2003). URL: https://www.iucr.org/resources/commissions/crystallographic-computing/newsletters/1.

Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 1174–1182 (2003). doi:10.1107/s0907444903009922.

Substructure search procedures for macromolecular structures. R. W. Grosse-Kunstleve and P. D. Adams. Acta Crystallogr D Biol Crystallogr 59, 1966–1973 (2003). doi:10.1107/s0907444903018043.

Computational aspects of high-throughput crystallographic macromolecular structure determination. P. D. Adams, R. W. Grosse-Kunstleve, A. T. Brunger. Methods Biochem Anal 44, 75–87 (2003). doi:10.1002/0471721204.ch4.

Automatic solution of heavy-atom substructures. C. M. Weeks, P. D. Adams, J. Berendzen, A. T. Brunger, E. J. Dodson, R. W. Grosse-Kunstleve, T. R. Schneider, G. M. Sheldrick, T. C. Terwilliger, M. G. Turkenburg, I. Usón. Meth Enzymol 374, 37–83 (2003). doi:10.1016/S0076-6879(03)74003-8.

Automated side-chain model building and sequence assignment by template matching. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 45–49 (2003). doi:10.1107/s0907444902018048.

TEXTAL system: artificial intelligence techniques for automated protein model building. T. R. Ioerger and J. C. Sacchettini. In Macromolecular crystallography, part D, volume 374 of Methods in Enzymology, pages 244–270. Elsevier (2003). doi:10.1016/S0076-6879(03)74012-9.

SOLVE and RESOLVE: automated structure solution and density modification. T. C. Terwilliger. In Macromolecular Crystallography, Part D, volume 374 of Methods in Enzymology, pages 22–37. Elsevier (2003). doi:10.1016/S0076-6879(03)74002-6.

TEXTAL: artificial intelligence techniques for automated protein structure determination. K. Gopal, R. Pai, T. Ioerger, T. Romo, J. Sacchettini. Proceedings of the 15th Conference on Innovative Applications of Artificial Intelligence (IAAI) pages 93–100 (2003).

Automated main-chain model building by template matching and iterative fragment extension. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 59, 38–44 (2003). doi:10.1107/s0907444902018036.

Automatic modeling of protein backbones in electron-density maps via prediction of calpha coordinates. T. R. Ioerger and J. C. Sacchettini. Acta Crystallogr D Biol Crystallogr 58, 2043–2054 (2002). doi:10.1107/s0907444902016724.

PHENIX: building new software for automated crystallographic structure determination. P. D. Adams, R. W. Grosse-Kunstleve, L. W. Hung, T. R. Ioerger, A. J. McCoy, N. W. Moriarty, R. J. Read, J. C. Sacchettini, N. K. Sauter, T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 58, 1948–1954 (2002). doi:10.1107/s0907444902016657.

The computational crystallography toolbox : crystallographic algorithms in a reusable software framework. R. W. Grosse-Kunstleve, N. K. Sauter, N. W. Moriarty, P. D. Adams. J Appl Crystallogr 35, 126–136 (2002). doi:10.1107/S0021889801017824.

Algorithms for deriving crystallographic space-group information. II. treatment of special positions. R. W. Grosse-Kunstleve and P. D. Adams. Acta Crystallogr, A, Found Crystallogr 58, 60–65 (2002). doi:10.1107/s0108767301016658.

Statistical density modification with non-crystallographic symmetry. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 58, 2082–2086 (2002). doi:10.1107/s0907444902016360.

Rapid automatic NCS identification using heavy-atom substructures. T. C. Terwilliger. Acta Crystallogr D Biol Crystallogr 58, 2213–2215 (2002). doi:10.1107/s0907444902016384.

Recent developments in software for the automation of crystallographic macromolecular structure determination. P. D. Adams and R. W. Grosse-Kunstleve. Curr Opin Struct Biol 10, 564–568 (2000). doi:10.1016/s0959-440x(00)00132-9.

Algorithms for deriving crystallographic space-group information. R. Grosse-Kunstleve. Acta Crystallogr, A, Found Crystallogr 55, 383–395 (1999). doi:10.1107/s0108767398010186.