Improved AlphaFold modeling with implicit experimental information
Terwilliger, Thomas C., Poon, Billy K., Afonine, Pavel V., Schlicksup, Christopher J., Croll, Tristan I., Millán, Claudia, Richardson, Jane. S., Read, Randy J., Adams, Paul D.
Published in Nature methods (01.11.2022)
Published in Nature methods (01.11.2022)
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MolProbity: More and better reference data for improved all‐atom structure validation
Williams, Christopher J., Headd, Jeffrey J., Moriarty, Nigel W., Prisant, Michael G., Videau, Lizbeth L., Deis, Lindsay N., Verma, Vishal, Keedy, Daniel A., Hintze, Bradley J., Chen, Vincent B., Jain, Swati, Lewis, Steven M., Arendall, W. Bryan, Snoeyink, Jack, Adams, Paul D., Lovell, Simon C., Richardson, Jane S., Richardson, David C.
Published in Protein science (01.01.2018)
Published in Protein science (01.01.2018)
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AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination
Terwilliger, Thomas C., Liebschner, Dorothee, Croll, Tristan I., Williams, Christopher J., McCoy, Airlie J., Poon, Billy K., Afonine, Pavel V., Oeffner, Robert D., Richardson, Jane S., Read, Randy J., Adams, Paul D.
Published in Nature methods (01.01.2024)
Published in Nature methods (01.01.2024)
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New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink “waters,” and NGL Viewer to recapture online 3D graphics
Prisant, Michael G., Williams, Christopher J., Chen, Vincent B., Richardson, Jane S., Richardson, David C.
Published in Protein science (01.01.2020)
Published in Protein science (01.01.2020)
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Journal Article
A New Generation of Crystallographic Validation Tools for the Protein Data Bank
Read, Randy J., Adams, Paul D., Arendall, W. Bryan, Brunger, Axel T., Emsley, Paul, Joosten, Robbie P., Kleywegt, Gerard J., Krissinel, Eugene B., Lütteke, Thomas, Otwinowski, Zbyszek, Perrakis, Anastassis, Richardson, Jane S., Sheffler, William H., Smith, Janet L., Tickle, Ian J., Vriend, Gert, Zwart, Peter H.
Published in Structure (London) (12.10.2011)
Published in Structure (London) (12.10.2011)
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MolProbity: all-atom structure validation for macromolecular crystallography
Chen, Vincent B., Arendall III, W. Bryan, Headd, Jeffrey J., Keedy, Daniel A., Immormino, Robert M., Kapral, Gary J., Murray, Laura W., Richardson, Jane S., Richardson, David C.
Published in Acta crystallographica. Section D, Biological crystallography. (01.01.2010)
Published in Acta crystallographica. Section D, Biological crystallography. (01.01.2010)
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Recommendations of the wwPDB NMR Validation Task Force
Montelione, Gaetano T., Nilges, Michael, Bax, Ad, Güntert, Peter, Herrmann, Torsten, Richardson, Jane S., Schwieters, Charles D., Vranken, Wim F., Vuister, Geerten W., Wishart, David S., Berman, Helen M., Kleywegt, Gerard J., Markley, John L.
Published in Structure (London) (03.09.2013)
Published in Structure (London) (03.09.2013)
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PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, Paul D., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Davis, Ian W., Echols, Nathaniel, Headd, Jeffrey J., Hung, Li-Wei, Kapral, Gary J., Grosse-Kunstleve, Ralf W., McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert, Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Zwart, Peter H.
Published in Acta crystallographica. Section D, Biological crystallography. (01.02.2010)
Published in Acta crystallographica. Section D, Biological crystallography. (01.02.2010)
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Journal Article
Seeing the PDB
Richardson, Jane S., Richardson, David C., Goodsell, David S.
Published in The Journal of biological chemistry (01.01.2021)
Published in The Journal of biological chemistry (01.01.2021)
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The Phenix software for automated determination of macromolecular structures
Adams, Paul D., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Echols, Nathaniel, Headd, Jeffrey J., Hung, Li-Wei, Jain, Swati, Kapral, Gary J., Grosse Kunstleve, Ralf W., McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D., Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Zwart, Peter H.
Published in Methods (San Diego, Calif.) (01.09.2011)
Published in Methods (San Diego, Calif.) (01.09.2011)
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Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding
Dunkle, Jack A., Wang, Leyi, Feldman, Michael B., Pulk, Arto, Chen, Vincent B., Kapral, Gary J., Noeske, Jonas, Richardson, Jane S., Blanchard, Scott C., Cate, Jamie H. Doudna
Published in Science (American Association for the Advancement of Science) (20.05.2011)
Published in Science (American Association for the Advancement of Science) (20.05.2011)
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Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
Tyka, Michael D., Keedy, Daniel A., André, Ingemar, DiMaio, Frank, Song, Yifan, Richardson, David C., Richardson, Jane S., Baker, David
Published in Journal of molecular biology (14.01.2011)
Published in Journal of molecular biology (14.01.2011)
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Scientific benchmarks for guiding macromolecular energy function improvement
Leaver-Fay, Andrew, O'Meara, Matthew J, Tyka, Mike, Jacak, Ron, Song, Yifan, Kellogg, Elizabeth H, Thompson, James, Davis, Ian W, Pache, Roland A, Lyskov, Sergey, Gray, Jeffrey J, Kortemme, Tanja, Richardson, Jane S, Havranek, James J, Snoeyink, Jack, Baker, David, Kuhlman, Brian
Published in Methods in enzymology (2013)
Published in Methods in enzymology (2013)
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Accelerating crystal structure determination with iterative AlphaFold prediction
Terwilliger, Thomas C., Afonine, Pavel V., Liebschner, Dorothee, Croll, Tristan I., McCoy, Airlie J., Oeffner, Robert D., Williams, Christopher J., Poon, Billy K., Richardson, Jane S., Read, Randy J., Adams, Paul D.
Published in Acta crystallographica. Section D, Biological crystallography. (01.03.2023)
Published in Acta crystallographica. Section D, Biological crystallography. (01.03.2023)
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OSPREY: protein design with ensembles, flexibility, and provable algorithms
Gainza, Pablo, Roberts, Kyle E, Georgiev, Ivelin, Lilien, Ryan H, Keedy, Daniel A, Chen, Cheng-Yu, Reza, Faisal, Anderson, Amy C, Richardson, David C, Richardson, Jane S, Donald, Bruce R
Published in Methods in enzymology (2013)
Published in Methods in enzymology (2013)
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Natural β-Sheet Proteins Use Negative Design to Avoid Edge-to-Edge Aggregation
Richardson, Jane S., Richardson, David C.
Published in Proceedings of the National Academy of Sciences - PNAS (05.03.2002)
Published in Proceedings of the National Academy of Sciences - PNAS (05.03.2002)
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