Publications : EMDataResource

2024-11-20 : 40312 EMDB map entries, 23557 PDB coordinate entries RCSB PDB | PDBe

Project Publications

PubMed Listing (GM079429)

2024 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008

2024

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Lawson C, Kryshtafovych A, Pintilie G, Burley S, Cerny J, Chen V, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read R, Richardson J, Rohou A, Schneider B, Sellers B, Shao C, Sourial E, Williams C, Williams C, Yang Y, Abbaraju V, Afonine PV, Baker M, Bond P, Blundell T, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan K, Dimaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc C, Hunte C, Igaev M, Joseph A, Kao W, Kihara D, Kumar D, Lang L, Lin S, Subramaniya SRMV, Mittal S, Mondal A, Moriarty N, Muenks A, Murshudov G, Nicholls R, Olek M, Palmer C, Perez A, Pohjolainen E, Pothula K, Rowley C, Sarkar D, Schäfer L, Schlicksup C, Schroeder G, Shekhar M, Si D, Singharoy A, Sobolev O, Terashi G, Vaiana A, Vedithi S, Verburgt J, Wang X, Warshamanage R, Winn M, Weyand S, Yamashita K, Zhao M, Schmid M, Berman H, Chiu W.(2024) Nature Methods, doi:10.1038/s41592-024-02321-7. doi
Community recommendations on cryoEM data archiving and validation. Kleywegt, G. J., Adams, P. D., Butcher, S. J., Lawson, C. L., Rohou, A., Rosenthal, P. B., Subramaniam, S., Topf, M., Abbott, S., Baldwin, P. R., Berrisford, J. M., Bricogne, G., Choudhary, P., Croll, T. I., Danev, R., Ganesan, S. J., Grant, T., Gutmanas, A., Henderson, R., Heymann, J. B., Huiskonen, J. T., Istrate, A., Kato, T., Lander, G. C., Lok, S.-M., Ludtke, S. J., Murshudov, G. N., Pye, R., Pintilie, G. D., Richardson, J. S., Sachse, C., Salih, O., Scheres, S. H. W., Schroeder, G. F., Sorzano, C. O. S., Stagg, S. M., Wang, Z., Warshamanage, R., Westbrook, J. D., Winn, M. D., Young, J. Y., Burley, S. K., Hoch, J. C., Kurisu, G., Morris, K., Patwardhan, A. & Velankar, S. (2024). Community recommendations on cryoEM data archiving and validation. IUCrJ, 11(2), 140-151. doi
EMDB-the Electron Microscopy Data Bank wwPDB Consortium. Nucleic Acids Res. 2024 Jan 5;52(D1):D456-D465. doi
Hub stability in the calcium calmodulin-dependent protein kinase II Chen, C-T, Puhl, H, Vogel SS, Molloy JE, Chiu W, Khan S Commun Biol 7, 766 (2024). doi
Cryogenic electron tomography reveals novel structures in the apical complex of Plasmodium falciparum. Sun SY, Segev-Zarko L-a, Pintilie GD, Kim CY, Staggers SR, Schmid MF, Egan ES, Chiu W, Boothroyd JC. mBio. 2024 Apr 10;15(4):e0286423. doi

2022

Topological crossing in the misfolded Tetrahymena ribozyme resolved by cryo-EM. Li S, Palo MZ, Pintilie G, Zhang X, Su Z, Kappel K, Chiu W, Zhang K, Das R. Proc Natl Acad Sci U S A. 2022 Sep 13;119(37):e2209146119. doi
Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures. Sun SY, Segev-Zarko LA, Chen M, Pintilie GD, Schmid MF, Ludtke SJ, Boothroyd JC, Chiu W. Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):e2111661119. doi
Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia. Zhang K, Horikoshi N, Li S, Powers AS, Hameedi MA, Pintilie GD, Chae HD, Khan YA, Suomivuori CM, Dror RO, Sakamoto KM, Chiu W, Wakatsuki S. ACS Cent Sci. 2022 Feb 23;8(2):214-222. doi
Developing Community Resources for Nucleic Acid Structures. Berman HM, Lawson CL, Schneider B. Life (Basel). 2022 Apr 6;12(4):540. doi
Oxidative stress protein Oxr1 promotes V-ATPase holoenzyme disassembly in catalytic activity-independent manner. Khan MM, Lee S, Couoh-Cardel S, Oot RA, Kim H, Wilkens S, Roh SH. EMBO J. 2022 Feb 1;41(3):e109360. doi
Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Gestaut D, Zhao Y, Park J, Ma B, Leitner A, Collier M, Pintilie G, Roh SH, Chiu W, Frydman J. Cell. 2022 Dec 8;185(25):4770-4787.e20. Erratum in: Cell. 2023 Apr 27;186(9):2038. doi

2021

Mapping the catalytic conformations of an assembly-line polyketide synthase module. Cogan DP, Zhang K, Li X, Li S, Pintilie GD, Roh SH, Craik CS, Chiu W, Khosla C. Science. 2021 Nov 5;374(6568):729-734. doi
Target highlights in CASP14: Analysis of models by structure providers. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. Proteins. 2021 Dec;89(12):1647-1672. doi
Validation, analysis and annotation of cryo-EM structures. Pintilie G, Chiu W. Acta Crystallogr D Struct Biol. 2021 Sep 1;77(Pt 9):1142-1152. doi: 10.1107/S2059798321006069. Epub 2021 Aug 31. doi
Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Zhang K, Zheludev IN, Hagey RJ, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Wu MT, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D'Souza V, Glenn JS, Chiu W, Das R. Nat Struct Mol Biol. 2021 Sep;28(9):747-754. doi
Cryo-EM targets in CASP14. Cragnolini T, Kryshtafovych A, Topf M. Proteins. 2021 Dec;89(12):1949-1958. doi
Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 A resolution. Su Z, Zhang K, Kappel K, Li S, Palo MZ, Pintilie GD, Rangan R, Luo B, Wei Y, Das R, Chiu W. Nature. 2021 Aug;596(7873):603-607. doi
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Sarkans U, Chiu W, Collinson L, Darrow MC, Ellenberg J, Grunwald D, Hériché JK, Iudin A, Martins GG, Meehan T, Narayan K, Patwardhan A, Russell MRG, Saibil HR, Strambio-De-Castillia C, Swedlow JR, Tischer C, Uhlmann V, Verkade P, Barlow M, Bayraktar O, Birney E, Catavitello C, Cawthorne C, Wagner-Conrad S, Duke E, Paul-Gilloteaux P, Gustin E, Harkiolaki M, Kankaanpää P, Lemberger T, McEntyre J, Moore J, Nicholls AW, Onami S, Parkinson H, Parsons M, Romanchikova M, Sofroniew N, Swoger J, Utz N, Voortman LM, Wong F, Zhang P, Kleywegt GJ, Brazma A. Nat Methods. 2021 Dec;18(12):1418-1422. doi
Evolution of standardization and dissemination of cryo-EM structures and data jointly by the community, PDB, and EMDB. Chiu W, Schmid MF, Pintilie GD, Lawson CL. J Biol Chem. 2021 Jan-Jun;296:100560. doi
The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion. Oliver SL, Xing Y, Chen DH, Roh SH, Pintilie GD, Bushnell DA, Sommer MH, Yang E, Carfi A, Chiu W, Arvin AM. PLoS Pathog. 2021 Jan 7;17(1):e1008961. doi
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA Jr, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. Nat Methods. 2021 Feb;18(2):156-164. Epub 2021 Feb 4. doi
Cryo-EM analysis of Ebola virus nucleocapsid-like assembly. Wang Y, Binning JM, Pintilie GD, Chiu W, Amarasinghe GK, Leung DW, Su Z. STAR Protoc. 2021 Dec 16;3(1):101030. doi

2020

Resolving individual atoms of protein complex by cryo-electron microscopy Zhang K, Pintilie GD, Li S, Schmid MF, Chiu W. Cell Res. 2020 Dec;30(12):1136-1139. doi
Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W. Sci Adv. 2020 Oct 7;6(41):eabb9605. doi
Full-length three-dimensional structure of the influenza A virus M1 protein and its organization into a matrix layer Selzer L, Su Z, Pintilie GD, Chiu W, Kirkegaard K. PLoS Biol. 2020 Sep 30;18(9):e3000827. doi
A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation Oliver SL, Xing Y, Chen DH, Roh SH, Pintilie GD, Bushnell DA, Sommer MH, Yang E, Carfi A, Chiu W, Arvin AM. Nat Commun. 2020 Aug 18;11(1):4141. doi
The data universe of structural biology Berman HM, Vallat B, Lawson CL. IUCrJ. 2020 May 28;7(Pt 4):630-638. doi
Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Nat Methods. 2020 Jul;17(7):699-707. doi
Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA Partin AC, Zhang K, Jeong BC, Herrell E, Li S, Chiu W, Nam Y. Mol Cell. 2020 May 7;78(3):411-422.e4. doi
Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR-Cas complex revealed by cryo-EM Zhang K, Wang S, Li S, Zhu Y, Pintilie GD, Mou TC, Schmid MF, Huang Z, Chiu W. Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7176-7182. doi
Evolving data standards for cryo-EM structures. Lawson CL, Berman HM, Chiu W. Struct Dyn. 2020 Jan 24;7(1):014701. doi
Measurement of Atom Resolvability in cryo-EM Maps With Q-scores. Pintilie G, Zhang K, Su Z, Li S, Schmid MF, Chiu W. Nat Methods. 2020;17(3):328–334. doi
Structure of the G Protein Chaperone and Guanine Nucleotide Exchange Factor Ric-8A Bound to Gαi1. McClelland, L. J., Zhang, K., Mou, T. C., Johnston, J., Yates-Hansen, C., Li, S., Thomas, C. J., Doukov, T. I., Triest, S., Wohlkonig, A., Tall, G. G., Steyaert, J., Chiu, W., & Sprang, S. R. Nat Commun. 2020;11(1):1077. doi

2019

Structure of Calcarisporiella thermophila Hsp104 Disaggregase that Antagonizes Diverse Proteotoxic Misfolding Events. Michalska K, Zhang K, March ZM, Hatzos-Skintges C, Pintilie G, Bigelow L, Castellano LM, Miles LJ, Jackrel ME, Chuang E, Jedrzejczak R, Shorter J, Chiu W, Joachimiak A. Structure. 2019 Mar 5;27(3):449-463.e7. doi
Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry. Guo M, Zhang K, Zhu Y, Pintilie GD, Guan X, Li S, Schmid MF, Ma Z, Chiu W, Huang Z. Cell Res. 2019 Apr;29(4):305-312. doi
Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution. Zhang K, Zhang H, Li S, Pintilie GD, Mou TC, Gao Y, Zhang Q, van den Bedem H, Schmid MF, Au SWN, Chiu W. Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):6800-6805. doi
The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis. Gestaut D, Roh SH, Ma B, Pintilie G, Joachimiak LA, Leitner A, Walzthoeni T, Aebersold R, Chiu W, Frydman J. Cell. 2019 Apr 18;177(3):751-765.e15 doi
Cryo-electron microscopy targets in CASP13: Overview and evaluation of results. Kryshtafovych A, Malhotra S, Monastyrskyy B, Cragnolini T, Joseph AP, Chiu W, Topf M. Proteins. Proteins. 2019 Dec;87(12):1128-1140. doi: 10.1002/prot.25817. Epub 2019 Oct 23. doi
Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Nat Commun. 2019 Dec 3;10(1):5511. doi
Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J. Nat Struct Mol Biol. 2019 Dec;26(12):1094-1105. Epub 2019 Nov 18. doi
Comparative Modeling in an 8.6-Å Cryo-EM Map of the Singapore Grouper Iridovirus. Pintilie G, Chen DH, Tran BN, Jakana J, Wu J, Hew CL, Chiu W. Structure. 2019 Oct 1;27(10):1561-1569.e4. Epub 2019 Aug 22. doi

2018

CryoEM Challenges Journal of Structural Biology Virtual Special Issue
Comparing cryo-EM structures. Lawson CL, Chiu W. J Struct Biol. 2018 Oct 13. pii: S1047-8477(18)30277-6. doi
Distribution of evaluation scores for the models submitted to the second cryo-EM model challenge. Kryshtafovych A, Monastyrskyy B, Adams PD, Lawson CL, Chiu W. Data Brief. 2018 Sep 8;20:1629-1638. doi
New software tools in EMAN2 inspired by EMDatabank map challenge. Bell JM, Chen M, Durmaz T, Fluty AC, Ludtke SJ. J Struct Biol. 2018 Nov;204(2):283-290. doi
The first single particle analysis Map Challenge: A summary of the assessments. Heymann JB, Marabini R, Kazemi M, Sorzano COS, Holmdahl M, Mendez JH, Stagg SM, Jonic S, Palovcak E, Armache JP, Zhao J, Cheng Y, Pintilie G, Chiu W, Patwardhan A, Carazo JM. J Struct Biol. 2018 Nov;204(2):291-300. doi
Evaluation system and web infrastructure for the second cryo-EM model challenge. Kryshtafovych A, Adams PD, Lawson CL, Chiu W. J Struct Biol. 2018 Oct;204(1):96-108. doi
Abbott S, Iudin A, Korir PK, Somasundharam S, Patwardhan A. EMDB Web Resources. Curr Protoc Bioinformatics. 2018 Mar;61(1):5.10.1-5.10.12. doi
Structural biology data archiving - where we are and what lies ahead. Kleywegt GJ, Velankar S, Patwardhan A. FEBS Lett. 2018 Jun;592(12):2153-2167. doi
Walsh RM Jr, Roh SH, Gharpure A, Morales-Perez CL, Teng J, Hibbs RE. Structural principles of distinct assemblies of the human α4β2 nicotin recept. Nature. 2018 May;557(7704):261-265. doi
The 3.5-Angstrom CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase V(o) Proton Channel. Roh SH, Stam NJ, Hryc CF, Couoh-Cardel S, Pintilie G, Chiu W, Wilkens S. Mol Cell. 2018 Mar 15;69(6):993-1004.e3. doi
Anticipating innovations in structural biology. Berman HM, Lawson CL, Vallat B, Gabanyi MJ Q Rev Biophys 2018 Jan;51:e8 doi

2017

Validation of Structures in the Protein Data Bank. Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Structure. 2017 Dec 5;25(12):1916-1927. doi
Structural and Functional Impacts of ER Coactivator Sequential Recruitment. Yi P, Wang Z, Feng Q, Chou CK, Pintilie GD, Shen H, Foulds CE, Fan G, Serysheva I, Ludtke SJ, Schmid MF, Hung MC, Chiu W, O'Malley BW. Mol Cell. 2017 Sep 7;67(5):733-743.e4. doi
Building bridges between cellular and molecular structural biology. Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Grünewald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. Elife. 2017 Jul 6;6. pii: e25835. doi
Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences. Dou H, Burrows DW, Baker ML, Ju T. Biophys J. 2017 Jun 20;112(12):2479-2493. doi
Trends in the Electron Microscopy Data Bank (EMDB). Patwardhan A. Acta Crystallogr D Struct Biol. 2017 Jun 1;73(Pt 6):503-508. doi
An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D. Elife. 2017 Mar 29;6. pii: e24905. doi
Accurate model annotation of a near-atomic resolution cryo-EM map. Hryc CF, Chen DH, Afonine PV, Jakana J, Wang Z, Haase-Pettingell C, Jiang W, Adams PD, King JA, Schmid MF, Chiu W. Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):3103-3108. doi
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive. Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PM, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. Structure. 2017 Mar 7;25(3):536-545. doi

2016

Databases and Archiving for CryoEM. Patwardhan A, Lawson CL. Methods Enzymol. 2016;579:393-412. doi
Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. DiMaio F, Chiu W. Methods Enzymol. 2016;579:255-76. doi
The archiving and dissemination of biological structure data. Berman HM, Burley SK, Kleywegt GJ, Markley JL, Nakamura H, Velankar S. Curr Opin Struct Biol. 2016 Oct;40:17-22. doi
De Novo modeling in cryo-EM density maps with Pathwalking. Chen M, Baldwin PR, Ludtke SJ, Baker ML. J Struct Biol. 2016 Dec;196(3):289-298. doi
Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms. Hecksel CW, Darrow MC, Dai W, Galaz-Montoya JG, Chin JA, Mitchell PG, Chen S, Jakana J, Schmid MF, Chiu W. Microsc Microanal. 2016 Jun;22(3):487-96. doi
EMPIAR: a public archive for raw electron microscopy image data. Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A. Nat Methods. 2016 May;13(5):387-8. doi
Web-based volume slicer for 3D electron-microscopy data from EMDB. Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. J Struct Biol. 2016 May;194(2):164-70. doi
The Electron Microscopy eXchange (EMX) initiative. arabini R, Ludtke SJ, Murray SC, Chiu W, de la Rosa-Trevín JM, Patwardhan A, Heymann JB, Carazo JM. J Struct Biol. 2016 May;194(2):156-63. doi
Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage. Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W. Biophys J. 2016 Feb 23;110(4):827-39. doi
EMDataBank unified data resource for 3DEM. Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. Nucleic Acids Res. 2016 Jan 4;44(D1):D396-403. doi
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB. Velankar S, van Ginkel G, Alhroub Y, Battle GM, Berrisford JM, Conroy MJ, Dana JM, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Lagerstedt I, Mir S, Fernandez Montecelo MA, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Sanz-García E, Sen S, Slowley RA, Wainwright ME, Deshpande MS, Iudin A, Sahni G, Salavert Torres J, Hirshberg M, Mak L, Nadzirin N, Armstrong DR, Clark AR, Smart OS, Korir PK, Kleywegt GJ. Nucleic Acids Res. 2016 Jan 4;44(D1):D385-95. doi

2015

Gating machinery of InsP3R channels revealed by electron cryomicroscopy. Fan G, Baker ML, Wang Z, Baker MR, Sinyagovskiy PA, Chiu W, Ludtke SJ, Serysheva II. Nature. 2015 Nov 19;527(7578):336-41. doi
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Structure. 2015 Jul 7;23(7):1156-67. doi
CTF Challenge: Result summary. Marabini R, Carragher B, Chen S, Chen J, Cheng A, Downing KH, Frank J, Grassucci RA, Bernard Heymann J, Jiang W, Jonic S, Liao HY, Ludtke SJ, Patwari S, Piotrowski AL, Quintana A, Sorzano CO, Stahlberg H, Vargas J, Voss NR, Chiu W, Carazo JM. J Struct Biol. 2015 Jun;190(3):348-59. doi
Structure of a biologically active estrogen receptor-coactivator complex on DNA. Yi P, Wang Z, Feng Q, Pintilie GD, Foulds CE, Lanz RB, Ludtke SJ, Schmid MF, Chiu W, O'Malley BW. Mol Cell. 2015 Mar 19;57(6):1047-58. doi
Collaborative computational project for electron cryo-microscopy. Wood C, Burnley T, Patwardhan A, Scheres S, Topf M, Roseman A, Winn M. Acta Crystallogr D Biol Crystallogr. 2015 Jan 1;71(Pt 1):123-6. doi
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank. Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J. Bioinformatics. 2015 Apr 15;31(8):1274-8. doi

2014

A 3D cellular context for the macromolecular world. Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. Nat Struct Mol Biol. 2014 Oct;21(10):841-5. doi
An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Wang Z, Hryc CF, Bammes B, Afonine PV, Jakana J, Chen DH, Liu X, Baker ML, Kao C, Ludtke SJ, Schmid MF, Adams PD, Chiu W. Nat Commun. 2014 Sep 4;5:4808. doi
Toward a high-resolution structure of IP₃R channel. Serysheva II. Cell Calcium. 2014 Sep;56(3):125-32. doi
The Protein Data Bank archive as an open data resource. Berman HM, Kleywegt GJ, Nakamura H, Markley JL. J Comput Aided Mol Des. 2014 Oct;28(10):1009-14. doi
Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Gipson P, Baker ML, Raytcheva D, Haase-Pettingell C, Piret J, King JA, Chiu W. Nat Commun. 2014 Jul 2;5:4278. doi Erratum
PDBe: Protein Data Bank in Europe. Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PM, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. Nucleic Acids Res. 2014 Jan;42(Database issue):D285-91. doi
Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank. Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM. Biopolymers. 2014 Jun;101(6):659-68. doi

2013

Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB. Lagerstedt I, Moore WJ, Patwardhan A, Sanz-García E, Best C, Swedlow JR, Kleywegt GJ. J Struct Biol. 2013 Nov;184(2):173-81. doi
How community has shaped the Protein Data Bank. Berman HM, Kleywegt GJ, Nakamura H, Markley JL. Structure. 2013 Sep 3;21(9):1485-91. doi
Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Baker ML, Hryc CF, Zhang Q, Wu W, Jakana J, Haase-Pettingell C, Afonine PV, Adams PD, King JA, Jiang W, Chiu W. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12301-6. doi
Validation of cryo-EM structure of IPR1 channel. Murray SC, Flanagan J, Popova OB, Chiu W, Ludtke SJ, Serysheva II. Structure. 2013 Jun 4;21(6):900-9. doi
The role of structural bioinformatics resources in the era of integrative structural biology. Gutmanas A, Oldfield TJ, Patwardhan A, Sen S, Velankar S, Kleywegt GJ. Acta Crystallogr D Biol Crystallogr. 2013 May;69(Pt 5):710-21. doi
Cryo-EM model validation using independent map reconstructions. DiMaio F, Zhang J, Chiu W, Baker D. Protein Sci. 2013 Jun;22(6):865-8. doi
Cryo-EM structure of a molluscan hemocyanin suggests its allosteric mechanism. Zhang Q, Dai X, Cong Y, Zhang J, Chen DH, Dougherty MT, Wang J, Ludtke SJ, Schmid MF, Chiu W. Structure. 2013 Apr 2;21(4):604-13.
Trendspotting in the Protein Data Bank. Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C. FEBS Lett. 2013 Apr 17;587(8):1036-45. doi

2012

Data management challenges in three-dimensional EM. Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-García E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Nat Struct Mol Biol. 2012 Dec;19(12):1203-7. doi
Comparison of Segger and other methods for segmentation and rigid-body docking of molecular components in cryo-EM density maps. Pintilie G, Chiu W. Biopolymers. 2012 Sep;97(9):742-60. doi
Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Baker ML, Baker MR, Hryc CF, Ju T, Chiu W. Biopolymers. 2012 Sep;97(9):655-68. doi
The 2010 cryo-EM modeling challenge. Ludtke SJ, Lawson CL, Kleywegt GJ, Berman H, Chiu W. Biopolymers. 2012 Sep;97(9):651-4. doi
Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking. Baker MR, Rees I, Ludtke SJ, Chiu W, Baker ML. Structure. 2012 Mar 7;20(3):450-63. doi
Outcome of the first electron microscopy validation task force meeting. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Structure. 2012 Feb 8;20(2):205-14. doi
Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. Chang J, Liu X, Rochat RH, Baker ML, Chiu W. Adv Exp Med Biol. 2012;726:49-90. doi
PDBe: Protein Data Bank in Europe. Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PM, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. Nucleic Acids Res. 2012 Jan;40(Database issue):D445-52. doi

2011

Near-atomic-resolution cryo-EM for molecular virology. Hryc CF, Chen DH, Chiu W. Curr Opin Virol. 2011 Aug;1(2):110-7. doi
4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus. Zhang R, Hryc CF, Cong Y, Liu X, Jakana J, Gorchakov R, Baker ML, Weaver SC, Chiu W. EMBO J. 2011 Aug 9;30(18):3854-63. doi
View-independent Contour Culling of 3D Density Maps for Far-field Viewing of Iso-surfaces. Feng P, Ju T, Warren J. Comput Graph. 2011 Jun;35(3):561-568.
The Protein Data Bank in Europe (PDBe): bringing structure to biology. Velankar S, Kleywegt GJ. Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):324-30. doi
Modeling protein structure at near atomic resolutions with Gorgon. Baker ML, Abeysinghe SS, Schuh S, Coleman RA, Abrams A, Marsh MP, Hryc CF, Ruths T, Chiu W, Ju T. J Struct Biol. 2011 May;174(2):360-73. doi
Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1355-60. doi
Workshop on the validation and modeling of electron cryo-microscopy structures of biological nanomachines. Ludtke SJ, Lawson CL, Kleywegt GJ, Berman HM, Chiu W. Pac Symp Biocomput. 2011:369-73.
PDBe: Protein Data Bank in Europe. Velankar S, Alhroub Y, Alili A, Best C, Boutselakis HC, Caboche S, Conroy MJ, Dana JM, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Penkett CJ, Pineda-Castillo J, Rinaldi L, Sahni G, Sawka G, Sen S, Slowley R, Sousa da Silva AW, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. Nucleic Acids Res. 2011 Jan;39(Database issue):D402-10. doi
EMDataBank.org: unified data resource for CryoEM. Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W. Nucleic Acids Res. 2011 Jan;39(Database issue):D456-64. doi

2010

Unified data resource for cryo-EM. Lawson CL. Methods Enzymol. 2010;483:73-90. doi
Analyses of subnanometer resolution cryo-EM density maps. Baker ML, Baker MR, Hryc CF, Dimaio F. Methods Enzymol. 2010;483:1-29. doi
Cryo-EM of macromolecular assemblies at near-atomic resolution. Baker ML, Zhang J, Ludtke SJ, Chiu W. Nat Protoc. 2010 Sep;5(10):1697-708. doi
Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus. Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W. Nat Struct Mol Biol. 2010 Jul;17(7):830-6. doi
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. Pintilie GD, Zhang J, Goddard TD, Chiu W, Gossard DC. J Struct Biol. 2010 Jun;170(3):427-38. doi
Mechanism of folding chamber closure in a group II chaperonin. Zhang J, Baker ML, Schröder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W. Nature. 2010 Jan 21;463(7279):379-83. doi
PDBe: Protein Data Bank in Europe. Velankar S, Best C, Beuth B, Boutselakis CH, Cobley N, Sousa Da Silva AW, Dimitropoulos D, Golovin A, Hirshberg M, John M, Krissinel EB, Newman R, Oldfield T, Pajon A, Penkett CJ, Pineda-Castillo J, Sahni G, Sen S, Slowley R, Suarez-Uruena A, Swaminathan J, van Ginkel G, Vranken WF, Henrick K, Kleywegt GJ. Nucleic Acids Res. 2010 Jan;38(Database issue):D308-17. doi

2009

Unifying Biological Image Formats with HDF5. Dougherty MT, Folk MJ, Zadok E, Bernstein HJ, Bernstein FC, Eliceiri KW, Benger W, Best C. Commun ACM. 2009 Oct 1;52(10):42-47.
Identifying Components in 3D Density Maps of Protein Nanomachines by Multi-scale Segmentation. Pintilie G, Zhang J, Chiu W, Gossard D. IEEE NIH Life Sci Syst Appl Workshop. 2009 Apr 1;2009:44-47.

2008

Representation of viruses in the remediated PDB archive. Lawson CL, Dutta S, Westbrook JD, Henrick K, Berman HM. Acta Crystallogr D Biol Crystallogr. 2008 Aug;D64(Pt 8):874-82. doi