Molecular Dynamics Flexible Fitting

Publications

Methodological articles and reviews

  1. Molecular dynamics-based model refinement and validation for sub-5Å cryo-electron microscopy maps.
    Abhishek Singharoy*, Ivan Teo*, Ryan McGreevy*, John E Stone, Jianhua Zhao, and Klaus Schulten. eLife, 2016

  2. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling.
    Ryan McGreevy, Ivan Teo, Abhishek Singharoy, and Klaus Schulten. Methods, 100, 50-60, 2016.

  3. Computational methodologies for real-space structural refinement of large macromolecular complexes.
    Boon Chong Goh*, Jodi A. Hadden*, Rafael C. Bernardi, Abhishek Singharoy, Ryan McGreevy, Till Rudack, C. Keith Cassidy, and Klaus Schulten. Annual Review of Biophysics, 45, 253-278, 2016.

  4. xMDFF: Molecular dynamics flexible fitting of low-resolution X-Ray structures.**
    Ryan McGreevy*, Abhishek Singharoy*, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, and Klaus Schulten. Acta Crystallographica D70, 2344-2355, 2014.

  5. GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting.
    John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten. Faraday Disc., 2014.

  6. Cryo-EM modeling by the molecular dynamics flexible fitting method.
    Kwok-Yan Chan, Leonardo G. Trabuco, Eduard Schreiner, and Klaus Schulten. Biopolymers, 97, 678-686, 2012.

  7. Parallel generalized Born implicit solvent calculations with NAMD.
    David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten. J. of Chem. Theory Comput., 7, 3635-3642, 2011.

  8. Symmetry-restrained flexible fitting for symmetric EM maps.
    Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, and Klaus Schulten. Structure, 19, 1211-1218, 2011.

  9. Stereochemical errors and their implications for molecular dynamics simulations.
    Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, and Klaus Schulten. BMC Bioinformatics, 12, 190, 2011.

  10. Applications of the molecular dynamics flexible fitting method.
    Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth Villa, and Klaus Schulten. J. Struct. Biol., 173, 420-427, 2011.

  11. Molecular Dynamics Flexible Fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography.
    Leonardo G. Trabuco*, Elizabeth Villa*, Eduard Schreiner, Christopher B. Harrison, and Klaus Schulten. Methods, 49, 174-180, 2009.

  12. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
    Leonardo G. Trabuco*, Elizabeth Villa*, Kakoli Mitra, Joachim Frank, and Klaus Schulten. Structure, 16, 673-683, 2008.

MDFF and xMDFF** applications by the TCBG group

  1. The structure of the human 26S proteasome at a resolution of 3.9Å.
    Andreas Schweitzer, Antje Aufderheide, Till Rudack, Florian Beck, Gunter Pfeifer, Jurgen M. Plitzko, Eri Sakata, Klaus Schulten, Friedrich Forster, and Wolfgang Baumeister. Proc. Natl. Acad. Sci. USA, 113 (28), 2016.

  2. Cyclophilin A stabilizes HIV-1 capsid through a novel non-canonical binding site.
    Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben Ramalho, Gregory Bedwell, In-Ja Byeon, Jinwoo Ahn, Jiong Shi, Angela Gronenborn, Peter Prevelige, Itay Rousso, Christopher Aiken, Tatyana Polenova, Klaus Schulten, and Peijun Zhang. Nature Communications, 7:10714, 2016.

  3. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling.
    C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten, and Peijun Zhang. eLife, 2015.

  4. Macromolecular crystallography for synthetic abiological molecules: Combining xMDFF and PHENIX for structure determination of cyanostar macrocycles.**
    Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G. Mayne, Chun-Hsing Chen, Adam Zlotnick, Klaus Schulten, and Amar H. Flood. Journal of the American Chemical Society, 137:8810-8818, 2015.

  5. A structural model of the active ribosome-bound membrane protein insertase YidC
    Stephan Wickles, Abhishek Singharoy, Jessica Andreani, Stefan Seemayer, Lukas Bischoff, Otto Berninghausen, Johannes Soeding, Klaus Schulten, Eli van der Sluis, and Roland Beckmann. eLife, 3:e03035, 2014.

  6. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain.**
    Qufei Li, Sherry Wanderling, Marcin Paduch, David Medovoy, Abhishek Singharoy, Ryan McGreevy, Carlos Villalba-Galea, Raymond E. Hulse, Benoit Roux, Klaus Schulten, Anthony Kossiakoff, and Eduardo Perozo. Nature Structure Molecular Biology, 21, 244-252, 2014.

  7. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
    Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken, and Peijun Zhang. Nature, 497, 643-646, 2013. doi:10.1038/nature12162.

  8. Flexible interwoven termini determine the thermal stability of thermosomes.
    Kai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten, Zhiyang Dong, and Fei Sun. Protein & Cell, 4, in press, 2013.

  9. Mechanism of tetracycline resistance by ribosomal protection protein Tet(O).
    Wen Li, Gemma C. Atkinson, Nehal S. Thakor, Ülar Allas, Chuao-chao Lu, Kwok-Yan Chan, Tanel Tenson, Klaus Schulten, Kevin S. Wilson, Vasili Hauryliuk, and Joachim Frank. Nature Communications, 4, 1477, 2013.

  10. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.
    Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, and Fei Sun. PLoS Pathogens, 9, e1003132, 2013.

  11. Mechanisms of SecM-mediated stalling in the ribosome.
    James Gumbart, Eduard Schreiner, Daniel N. Wilson, Roland Beckmann, and Klaus Schulten. Biophysical Journal, 103, 331-341, 2012.

  12. Structural characterization of mRNA-tRNA translocation intermediates.
    Xabier Agirrezabala, Hstau Liao, Eduard Schreiner, Jie Fu, Rodrigo Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank. Proc. Natl. Acad. Sci. USA, 109, 6094-6099, 2012.

  13. Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
    Jens Frauenfeld, James Gumbart, Eli O. van der Sluis, Soledad Funes, Marco Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas Becker, Klaus Schulten, and Roland Beckmann. Nat. Struct. Mol. Biol., 18, 614-621, 2011.

  14. Structural insights into cognate vs. near-cognate discrimination during decoding.
    Xabier Agirrezabala, Eduard Scheiner, Leonardo G. Trabuco, Jianlin Lei, Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank. EMBO J., 30, 1497-1507, 2011.

  15. Molecular dynamics of EF-G during translocation.
    Wen Li, Leonardo G. Trabuco, Klaus Schulten, and Joachim Frank. Proteins, 79, 1478-1486, 2011.

  16. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain.
    HyeongJun Kim*, Jen Hsin*, Yanxin Liu*, Paul R. Selvin, and Klaus Schulten. Structure, 18, 1443-1449, 2010.

  17. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle.
    Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha, Zaida Luthey-Schulten, and Klaus Schulten. J. Mol. Biol., 402, 741-760, 2010.

  18. Recognition of the regulatory nascent chain TnaC by the ribosome.
    Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus Schulten. Structure, 18, 627-637, 2010.

  19. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
    Thomas Becker, Elisabet Mandon, Shashi Bhushan, Alexander Jarasch, Jean-Paul Armache, Soledad Funes, Fabrice Jossinet, James Gumbart, Thorsten Mielke, Otto Berninghausen, Klaus Schulten, Eric Westhof, Reid Gilmore, and Roland Beckmann. Science, 326, 1369-1373, 2009.

  20. Structural insight into nascent polypeptide chain-mediated translational stalling.
    Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean-Paul Armache, Elizabeth Villa, Leonardo G. Trabuco, Thomas Becker, Thorsten Mielke, Klaus Schulten, Thomas A. Steitz, and Roland Beckmann. Science, 326, 1412-1415, 2009.

  21. Regulation of the protein-conducting channel by a bound ribosome.
    James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and Klaus Schulten. Structure, 17, 1453-1464, 2009.

  22. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.
    Jen Hsin, James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Biophys. J., 97, 321-329, 2009.

  23. Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides.
    Melih K. Sener*, Jen Hsin*, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Chem. Phys., 357, 188-197, 2009.

  24. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis.
    Elizabeth Villa*, Jayati Sengupta*, Leonardo G. Trabuco, Jamie LeBarron, William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen, Måns Ehrenberg, Klaus Schulten, and Joachim Frank. Proc. Natl. Acad. Sci. USA, 106, 1063-1068, 2009.

Selected third-party publications employing MDFF

  1. Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex.
    Eva Nogales, Robert K Louder, Yuan He. Current Opinion in Structural Biology, 40, 120-127, 2016

  2. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM.
    Matthew G. Iadanza, Anna J. Higgins, Bob Schiffrin, Antonio N. Calabrese, David J. Brockwell, Alison E. Ashcroft, Sheena E. Radford and Neil A. Ranson. Nature Communications, 7, 2016

  3. Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps.
    Ramachandran Rakesh, Agnel Praveen Joseph, Ramachandra M. Bhaskara and Narayanaswamy Srinivasan. RNA Biology, 13, 1025-1040, 2016

  4. Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility.
    Masahiko Yamagishi, Hideki Shigematsu, Takeshi Yokoyama, Masahide Kikkawa, Mitsuhiro Sugawa, Mari Aoki, Mikako Shirouzu, Junichiro Yajima, Ryo Nitta. Structure, 24, 1322-1334, 2016

  5. Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase.
    Kliment A. Verba, Ray Yu-Ruei Wang, Akihiko Arakawa, Yanxin Liu, Mikako Shirouzu, Shigeyuki Yokoyama, David A. Agard. Science, 352, 2016

  6. The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.
    Zhihai Li, Xiaodong Yan, Hai Yu, Daning Wang, Shuo Song, Yunbing Li, Maozhou He, Qiyang Hong, Qingbing Zheng, Qinjian Zhao, Ying Gu, Jun Zhang, Mandy E.W. Janssen, Giovanni Cardone, Norman H. Olson, Timothy S. Baker, Shaowei Li, Ningshao Xia. Structure, 24, 874-885, 2016

  7. CryoEM structure of yeast cytoplasmic exosome complex.
    Jun-Jie Liu, Chu-Ya Niu1, Yao Wu3, Dan Tan, Yang Wang, Ming-Da Ye, Yang Liu, Wenwei Zhao, Ke Zhou, Quan-Sheng Liu, Junbiao Dai, Xuerui Yang, Meng-Qiu Dong, Niu Huang and Hong-Wei Wang. Cell Research, 26, 822-837, 2016

  8. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.
    Rui Huang, Zev A. Ripstein, Rafal Augustyniak, Michal Lazniewski, Krzysztof Ginalski, Lewis E. Kay, and John L. Rubinstein. Proc. Natl. Acad. Sci. USA, 113, E4190--E4199, 2016

  9. Near-atomic resolution visualization of human transcription promoter opening.
    Yuan He, Chunli Yan, Jie Fang, Carla Inouye, Robert Tjian, Ivaylo Ivanov and Eva Nogales. Nature, 533, 359-365, 2016

  10. Secondary Interaction Interfaces with PCNA Control Conformational Switching of DNA Polymerase PolB from Polymerization to Editing.
    Xiaojun Xu, Chunli Yan, Bradley R. Kossmann, and Ivaylo Ivanov. The Journal of Physical Chemistry B, 120, 8379-8388, 2016

  11. Paired octamer rings of retinoschisin suggest a junctional model for cell-cell adhesion in the retina.
    GÖkhan Tolun, Camasamudram Vijayasarathy, Rick Huang, Yong Zeng, Yan Li, Alasdair C. Steven, Paul A. Sieving, and J. Bernard Heymann. Proc. Natl. Acad. Sci. USA, 113, 5287-5292, 2016

  12. Force-producing ADP state of myosin bound to actin.
    Sarah F. Wulf, Virginie Ropars, Setsuko Fujita-Becker, Marco Oster, Goetz Hofhaus, Leonardo G. Trabuco, Olena Pylypenko, H. Lee Sweeney, Anne M. Houdusse, and Rasmus R. S SchrÖder. Proc. Natl. Acad. Sci. USA, 113, E1844-E1852, 2016

  13. Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance.
    Daniel G. Schep, Jianhua Zhao, and John L. Rubinstein. Proc. Natl. Acad. Sci. USA, 113, 3245-3250, 2016

  14. New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy.
    Daniel L. Hurdiss, Ethan L. Morgan, Rebecca F. Thompson, Emma L. Prescott, Margarita M. Panou, Andrew Macdonald, Neil A. Ranson. Structure, 24, 528-536, 2016

  15. Structure- and function-based design of Plasmodium-selective proteasome inhibitors.
    Hao Li, Anthony J. O'Donoghue, Wouter A. van der Linden, Stanley C. Xie, Euna Yoo, Ian T. Foe, Leann Tilley, Charles S. Craik, Paula C. A. da Fonseca and Matthew Bogyo. Nature, 530, 233-236, 2016

  16. Structure of the poly-C9 component of the complement membrane attack complex .
    Natalya V. Dudkina, Bradley A. Spicer, Cyril F. Reboul, Paul J. Conroy, Natalya Lukoyanova, Hans Elmlund, Ruby H. P. Law, Susan M. Ekkel, Stephanie C. Kondos, Robert J. A. Goode, Georg Ramm, James C. Whisstock, Helen R. Saibil and Michelle A. Dunstone. Nature Communications, 7, 2016

  17. Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.
    Grigore Pintilie, Dong-Hua Chen, Cameron A. Haase-Pettingell, Jonathan A. King, and Wah Chiu. Biophysical Journal, 110, 827-839, 2016

  18. Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling.
    Clara Barrio-Garcia, Matthias Thoms, Dirk Flemming, Lukas Kater, Otto Berninghausen, Jochen Baszler, Roland Beckmann, and Ed Hurt. Nat. Struct. Mol. Biol., 23, 37-44, 2016

  19. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.
    Anna Zhou, Alexis Rohou, Daniel G Schep, John V Bason, Martin G Montgomery, John E Walker, Nikolaus Grigorieff, John L Rubinstein . eLife, 4, 2015

  20. High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation.
    Zhiguo Shang, Kaifeng Zhou, Chen Xu, Roseann Csencsits, Jared C Cochran, and Charles V Sindelar. eLife, 2014

  21. Flexibility in the Insulin Receptor Ectodomain Enables Docking of Insulin in Crystallographic Conformation Observed in a Hormone-Bound Microreceptor .
    Harish Vashisth. Membranes, 4, 730-746, 2014

  22. Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA .
    Agnel Praveen Joseph, Prasanna Bhat, Saumitra Das and Narayanaswamy Srinivasan. RNA Biology, 11, 891-905, 2014

  23. Decrypting the structural, dynamic and energetic basis of a monomeric kinesin interacting with a tubulin dimer in three ATPase states by all-atom molecular dynamics simulation .
    Wenjun Zheng. Biochemistry, 2014

  24. Cryo-EM Structure of Isomeric Molluscan Hemocyanin Triggered by Viral Infection .
    Hongtao Zhu , Jun Zhuang , Hongli Feng, Rongfeng Liang, Jiangyong Wang, Lianhui Xie, Ping Zhu. PLOS One, 2014

  25. Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly .
    Xiaoxiao Zhang, Kaige Yan, Yixiao Zhang, Ningning Li, Chengying Ma, Zhifei Li, Yanqing Zhang, Boya Feng, Jing Liu, Yadong Sun, Yanji Xu, Jianlin Lei, and Ning Gao. Nucl. Acids Res., 42, 13430-13439, 2014

  26. Structural and Biochemical Characterization of the Cop9 Signalosome CSN5/CSN6 Heterodimer .
    Melissa Birol, Radoslav Ivanov Enchev, André Padilla, Florian Stengel, Ruedi Aebersold, Stéphanie Betzi, Yinshan Yang, François Hoh, Matthias Peter Christian Dumas, Aude Echalier. PLOS One, 2014

  27. Functional Conformations for Pyruvate Carboxylase during Catalysis Explored by Cryoelectron Microscopy .
    Gorka Lasso, Linda P.C. Yu, David Gil, Melisa Lázaro, Liang Tong, and Mikel Valle. Structure, 22, 911-922, 2014

  28. A New Model for Pore Formation by Cholesterol-Dependent Cytolysins .
    Cyril F. Reboul, James C. Whisstock, Michelle A. Dunstone. PLOS Comp. Biol., 2014

  29. Structural basis for interaction of a cotranslational chaperone with the eukaryotic ribosome .
    Yixiao Zhang, Chengying Ma, Yi Yuan, Jing Zhu, Ningning Li, Chu Chen, Shan Wu, Li Yu, Jianlin Lei and Ning Gao. Nat. Struct. Mol. Biol., 21,1042-1046, 2014

  30. Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions.
    Fei Guo, Zheng Liu, Ping-An Fang, Qinfen Zhang, Elena T. Wright, Weimin Wu, Ci Zhang, Frank Vago, Yue Ren, Joanita Jakana, Wah Chiu, Philip Serwer, and Wen Jiang. Proc. Natl. Acad. Sci. USA, 111,E4606-E4614, 2014

  31. Function and dynamics of macromolecular complexes explored by integrative structural and computational biology.
    Michael D Purdy, Brad C Bennett, William E McIntire, Ali K. Khan, Peter M Kasson, Mark Yeager. Current Opinion in Structural Biology, 27, 138-148, 2014

  32. EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics.
    Bo Chen, Grégory Boël, Yaser Hashem, Wei Ning, Jingyi Fei, Chi Wang, Ruben L Gonzalez Jr, John F Hunt and Joachim Frank. Nat. Struct. Mol. Biol., 21, 152-159, 2014

  33. Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling.
    Harish Vashisth, Georgios Skiniotis, and Charles Lee Brooks, III. Chemical Reviews, 114, 3353-3365, 2014

  34. 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
    Christoph Leidig, Matthias Thoms, Iris Holdermann, Bettina Bradatsch, Otto Berninghausen, Gert Bange, Irmgard Sinning, Ed Hurt and Roland Beckmann. Nature Communications, 5, Article number: 3491, 2014

  35. Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion.
    Marko Gogala, Thomas Becker, Birgitta Beatrix, Jean-Paul Armache, Clara Barrio-Garcia, Otto Berninghausen and Roland Beckmann. Nature, 506, 107-110, 2014

  36. Bacterial tubulin TubZ-Bt transitions between a two-stranded intermediate and a four-stranded filament upon GTP hydrolysis.
    Elizabeth A. Montabana and David A. Agard. Proc. Natl. Acad. Sci. USA, 111, 3407-3412, 2014

  37. Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome.
    Pia Unverdorben, Florian Beck, Paweł Śledź, Andreas Schweitzer, Günter Pfeifer, Jürgen M. Plitzko, Wolfgang Baumeister, and Friedrich Förster. Proc. Natl. Acad. Sci. USA, 111, 5544-5549, 2014

  38. Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter.
    JungMin Kim, Shenping Wu, Thomas M. Tomasiak, Claudia Mergel, Michael B. Winter, Sebastian B. Stiller, Yaneth Robles-Colmanares, Robert M. Stroud, Robert Tampé, Charles S. Craik and Yifan Cheng. Nature, 2014

  39. Cryo-electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly.
    Tanmay A. M. Bharat, Luis R. Castillo Menendez, Wim J. H. Hagen, Vanda Lux, Sebastien Igonet, Martin Schorb, Florian K. M. Schur, Hans-Georg Kräusslich, and John A. G. Briggs. Proc. Natl. Acad. Sci. USA, 111, 8233-8238, 2014

  40. Structure of the SecY channel during initiation of protein translocation.
    Eunyong Park, Jean-François Ménétret, James C. Gumbart, Steven J. Ludtke, Weikai Li, Andrew Whynot, Tom A. Rapoport and Christopher W. Akey. Nature, 506, 102-106, 2014

  41. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.
    Yaser Hashem, Amedee des Georges, Jie Fu, Sarah N. Buss, Fabrice Jossinet, Amy Jobe, Qin Zhang, Hstau Y. Liao, Robert A. Grassucci, Chandrajit Bajaj, Eric Westhof, Susan Madison-Antenucci, and Joachim Frank. Nature, 494, 385-389, 2013

  42. The backbone model of the Arabis mosaic virus reveals new insights into functional domains of Nepovirus capsid.
    Joséphine Lai-Kee-Him, Pascale Schellenberger, Christian Dumas, Eric Richard, Stefano Trapani, Véronique Komar, Gerard Demangeat, Christophe Ritzenthaler, and Patrick Bron. J. Struct. Biol., 182, 1-9, 2013

  43. Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.
    Nicolas Coudray, Salvatore Valvo, Minghui Hu, Ralph Lasala, Changki Kim, Martin Vink, Ming Zhou, Davide Provasi, Marta Filizola, Juoehi Tao, Jia Fang, Pawel A. Penczek, Iban Ubarretxena-Belandia, and David L. Stokes. Proc. Natl. Acad. Sci., 110, 2140-2145, 2013

  44. A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry.
    Alex J Noble, Qian Zhang, Jason O'Donnell, Hanaa Hariri, Nilakshee Bhattacharya, Alan G Marshall, and Scott M Stagg. Nat. Struct. Mol. Biol., 20, 167-173, 2013

  45. Modeling a Ryanodine Receptor N-terminal Domain Connecting the Central Vestibule and the Corner Clamp Region.
    Li Zhu, Xiaowei Zhong, S. R. Wayne Chen, Nilesh Banavali, and Zheng Liu. J. Biol. Chem., 288, 903-914, 2013

  46. Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.
    Jean-Paul Armache, Andreas M. Anger, Viter Márquez, Sibylle Franckenberg, Thomas Fröhlich, Elizabeth Villa, Otto Berninghausen, Michael Thomm, Georg J. Arnold, Roland Beckmann, and Daniel N. Wilson. Nucl. Acids Res., 41, 1284-1293, 2013

  47. All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps.
    Minghui Li and Wenjun Zheng. Biochemistry, 51, 5022-5032, 2012

  48. ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit.
    Sébastien Ferreira-Cerca, Vatsala Sagar, Thorsten Schäfer, Momar Diop, Anne-Maria Wesseling, Haiyun Lu, Eileen Chai, Ed Hurt, and Nicole LaRonde-LeBlanc. Nat. Struct. Mol. Biol., 19, 1316-1323, 2012

  49. CryoEM Visualization of an Adenovirus Capsid-Incorporated HIV Antigen.
    Justin W. Flatt, Tara L. Fox, Natalia Makarova. Jerry L. Blackwell, Igor P. Dmitriev, Elena A. Kashentseva, David T. Curiel, and Phoebe L. Stewart. PLoS ONE, 7(11), e49607, 2012

  50. Coagulation Factor X Activates Innate Immunity to Human Species C Adenovirus.
    Konstantin Doronin, Justin W. Flatt, Nelson C. Di Paolo, Reeti Khare, Oleksandr Kalyuzhniy, Mauro Acchione, John P. Sumida, Umeharu Ohto, Toshiyuki Shimizu, Sachiko Akashi-Takamura, Kensuke Miyake, James W. MacDonald, Theo K. Bammler, Richard P. Beyer, Frederico M. Farin, Phoebe L. Stewart, and Dmitry M. Shayakhmetov. Science, 338, 795-798, 2012

  51. Structural Basis for Microtubule Binding and Release by Dynein.
    William B. Redwine, Rogelio Hernández-López, Sirui Zou, Julie Huang, Samara L. Reck-Peterson, and Andres E. Leschziner. Science, 337, 1532-1536, 2012

  52. Near-atomic resolution structural model of the yeast 26S proteasome.
    Florian Beck, Pia Unverdorben, Stefan Bohn, Andreas Schweitzer, Günter Pfeifer, Eri Sakata, Stephan Nickell, Jürgen M. Plitzko, Elizabeth Villa, Wolfgang Baumeister, and Friedrich Förster. Proc. Natl. Acad. Sci. USA, 109, 14870-14875, 2012

  53. All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps.
    Minghui Li and Wenjun Zheng. Biochemistry, 51, 5022-5032, 2012

  54. Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability.
    Jordi Querol-Audí, Chunli Yan, Xiaojun Xu, Susan E. Tsutakawa, Miaw-Sheue Tsai, John A. Tainer, Priscilla K. Cooper, Eva Nogales, and Ivaylo Ivanov. Proc. Natl. Acad. Sci. USA, 109, 8528-8533, 2012

  55. The Structure of Human Tripeptidyl Peptidase II as Determined by a Hybrid Approach.
    Anne-Marie Schonegge, Elizabeth Villa, Friedrich Forster, Reiner Hegerl, Jurgen Peters, Wolfgang Baumeister, and Beate Rockel. Structure, 20, 593-603, 2012

  56. Structural insights into initial and intermediate steps of the ribosome-recycling process.
    Takeshi Yokoyama, Tanvir R Shaikh, Nobuhiro Iwakura, Hideko Kaji, Akira Kaji and Rajendra K Agrawal. EMBO J., 31, 1836-1846, 2012

  57. Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability.
    Jordi Querol-Audí, Chunli Yan, Xiaojun Xu, Susan E. Tsutakawa, Miaw-Sheue Tsai, John A. Tainer, Priscilla K. Cooper, Eva Nogales and Ivaylo Ivanov. Proc. Natl. Acad. Sci. USA, 109, 8528-8533, 2012

  58. All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps.
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* Equal contribution.

** xMDFF publication.