Subfield · Structural Biology
Most cited papers in Structural Biology
What are the most cited papers in Structural Biology?
The most cited paper in Structural Biology is "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales" (Aidan P. Thompson, Hasan Metin Aktulga, Richard A. Berger et al., 2021), with 12,569 citations. Next come "cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination" (11,217) and "Jalview Version 2—a multiple sequence alignment editor and analysis workbench" (11,179).
Showing 50 of 100 papers. Every paper with more than 1,046 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Aidan P. Thompson, Hasan Metin Aktulga, Richard A. Berger et al. · Computer Physics Communications | 22 Sep 2021 | 12,569 |
| 2 | cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Ali Punjani, John L. Rubinstein, David J. Fleet et al. · Nature Methods | 6 Feb 2017 | 11,217 |
| 3 | Jalview Version 2—a multiple sequence alignment editor and analysis workbench Andrew Mark Waterhouse, James B Procter, David M. A. Martin et al. · Bioinformatics | 16 Jan 2009 | 11,179 |
| 4 | UCSF ChimeraX : Structure visualization for researchers, educators, and developers Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Protein Science | 3 Sep 2020 | 10,674 |
| 5 | MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Shawn Q. Zheng, Eugene J. Palovcak, Jean‐Paul Armache et al. · Nature Methods | 27 Feb 2017 | 9,180 |
| 6 | Imaging Intracellular Fluorescent Proteins at Nanometer Resolution Eric Betzig, George H. Patterson, Rachid Sougrat et al. · Science | 10 Aug 2006 | 9,061 |
| 7 | Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Dorothee Claudia Liebschner et al. · Acta Crystallographica Section D Structural Biology | Oct 2019 | 7,679 |
| 8 | ImageJ2: ImageJ for the next generation of scientific image data Curtis Rueden, Johannes Schindelin, Mark Hiner et al. · BMC Bioinformatics | 29 Nov 2017 | 6,379 |
| 9 | Computer Visualization of Three-Dimensional Image Data Using IMOD James R. Kremer, David N. Mastronarde, J. Richard McIntosh · Journal of Structural Biology | 1996 | 6,195 |
| 10 | Automated electron microscope tomography using robust prediction of specimen movements David N. Mastronarde · Journal of Structural Biology | 25 Aug 2005 | 6,180 |
| 11 | RELION: Implementation of a Bayesian approach to cryo-EM structure determination Sjors H. W. Scheres · Journal of Structural Biology | 19 Sep 2012 | 6,175 |
| 12 | CTFFIND4: Fast and accurate defocus estimation from electron micrographs Alexis L. Rohou, Nikolaus Grigorieff · Journal of Structural Biology | 13 Aug 2015 | 5,758 |
| 13 | A guided tour into subcellular colocalization analysis in light microscopy Susanne Bolte, Fabrice P. Cordelières · Journal of Microscopy | Dec 2006 | 5,686 |
| 14 | Phase retrieval algorithms: a comparison James R. Fienup · Applied Optics | Aug 1982 | 5,681 |
| 15 | Gwyddion: an open-source software for SPM data analysis David Nečas, Petr Klapetek · Open Physics | 16 Nov 2011 | 4,514 |
| 16 | Gctf: Real-time CTF determination and correction Kai Zhang · Journal of Structural Biology | 20 Nov 2015 | 4,155 |
| 17 | Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy Mats G. Gustafsson · Journal of Microscopy | May 2000 | 3,882 |
| 18 | Real-space refinement in PHENIX for cryo-EM and crystallography Pavel V. Afonine, Billy K. Poon, Randy J. Read et al. · Acta Crystallographica Section D Structural Biology | 30 May 2018 | 3,869 |
| 19 | Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy Samuel T. Hess, Thanu Prabha Kalambur Girirajan, Michael D. Mason · Biophysical Journal | 15 Sep 2006 | 3,705 |
| 20 | Electron Energy-Loss Spectroscopy in the Electron Microscope Ray F. Egerton, Dale E. Newbury · Physics Today | Nov 1987 | 3,431 |
| 21 | Embedding in Epoxy Resins for Ultrathin Sectioning in Electron Microscopy Keith C. Richardson, Leonard Jarett, E. H. Finke · Stain Technology | 1960 | 3,318 |
| 22 | EMAN2: An extensible image processing suite for electron microscopy Guang Yi Tang, Liwei Peng, Philip Rupert Baldwin et al. · Journal of Structural Biology | 11 Jun 2006 | 3,274 |
| 23 | Far-Field Optical Nanoscopy Stefan W. Hell · Science | 25 May 2007 | 3,002 |
| 24 | iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM T. Geoff G. Battye, Luke Kontogiannis, Owen Johnson et al. · Acta Crystallographica Section D Biological Crystallography | 17 Mar 2011 | 2,958 |
| 25 | Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography Richard Gordon, Robert Bender, Gábor T. Herman · Journal of Theoretical Biology | Dec 1970 | 2,796 |
| 26 | Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy Peter B. Rosenthal, Richard A. Henderson · Journal of Molecular Biology | Oct 2003 | 2,705 |
| 27 | Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification Ignacio Arganda‐Carreras, Verena Kaynig, Curtis Rueden et al. · Bioinformatics | 28 Mar 2017 | 2,553 |
| 28 | Ultrafast Spin Dynamics in Ferromagnetic Nickel Emmanuel Beaurepaire, J.‐C. Merle, A. Daunois et al. · Physical Review Letters | 27 May 1996 | 2,463 |
| 29 | EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions Steven J. Ludtke, Philip Rupert Baldwin, Wah Keung Chiu · Journal of Structural Biology | Dec 1999 | 2,442 |
| 30 | Cryo-electron microscopy of vitrified specimens Jacques Dubochet, Marc Adrian, Jiin-Ju Chang et al. · Quarterly Reviews of Biophysics | May 1988 | 2,424 |
| 31 | Automated protein model building combined with iterative structure refinement. Anastassis Perrakis, Richard James Morris, Victor S. Lamzin · Nature Structural Biology | May 1999 | 2,424 |
| 32 | Maximally localized Wannier functions for entangled energy bands Ivo Souza, Nicola Marzari, David Vanderbilt · Physical review. B, Condensed matter | 19 Dec 2001 | 2,272 |
| 33 | A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography Oleg Kuybeda, Gabriel A. Frank, Alberto Bartesaghi et al. · Journal of Structural Biology | 27 Oct 2012 | 2,247 |
| 34 | Advanced methods of microscope control using μManager software Arthur Edelstein, Mark A. Tsuchida, Nenad Amodaj et al. · Journal of Biological Methods | 7 Nov 2014 | 2,234 |
| 35 | Attosecond science P. B. Corkum, Ferenc Krausz · Nature Physics | Jun 2007 | 2,150 |
| 36 | Femtosecond X-ray protein nanocrystallography Henry N. Chapman et al. · Nature | Feb 2011 | 2,130 |
| 37 | Accurate and efficient algorithm for Bader charge integration Min Yu, Dallas R. Trinkle · The Journal of Chemical Physics | 10 Feb 2011 | 2,108 |
| 38 | Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution Bi‐Chang Chen et al. · Science | 23 Oct 2014 | 2,103 |
| 39 | XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density Duncan E. McRee · Journal of Structural Biology | Apr 1999 | 2,102 |
| 40 | Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object David M. Paganin, Sheridan C. Mayo, Timur E. Gureyev et al. · Journal of Microscopy | Apr 2002 | 2,083 |
| 41 | SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields Joachim Frank, Michael Radermacher, Pawel A. Penczek et al. · Journal of Structural Biology | 1996 | 2,077 |
| 42 | Quantifying the local resolution of cryo-EM density maps Alp Kucukelbir, Fred J. Sigworth, Hemant D. Tagare · Nature Methods | 10 Nov 2013 | 2,053 |
| 43 | Automated molecular microscopy: The new Leginon system Christian J. M. Suloway, James Pulokas, Denis Fellmann et al. · Journal of Structural Biology | 21 Apr 2005 | 2,048 |
| 44 | Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens Jianwei Miao, Pambos S. Charalambous, Janos Kirz et al. · Nature | Jul 1999 | 1,983 |
| 45 | Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM Xueming Li, Paul E. Mooney, Shawn Q. Zheng et al. · Nature Methods | 3 May 2013 | 1,968 |
| 46 | Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction Ali Punjani, Haowei Zhang, David J. Fleet · Nature Methods | 30 Nov 2020 | 1,940 |
| 47 | 7 × 7 Reconstruction on Si(111) Resolved in Real Space Gerd K. Binnig, Heinrich Rohrer, Ch. Gerber et al. · Physical Review Letters | 10 Jan 1983 | 1,904 |
| 48 | Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs Tristan Bepler, Andrew Morin, Micah Rapp et al. · Nature Methods | 7 Oct 2019 | 1,871 |
| 49 | Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure Winfried T. Denk, Heinz Horstmann · PLoS Biology | 14 Oct 2004 | 1,735 |
| 50 | ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging Martin Ovesný, Pavel Křížek, Josef Borkovec et al. · Bioinformatics | 26 Apr 2014 | 1,704 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.