Topic · Protein Structure and Dynamics
Most cited papers in Protein Structure and Dynamics
What are the most cited papers in Protein Structure and Dynamics?
The most cited paper in Protein Structure and Dynamics is "Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4" (Ulrich K. Laemmli, 1970), with 252,153 citations. Next come "A short history of SHELX" (87,903) and "VMD: Visual molecular dynamics" (68,537).
Showing 50 of 99 papers. Every paper with more than 5,331 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 Ulrich K. Laemmli · Nature | Aug 1970 | 252,153 |
| 2 | A short history of SHELX George M. Sheldrick · Acta Crystallographica Section A Foundations of Crystallography | 21 Dec 2007 | 87,903 |
| 3 | VMD: Visual molecular dynamics William F Humphrey Jr, Andrew Dalke, Klaus J. Schulten · Journal of Molecular Graphics | Feb 1996 | 68,537 |
| 4 | UCSF Chimera—A visualization system for exploratory research and analysis Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Journal of Computational Chemistry | Jul 2004 | 48,801 |
| 5 | Highly accurate protein structure prediction with AlphaFold John Jumper et al. · Nature | 15 Jul 2021 | 47,486 |
| 6 | The Protein Data Bank Helen Miriam Berman · Nucleic Acids Research | 2000 | 40,564 |
| 7 | AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading Oleg Trott, Arthur J. Olson · Journal of Computational Chemistry | 4 Jun 2009 | 38,730 |
| 8 | Coot : model-building tools for molecular graphics Paul Emsley, Kevin D. Cowtan · Acta Crystallographica Section D Biological Crystallography | 26 Nov 2004 | 31,846 |
| 9 | Features and development of Coot Paul Emsley, Bernhard Lohkamp, William G. Scott et al. · Acta Crystallographica Section D Biological Crystallography | 23 Mar 2010 | 30,245 |
| 10 | PHENIX : a comprehensive Python-based system for macromolecular structure solution Paul D. Adams, Pavel V. Afonine, G. Bunkóczi et al. · Acta Crystallographica Section D Biological Crystallography | 21 Jan 2010 | 24,924 |
| 11 | Canonical dynamics: Equilibrium phase-space distributions William Graham Hoover · Physical Review A | Mar 1985 | 23,918 |
| 12 | A smooth particle mesh Ewald method Ulrich Essmann, L. Perera, Max L. Berkowitz et al. · The Journal of Chemical Physics | 15 Nov 1995 | 23,377 |
| 13 | A simple method for displaying the hydropathic character of a protein Jack Kyte, Russell F. Doolittle · Journal of Molecular Biology | May 1982 | 23,233 |
| 14 | Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease John M. Chirgwin, Alan Przybyla, Raymond J. MacDonald et al. · Biochemistry | Nov 1979 | 22,217 |
| 15 | Phaser crystallographic software Airlie J. McCoy, Ralf W. Grosse‐Kunstleve, Paul D. Adams et al. · Journal of Applied Crystallography | 13 Jul 2007 | 21,198 |
| 16 | Polymorphic transitions in single crystals: A new molecular dynamics method Michele Parrinello, Ananda Fathur Rahman · Journal of Applied Physics | Dec 1981 | 20,747 |
| 17 | The Reliability of Molecular Weight Determinations by Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis Karolin Weber, Mary Osborn · Journal of Biological Chemistry | Aug 1969 | 20,350 |
| 18 | Development and testing of a general amber force field Junmei Wang, Romain M. Wolf, James W. Caldwell et al. · Journal of Computational Chemistry | 13 Apr 2004 | 20,214 |
| 19 | GROMACS: Fast, flexible, and free David van der Spoel, Erik R. Lindahl, Berk Hess et al. · Journal of Computational Chemistry | 6 Oct 2005 | 19,617 |
| 20 | Canonical sampling through velocity rescaling Giovanni Bussi, Davide Donadio, Michele Parrinello · The Journal of Chemical Physics | 3 Jan 2007 | 19,040 |
| 21 | Minimap2: pairwise alignment for nucleotide sequences Heng Li · Bioinformatics | 4 May 2018 | 17,673 |
| 22 | Scalable molecular dynamics with NAMD James Christopher Phillips, Rosemary Braun, Wei Wang et al. · Journal of Computational Chemistry | 12 Oct 2005 | 17,545 |
| 23 | LINCS: A linear constraint solver for molecular simulations Berk Hess, Henk Bekker, Herman J. C. Berendsen et al. · Journal of Computational Chemistry | Sep 1997 | 17,504 |
| 24 | NMRPipe: A multidimensional spectral processing system based on UNIX pipes Frank Delaglio, Stephan Grzesiek, Geerten W. Vuister et al. · Journal of Biomolecular NMR | Nov 1995 | 16,465 |
| 25 | GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Berk Hess, Carsten Kutzner, David van der Spoel et al. · Journal of Chemical Theory and Computation | 2 Feb 2008 | 16,214 |
| 26 | Accurate structure prediction of biomolecular interactions with AlphaFold 3 Josh Abramson et al. · Nature | 8 May 2024 | 15,959 |
| 27 | Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features Wolfgang Kabsch, Christian Sander · Biopolymers | Dec 1983 | 15,893 |
| 28 | Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination Axel T. Brünger, Paul D. Adams, G. Marius Clore et al. · Acta Crystallographica Section D Biological Crystallography | Sep 1998 | 15,809 |
| 29 | CHARMM : A program for macromolecular energy, minimization, and dynamics calculations Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson et al. · Journal of Computational Chemistry | Jun 1983 | 15,019 |
| 30 | MolProbity : all-atom structure validation for macromolecular crystallography Vincent B. Chen, W.B. Arendall, Jeffrey J. Headd et al. · Acta Crystallographica Section D Biological Crystallography | 21 Dec 2009 | 14,901 |
| 31 | All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins Alexander D. MacKerell et al. · The Journal of Physical Chemistry B | Apr 1998 | 14,659 |
| 32 | The Pfam Protein Families Database Alex Bateman · Nucleic Acids Research | 2002 | 14,221 |
| 33 | MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures Per Juris Kraulis · Journal of Applied Crystallography | Oct 1991 | 14,158 |
| 34 | SWISS-MODEL: homology modelling of protein structures and complexes Andrew Mark Waterhouse, Martino Bertoni, Stefan Bienert et al. · Nucleic Acids Research | 7 May 2018 | 14,049 |
| 35 | Comparative Protein Modelling by Satisfaction of Spatial Restraints Andrej Šali, Tom L. Blundell · Journal of Molecular Biology | Dec 1993 | 13,351 |
| 36 | Squeeze-and-Excitation Networks Jie Hu, Li Shen, Samuel Albanie et al. · IEEE Transactions on Pattern Analysis and Machine Intelligence | 2 May 2019 | 12,749 |
| 37 | Overview of the CCP 4 suite and current developments Martyn Winn, Charles C. Ballard, Kevin D. Cowtan et al. · Acta Crystallographica Section D Biological Crystallography | 17 Mar 2011 | 12,694 |
| 38 | Improved methods for building protein models in electron density maps and the location of errors in these models T. Alwyn Jones, Jin-yu Zou, Sandra W. Cowan et al. · Acta Crystallographica Section A Foundations of Crystallography | Mar 1991 | 12,692 |
| 39 | ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB James Maier, Carmenza Martinez, Koushik Kasavajhala et al. · Journal of Chemical Theory and Computation | 7 Jul 2015 | 11,534 |
| 40 | Evolution of Protein Molecules Thomas H. Jukes, Charles R. Cantor · Elsevier eBooks | 1969 | 11,260 |
| 41 | Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function Garrett M. Morris, David S. Goodsell, Robert S. Halliday et al. · Journal of Computational Chemistry | 15 Nov 1998 | 10,945 |
| 42 | Avogadro: an advanced semantic chemical editor, visualization, and analysis platform Marcus D. Hanwell, Donald Ephraim Curtis, David C. Lonie et al. · Journal of Cheminformatics | 13 Aug 2012 | 10,759 |
| 43 | GROMACS: A message-passing parallel molecular dynamics implementation Herman J. C. Berendsen, David van der Spoel, Rudi van Drunen · Computer Physics Communications | Sep 1995 | 10,722 |
| 44 | Inference of Macromolecular Assemblies from Crystalline State Evgeny Krissinel, Kim Henrick · Journal of Molecular Biology | 15 May 2007 | 10,600 |
| 45 | The Phyre2 web portal for protein modeling, prediction and analysis Lawrence A. Kelley, Stefans Mezulis, Christopher M. Yates et al. · Nature Protocols | 7 May 2015 | 10,412 |
| 46 | Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy Richard A. Friesner, Jay L. Banks, Robert B. Murphy et al. · Journal of Medicinal Chemistry | 27 Feb 2004 | 10,177 |
| 47 | CHARMM‐GUI: A web‐based graphical user interface for CHARMM Sunhwan Jo, Taehoon Kim, Vidyashankara Iyer et al. · Journal of Computational Chemistry | 19 Mar 2008 | 10,125 |
| 48 | ColabFold: making protein folding accessible to all Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki et al. · Nature Methods | 30 May 2022 | 10,120 |
| 49 | P ACKMOL : A package for building initial configurations for molecular dynamics simulations Leandro Martı́nez, Ricardo Andrade, Ernesto G. Birgin et al. · Journal of Computational Chemistry | 19 Feb 2009 | 9,884 |
| 50 | The Amber biomolecular simulation programs David Andrew Case, Thomas E. Cheatham, Tom Darden et al. · Journal of Computational Chemistry | 30 Sep 2005 | 9,778 |
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.