A citation-based method for searching scientific literature

O S Smart, J G Neduvelil, X Wang, B A Wallace, M S Sansom. J Mol Graph 1996
Times Cited: 1001







List of co-cited articles
631 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
48

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
38

New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
36

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
36

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
34

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
32


CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
22

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Paul D Adams, Pavel V Afonine, Gábor Bunkóczi, Vincent B Chen, Ian W Davis, Nathaniel Echols, Jeffrey J Headd, Li-Wei Hung, Gary J Kapral, Ralf W Grosse-Kunstleve,[...]. Acta Crystallogr D Biol Crystallogr 2010
20

MolProbity: all-atom structure validation for macromolecular crystallography.
Vincent B Chen, W Bryan Arendall, Jeffrey J Headd, Daniel A Keedy, Robert M Immormino, Gary J Kapral, Laura W Murray, Jane S Richardson, David C Richardson. Acta Crystallogr D Biol Crystallogr 2010
17

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
17

CHARMM36m: an improved force field for folded and intrinsically disordered proteins.
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig, Bert L de Groot, Helmut Grubmüller, Alexander D MacKerell. Nat Methods 2017
17

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.
Jeffery B Klauda, Richard M Venable, J Alfredo Freites, Joseph W O'Connor, Douglas J Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D MacKerell, Richard W Pastor. J Phys Chem B 2010
17

Coot: model-building tools for molecular graphics.
Paul Emsley, Kevin Cowtan. Acta Crystallogr D Biol Crystallogr 2004
16

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.
Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable,[...]. J Comput Chem 2014
16

Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams. Acta Crystallogr D Struct Biol 2018
924
14

UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
14

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
13


Quantifying the local resolution of cryo-EM density maps.
Alp Kucukelbir, Fred J Sigworth, Hemant D Tagare. Nat Methods 2014
11

MolProbity: More and better reference data for improved all-atom structure validation.
Christopher J Williams, Jeffrey J Headd, Nigel W Moriarty, Michael G Prisant, Lizbeth L Videau, Lindsay N Deis, Vishal Verma, Daniel A Keedy, Bradley J Hintze, Vincent B Chen,[...]. Protein Sci 2018
11


Scalable molecular dynamics with NAMD.
James C Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D Skeel, Laxmikant Kalé, Klaus Schulten. J Comput Chem 2005
10

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
10

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
Robert B Best, Xiao Zhu, Jihyun Shim, Pedro E M Lopes, Jeetain Mittal, Michael Feig, Alexander D Mackerell. J Chem Theory Comput 2012
10


CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter K Eastman, Justin A Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,[...]. J Chem Theory Comput 2016
10

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
9

SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse, Martino Bertoni, Stefan Bienert, Gabriel Studer, Gerardo Tauriello, Rafal Gumienny, Florian T Heer, Tjaart A P de Beer, Christine Rempfer, Lorenza Bordoli,[...]. Nucleic Acids Res 2018
9

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.
Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum,[...]. Commun Biol 2019
402
9

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
9

CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.
Sunhwan Jo, Joseph B Lim, Jeffery B Klauda, Wonpil Im. Biophys J 2009
908
8


CHARMM: the biomolecular simulation program.
B R Brooks, C L Brooks, A D Mackerell, L Nilsson, R J Petrella, B Roux, Y Won, G Archontis, C Bartels, S Boresch,[...]. J Comput Chem 2009
8

Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C Phillips, David J Hardy, Julio D C Maia, John E Stone, João V Ribeiro, Rafael C Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang,[...]. J Chem Phys 2020
554
7

electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation.
Nigel W Moriarty, Ralf W Grosse-Kunstleve, Paul D Adams. Acta Crystallogr D Biol Crystallogr 2009
719
7

Screening and large-scale expression of membrane proteins in mammalian cells for structural studies.
April Goehring, Chia-Hsueh Lee, Kevin H Wang, Jennifer Carlisle Michel, Derek P Claxton, Isabelle Baconguis, Thorsten Althoff, Suzanne Fischer, K Christopher Garcia, Eric Gouaux. Nat Protoc 2014
325
7


Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs.
Arvind Kumar, Sandip Basak, Shanlin Rao, Yvonne Gicheru, Megan L Mayer, Mark S P Sansom, Sudha Chakrapani. Nat Commun 2020
38
18


EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.
Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, James S Fraser. Nat Methods 2015
486
6

PHENIX: building new software for automated crystallographic structure determination.
Paul D Adams, Ralf W Grosse-Kunstleve, Li Wei Hung, Thomas R Ioerger, Airlie J McCoy, Nigel W Moriarty, Randy J Read, James C Sacchettini, Nicholas K Sauter, Thomas C Terwilliger. Acta Crystallogr D Biol Crystallogr 2002
6

The pore dimensions of gramicidin A.
O S Smart, J M Goodfellow, B A Wallace. Biophys J 1993
473
6

MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, Oliver Beckstein. J Comput Chem 2011
6

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.
K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, E Darian, O Guvench, P Lopes, I Vorobyov,[...]. J Comput Chem 2010
6

GABAA receptor signalling mechanisms revealed by structural pharmacology.
Simonas Masiulis, Rooma Desai, Tomasz Uchański, Itziar Serna Martin, Duncan Laverty, Dimple Karia, Tomas Malinauskas, Jasenko Zivanov, Els Pardon, Abhay Kotecha,[...]. Nature 2019
233
6

Cryo-EM structure of the human α1β3γ2 GABAA receptor in a lipid bilayer.
Duncan Laverty, Rooma Desai, Tomasz Uchański, Simonas Masiulis, Wojciech J Stec, Tomas Malinauskas, Jasenko Zivanov, Els Pardon, Jan Steyaert, Keith W Miller,[...]. Nature 2019
166
6

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.
Jasenko Zivanov, Takanori Nakane, Sjors H W Scheres. IUCrJ 2019
336
6

Collaboration gets the most out of software.
Andrew Morin, Ben Eisenbraun, Jason Key, Paul C Sanschagrin, Michael A Timony, Michelle Ottaviano, Piotr Sliz. Elife 2013
548
6

TRPV1 structures in distinct conformations reveal activation mechanisms.
Erhu Cao, Maofu Liao, Yifan Cheng, David Julius. Nature 2013
679
5


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.