A citation-based method for searching scientific literature

A Sali, T L Blundell. J Mol Biol 1993
Times Cited: 9622







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



Times Cited
  Times     Co-cited
Similarity


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
20

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
17


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
11

Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
11

GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
9

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
8

The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
8

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
8

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
8

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility.
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
7

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
7

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Fabian Sievers, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding,[...]. Mol Syst Biol 2011
6

The FoldX web server: an online force field.
Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano. Nucleic Acids Res 2005
6

Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
6

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
6

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
6



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
5

CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
5


ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
5



Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
4

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G C P van Zundert, J P G L M Rodrigues, M Trellet, C Schmitz, P L Kastritis, E Karaca, A S J Melquiond, M van Dijk, S J de Vries, A M J J Bonvin. J Mol Biol 2016
4


TM-align: a protein structure alignment algorithm based on the TM-score.
Yang Zhang, Jeffrey Skolnick. Nucleic Acids Res 2005
4

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
4

Inference of macromolecular assemblies from crystalline state.
Evgeny Krissinel, Kim Henrick. J Mol Biol 2007
4

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
4

Modeling of loops in protein structures.
A Fiser, R K Do, A Sali. Protein Sci 2000
4

All-atom empirical potential for molecular modeling and dynamics studies of proteins.
A D MacKerell, D Bashford, M Bellott, R L Dunbrack, J D Evanseck, M J Field, S Fischer, J Gao, H Guo, S Ha,[...]. J Phys Chem B 1998
4



Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
Jun Lan, Jiwan Ge, Jinfang Yu, Sisi Shan, Huan Zhou, Shilong Fan, Qi Zhang, Xuanling Shi, Qisheng Wang, Linqi Zhang,[...]. Nature 2020
4

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Daniel Wrapp, Nianshuang Wang, Kizzmekia S Corbett, Jory A Goldsmith, Ching-Lin Hsieh, Olubukola Abiona, Barney S Graham, Jason S McLellan. Science 2020
4

Improved protein structure prediction using predicted interresidue orientations.
Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker. Proc Natl Acad Sci U S A 2020
428
4



MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, Takashi Miyata. Nucleic Acids Res 2002
3

CD-HIT: accelerated for clustering the next-generation sequencing data.
Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, Weizhong Li. Bioinformatics 2012
3

Template-based protein structure modeling using the RaptorX web server.
Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu, Jinbo Xu. Nat Protoc 2012
964
3

PyMod 3: a complete suite for structural bioinformatics in PyMOL.
Giacomo Janson, Alessandro Paiardini. Bioinformatics 2021
20
15

Electrostatics of nanosystems: application to microtubules and the ribosome.
N A Baker, D Sept, S Joseph, M J Holst, J A McCammon. Proc Natl Acad Sci U S A 2001
3

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.
Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal. Nucleic Acids Res 2016
3

Anisotropy of fluctuation dynamics of proteins with an elastic network model.
A R Atilgan, S R Durell, R L Jernigan, M C Demirel, O Keskin, I Bahar. Biophys J 2001
3

Plasma Hsp90 levels in patients with systemic sclerosis and relation to lung and skin involvement: a cross-sectional and longitudinal study.
Hana Štorkánová, Sabína Oreská, Maja Špiritović, Barbora Heřmánková, Kristýna Bubová, Martin Komarc, Karel Pavelka, Jiří Vencovský, Jörg H W Distler, Ladislav Šenolt,[...]. Sci Rep 2021
3

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
438
3


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.