A citation-based method for searching scientific literature

Charles C David, Donald J Jacobs. Methods Mol Biol 2014
Times Cited: 270







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



Times Cited
  Times     Co-cited
Similarity


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
28


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

Essential dynamics of proteins.
A Amadei, A B Linssen, H J Berendsen. Proteins 1993
15


Bio3d: an R package for the comparative analysis of protein structures.
Barry J Grant, Ana P C Rodrigues, Karim M ElSawy, J Andrew McCammon, Leo S D Caves. Bioinformatics 2006
753
13

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
12

PRODRG: a tool for high-throughput crystallography of protein-ligand complexes.
Alexander W Schüttelkopf, Daan M F van Aalten. Acta Crystallogr D Biol Crystallogr 2004
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
11

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
10

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
10

The Amber biomolecular simulation programs.
David A Case, Thomas E Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J Woods. J Comput Chem 2005
10

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R Shirts, Jeremy C Smith, Peter M Kasson, David van der Spoel,[...]. Bioinformatics 2013
9


Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
7

Canonical sampling through velocity rescaling.
Giovanni Bussi, Davide Donadio, Michele Parrinello. J Chem Phys 2007
7

Current updates on computer aided protein modeling and designing.
Faez Iqbal Khan, Dong-Qing Wei, Ke-Ren Gu, Md Imtaiyaz Hassan, Shams Tabrez. Int J Biol Macromol 2016
58
12

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
7

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



Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
993
7

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng,[...]. Nature 2020
7



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

Principal component analysis for protein folding dynamics.
Gia G Maisuradze, Adam Liwo, Harold A Scheraga. J Mol Biol 2009
171
6



Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
P A Kollman, I Massova, C Reyes, B Kuhn, S Huo, L Chong, M Lee, T Lee, Y Duan, W Wang,[...]. Acc Chem Res 2000
6

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.
Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison. J Cheminform 2012
6

Molecular Dynamics Simulation for All.
Scott A Hollingsworth, Ron O Dror. Neuron 2018
206
6

Molecular dynamics simulations of biomolecules.
Martin Karplus, J Andrew McCammon. Nat Struct Biol 2002
6


Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d.
Hua Wan, Jian-ping Hu, Xu-hong Tian, Shan Chang. Phys Chem Chem Phys 2013
38
13


Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs.
Yun-Wei Dong, Ming-Ling Liao, Xian-Liang Meng, George N Somero. Proc Natl Acad Sci U S A 2018
74
6

Automatic atom type and bond type perception in molecular mechanical calculations.
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
5

Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII.
Faez Iqbal Khan, Mohd Shahbaaz, Krishna Bisetty, Abdul Waheed, William S Sly, Faizan Ahmad, Md Imtaiyaz Hassan. Gene 2016
51
9


Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Paul Shannon, Andrew Markiel, Owen Ozier, Nitin S Baliga, Jonathan T Wang, Daniel Ramage, Nada Amin, Benno Schwikowski, Trey Ideker. Genome Res 2003
5

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
5

LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
Roman A Laskowski, Mark B Swindells. J Chem Inf Model 2011
5


GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
Tai-Sung Lee, David S Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J Giese, Adrian Roitberg, David A Case, Ross C Walker, Darrin M York. J Chem Inf Model 2018
94
5



ProDy: protein dynamics inferred from theory and experiments.
Ahmet Bakan, Lidio M Meireles, Ivet Bahar. Bioinformatics 2011
521
4

Structure prediction and functional analyses of a thermostable lipase obtained from Shewanella putrefaciens.
Faez Iqbal Khan, Bilal Nizami, Razique Anwer, Ke-Ren Gu, Krishna Bisetty, Md Imtaiyaz Hassan, Dong-Qing Wei. J Biomol Struct Dyn 2017
23
17

Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus.
Vashni Gramany, Faez Iqbal Khan, Algasan Govender, Krishna Bisetty, Suren Singh, Kugenthiren Permaul. J Biomol Struct Dyn 2016
30
13


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.