A citation-based method for searching scientific literature

Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
Times Cited: 1672







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



Times Cited
  Times     Co-cited
Similarity



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
39

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
37

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
22

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
21

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
19

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
17


End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
415
16

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
14

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
12



Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
10

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
9

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
9

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
9

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
Andreas W Götz, Mark J Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2012
9

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
8


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
7

Comparison of multiple Amber force fields and development of improved protein backbone parameters.
Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling. Proteins 2006
7


GLYCAM06: a generalizable biomolecular force field. Carbohydrates.
Karl N Kirschner, Austin B Yongye, Sarah M Tschampel, Jorge González-Outeiriño, Charlisa R Daniels, B Lachele Foley, Robert J Woods. J Comput Chem 2008
7

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.
Chuan Tian, Koushik Kasavajhala, Kellon A A Belfon, Lauren Raguette, He Huang, Angela N Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu,[...]. J Chem Theory Comput 2020
209
7



g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
6

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor.
Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder, Nadine Krüger, Tanja Herrler, Sandra Erichsen, Tobias S Schiergens, Georg Herrler, Nai-Huei Wu, Andreas Nitsche,[...]. Cell 2020
6

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
6

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.
Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl. J Chem Theory Comput 2008
6

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
6

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.
Mats H M Olsson, Chresten R Søndergaard, Michal Rostkowski, Jan H Jensen. J Chem Theory Comput 2011
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

Comparative Protein Structure Modeling Using MODELLER.
Benjamin Webb, Andrej Sali. Curr Protoc Bioinformatics 2016
6

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
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


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, Thomas A Halgren, Jasna J Klicic, Daniel T Mainz, Matthew P Repasky, Eric H Knoll, Mee Shelley, Jason K Perry,[...]. J Med Chem 2004
5

Molecular docking: a powerful approach for structure-based drug discovery.
Xuan-Yu Meng, Hong-Xing Zhang, Mihaly Mezei, Meng Cui. Curr Comput Aided Drug Des 2011
695
5


Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2.
Renhong Yan, Yuanyuan Zhang, Yaning Li, Lu Xia, Yingying Guo, Qiang Zhou. Science 2020
5

Open Babel: An open chemical toolbox.
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
5



Molecular properties that influence the oral bioavailability of drug candidates.
Daniel F Veber, Stephen R Johnson, Hung-Yuan Cheng, Brian R Smith, Keith W Ward, Kenneth D Kopple. J Med Chem 2002
5

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.
G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
4

Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods.
Canrong Wu, Yang Liu, Yueying Yang, Peng Zhang, Wu Zhong, Yali Wang, Qiqi Wang, Yang Xu, Mingxue Li, Xingzhou Li,[...]. Acta Pharm Sin B 2020
4

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
4


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.