A citation-based method for searching scientific literature

Lei Xu, Huiyong Sun, Youyong Li, Junmei Wang, Tingjun Hou. J Phys Chem B 2013
Times Cited: 278







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



Times Cited
  Times     Co-cited
Similarity




Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring.
Huiyong Sun, Youyong Li, Mingyun Shen, Sheng Tian, Lei Xu, Peichen Pan, Yan Guan, Tingjun Hou. Phys Chem Chem Phys 2014
242
46


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
42

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
37


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
28

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
27

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
24

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
23

Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches.
Huiyong Sun, Lili Duan, Fu Chen, Hui Liu, Zhe Wang, Peichen Pan, Feng Zhu, John Z H Zhang, Tingjun Hou. Phys Chem Chem Phys 2018
96
22

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
21

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


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
18


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
204
15

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
14

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.
Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee,[...]. J Comput Chem 2003
14

Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power.
Zhe Wang, Huiyong Sun, Xiaojun Yao, Dan Li, Lei Xu, Youyong Li, Sheng Tian, Tingjun Hou. Phys Chem Chem Phys 2016
269
13

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.
Fu Chen, Huiyong Sun, Junmei Wang, Feng Zhu, Hui Liu, Zhe Wang, Tailong Lei, Youyong Li, Tingjun Hou. RNA 2018
32
40


The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling.
Jianing Li, Robert Abel, Kai Zhu, Yixiang Cao, Suwen Zhao, Richard A Friesner. Proteins 2011
332
12




Validation and use of the MM-PBSA approach for drug discovery.
Bernd Kuhn, Paul Gerber, Tanja Schulz-Gasch, Martin Stahl. J Med Chem 2005
293
11





Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes.
Richard A Friesner, Robert B Murphy, Matthew P Repasky, Leah L Frye, Jeremy R Greenwood, Thomas A Halgren, Paul C Sanschagrin, Daniel T Mainz. J Med Chem 2006
9

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
9


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
8

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
8

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
Lingle Wang, Yujie Wu, Yuqing Deng, Byungchan Kim, Levi Pierce, Goran Krilov, Dmitry Lupyan, Shaughnessy Robinson, Markus K Dahlgren, Jeremy Greenwood,[...]. J Am Chem Soc 2015
482
8

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.
Aaron Weis, Kambiz Katebzadeh, Pär Söderhjelm, Ingemar Nilsson, Ulf Ryde. J Med Chem 2006
184
7


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

Virtual screening using molecular simulations.
Tianyi Yang, Johnny C Wu, Chunli Yan, Yuanfeng Wang, Ray Luo, Michael B Gonzales, Kevin N Dalby, Pengyu Ren. Proteins 2011
109
7

Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA.
Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti, Miriam Sgobba. J Comput Chem 2010
332
7


Development and validation of a genetic algorithm for flexible docking.
G Jones, P Willett, R C Glen, A R Leach, R Taylor. J Mol Biol 1997
6

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.
Michael M Mysinger, Michael Carchia, John J Irwin, Brian K Shoichet. J Med Chem 2012
737
6

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
858
6



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.