A citation-based method for searching scientific literature

Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
Times Cited: 2605







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



Times Cited
  Times     Co-cited
Similarity


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
50

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
36

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
35

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
28

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
22

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
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
17

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
15

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

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
12

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
12



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
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
954
8

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
7



Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.
Jianyin Shao, Stephen W Tanner, Nephi Thompson, Thomas E Cheatham. J Chem Theory Comput 2007
511
7

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
7

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

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
845
6

A modified TIP3P water potential for simulation with Ewald summation.
Daniel J Price, Charles L Brooks. J Chem Phys 2004
510
6


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
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

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
Thomas A Halgren, Robert B Murphy, Richard A Friesner, Hege S Beard, Leah L Frye, W Thomas Pollard, Jay L Banks. J Med Chem 2004
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
5

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Edward Harder, Wolfgang Damm, Jon Maple, Chuanjie Wu, Mark Reboul, Jin Yu Xiang, Lingle Wang, Dmitry Lupyan, Markus K Dahlgren, Jennifer L Knight,[...]. J Chem Theory Comput 2016
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
128
5

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
339
5

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
5

Langevin thermostat for rigid body dynamics.
Ruslan L Davidchack, Richard Handel, M V Tretyakov. J Chem Phys 2009
82
4

Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.
Yinglong Miao, William Sinko, Levi Pierce, Denis Bucher, Ross C Walker, J Andrew McCammon. J Chem Theory Comput 2014
201
4

Lipid14: The Amber Lipid Force Field.
Callum J Dickson, Benjamin D Madej, Age A Skjevik, Robin M Betz, Knut Teigen, Ian R Gould, Ross C Walker. J Chem Theory Comput 2014
651
4

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.
Yinglong Miao, Victoria A Feher, J Andrew McCammon. J Chem Theory Comput 2015
255
4

ZINC 15--Ligand Discovery for Everyone.
Teague Sterling, John J Irwin. J Chem Inf Model 2015
4

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
4

Lead- and drug-like compounds: the rule-of-five revolution.
Christopher A Lipinski. Drug Discov Today Technol 2004
4

Stereochemistry of polypeptide chain configurations.
G N RAMACHANDRAN, C RAMAKRISHNAN, V SASISEKHARAN. J Mol Biol 1963
4



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
144
4

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
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

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
4

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
4

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