A citation-based method for searching scientific literature

Seung-gu Kang, Payel Das, Scott J McGrane, Alan J Martin, Tien Huynh, Ajay K Royyuru, Andrew J Taylor, Paul G Jones, Ruhong Zhou. J Phys Chem B 2014
Times Cited: 2







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



Times Cited
  Times     Co-cited
Similarity


Fragment-based drug discovery using a multidomain, parallel MD-MM/PBSA screening protocol.
Tian Zhu, Hyun Lee, Hao Lei, Christopher Jones, Kavankumar Patel, Michael E Johnson, Kirk E Hevener. J Chem Inf Model 2013
15
50



Best practices in free energy calculations for drug design.
Michael R Shirts. Methods Mol Biol 2012
25
50


Alchemical free energy methods for drug discovery: progress and challenges.
John D Chodera, David L Mobley, Michael R Shirts, Richard W Dixon, Kim Branson, Vijay S Pande. Curr Opin Struct Biol 2011
325
50

Structural and enzymatic analyses reveal the binding mode of a novel series of Francisella tularensis enoyl reductase (FabI) inhibitors.
Shahila Mehboob, Kirk E Hevener, Kent Truong, Teuta Boci, Bernard D Santarsiero, Michael E Johnson. J Med Chem 2012
17
50


Thermodynamic integration to predict host-guest binding affinities.
Morgan Lawrenz, Jeff Wereszczynski, Juan Manuel Ortiz-Sánchez, Sara E Nichols, J Andrew McCammon. J Comput Aided Mol Des 2012
16
50



R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.
Enguerran Vanquelef, Sabrina Simon, Gaelle Marquant, Elodie Garcia, Geoffroy Klimerak, Jean Charles Delepine, Piotr Cieplak, François-Yves Dupradeau. Nucleic Acids Res 2011
403
50

Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package.
Joseph W Kaus, Levi T Pierce, Ross C Walker, J Andrew McCammont. J Chem Theory Comput 2013
71
50


Metabolism-directed structure optimization of benzimidazole-based Francisella tularensis enoyl-reductase (FabI) inhibitors.
Yan-Yan Zhang, Yong Liu, Shahila Mehboob, Jin-Hua Song, Teuta Boci, Michael E Johnson, Arun K Ghosh, Hyunyoung Jeong. Xenobiotica 2014
4
50

Halogen atoms in the modern medicinal chemistry: hints for the drug design.
Marcelo Zaldini Hernandes, Suellen Melo T Cavalcanti, Diogo Rodrigo M Moreira, Walter Filgueira de Azevedo Junior, Ana Cristina Lima Leite. Curr Drug Targets 2010
292
50


Towards accurate free energy calculations in ligand protein-binding studies.
Thomas Steinbrecher, Andreas Labahn. Curr Med Chem 2010
100
50


Ab initio calculations on halogen-bonded complexes and comparison with density functional methods.
Yun-Xiang Lu, Jian-Wei Zou, Ji-Cai Fan, Wen-Na Zhao, Yong-Jun Jiang, Qing-Sen Yu. J Comput Chem 2009
49
50

A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.
Paulius Mikulskis, Samuel Genheden, Ulf Ryde. J Chem Inf Model 2014
48
50

A medicinal chemist's guide to molecular interactions.
Caterina Bissantz, Bernd Kuhn, Martin Stahl. J Med Chem 2010
781
50

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
348
50

A polarizable ellipsoidal force field for halogen bonds.
Likai Du, Jun Gao, Fuzhen Bi, Lili Wang, Chengbu Liu. J Comput Chem 2013
18
50

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.
Samuel Genheden, Ingemar Nilsson, Ulf Ryde. J Chem Inf Model 2011
55
50

Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching.
Kirk E Hevener, Shahila Mehboob, Pin-Chih Su, Kent Truong, Teuta Boci, Jiangping Deng, Mahmood Ghassemi, James L Cook, Michael E Johnson. J Med Chem 2012
47
50

Calculation of binding free energies of inhibitors to plasmepsin II.
Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F van Gunsteren. J Comput Chem 2011
18
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
50



Tularemia: current diagnosis and treatment options.
Matthew J Hepburn, Andrew J H Simpson. Expert Rev Anti Infect Ther 2008
64
50

Lambda-dynamics free energy simulation methods.
Jennifer L Knight, Charles L Brooks. J Comput Chem 2009
116
50

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.
Frithjof Godschalk, Samuel Genheden, Pär Söderhjelm, Ulf Ryde. Phys Chem Chem Phys 2013
39
50


The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.
François-Yves Dupradeau, Adrien Pigache, Thomas Zaffran, Corentin Savineau, Rodolphe Lelong, Nicolas Grivel, Dimitri Lelong, Wilfried Rosanski, Piotr Cieplak. Phys Chem Chem Phys 2010
496
50






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
50

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
50

Let's get honest about sampling.
David L Mobley. J Comput Aided Mol Des 2012
59
50

Efficient discovery of potent anti-HIV agents targeting the Tyr181Cys variant of HIV reverse transcriptase.
William L Jorgensen, Mariela Bollini, Vinay V Thakur, Robert A Domaoal, Krasimir A Spasov, Karen S Anderson. J Am Chem Soc 2011
46
50

Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context.
Nadine Homeyer, Friederike Stoll, Alexander Hillisch, Holger Gohlke. J Chem Theory Comput 2014
85
50

Structural and biological evaluation of a novel series of benzimidazole inhibitors of Francisella tularensis enoyl-ACP reductase (FabI).
Shahila Mehboob, Jinhua Song, Kirk E Hevener, Pin-Chih Su, Teuta Boci, Libby Brubaker, Lena Truong, Tina Mistry, Jiangping Deng, James L Cook,[...]. Bioorg Med Chem Lett 2015
14
50

Perspective: Alchemical free energy calculations for drug discovery.
David L Mobley, Pavel V Klimovich. J Chem Phys 2012
114
50

Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations.
Thomas Steinbrecher, InSuk Joung, David A Case. J Comput Chem 2011
110
50




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.