A citation-based method for searching scientific literature

G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
Times Cited: 2164







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



Times Cited
  Times     Co-cited
Similarity


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
33

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
33

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
27

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
21

VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
15

A hierarchical approach to all-atom protein loop prediction.
Matthew P Jacobson, David L Pincus, Chaya S Rapp, Tyler J F Day, Barry Honig, David E Shaw, Richard A Friesner. Proteins 2004
14


Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules.
John C Shelley, Anuradha Cholleti, Leah L Frye, Jeremy R Greenwood, Mathew R Timlin, Makoto Uchimaya. J Comput Aided Mol Des 2007
834
10


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

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.
Jeremy R Greenwood, David Calkins, Arron P Sullivan, John C Shelley. J Comput Aided Mol Des 2010
424
8

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
8

On the role of the crystal environment in determining protein side-chain conformations.
Matthew P Jacobson, Richard A Friesner, Zhexin Xiang, Barry Honig. J Mol Biol 2002
611
8

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

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
7

OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.
Katarina Roos, Chuanjie Wu, Wolfgang Damm, Mark Reboul, James M Stevenson, Chao Lu, Markus K Dahlgren, Sayan Mondal, Wei Chen, Lingle Wang,[...]. J Chem Theory Comput 2019
289
7

PHASE: a novel approach to pharmacophore modeling and 3D database searching.
Steven L Dixon, Alexander M Smondyrev, Shashidhar N Rao. Chem Biol Drug Des 2006
338
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
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


PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results.
Steven L Dixon, Alexander M Smondyrev, Eric H Knoll, Shashidhar N Rao, David E Shaw, Richard A Friesner. J Comput Aided Mol Des 2006
635
6


Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
6

New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies.
Ramy Farid, Tyler Day, Richard A Friesner, Robert A Pearlstein. Bioorg Med Chem 2006
282
6

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
6

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
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


Prediction of drug solubility from structure.
William L Jorgensen, Erin M Duffy. Adv Drug Deliv Rev 2002
384
5

A new and rapid colorimetric determination of acetylcholinesterase activity.
G L ELLMAN, K D COURTNEY, V ANDRES, R M FEATHER-STONE. Biochem Pharmacol 1961
5

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
400
5

PubChem Substance and Compound databases.
Sunghwan Kim, Paul A Thiessen, Evan E Bolton, Jie Chen, Gang Fu, Asta Gindulyte, Lianyi Han, Jane He, Siqian He, Benjamin A Shoemaker,[...]. Nucleic Acids Res 2016
5

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
5

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

XDS.
Wolfgang Kabsch. Acta Crystallogr D Biol Crystallogr 2010
5

Phaser crystallographic software.
Airlie J McCoy, Ralf W Grosse-Kunstleve, Paul D Adams, Martyn D Winn, Laurent C Storoni, Randy J Read. J Appl Crystallogr 2007
5

Novel procedure for modeling ligand/receptor induced fit effects.
Woody Sherman, Tyler Day, Matthew P Jacobson, Richard A Friesner, Ramy Farid. J Med Chem 2006
5

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
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



Investigation of anticancer properties of caffeinated complexes via computational chemistry methods.
Koray Sayin, Ayhan Üngördü. Spectrochim Acta A Mol Biomol Spectrosc 2018
20
20

SwissParam: a fast force field generation tool for small organic molecules.
Vincent Zoete, Michel A Cuendet, Aurélien Grosdidier, Olivier Michielin. J Comput Chem 2011
765
4

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.
Rashmi Kumari, Rajendra Kumar, Andrew Lynn. J Chem Inf Model 2014
4

Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds.
Anh-Tien Ton, Francesco Gentile, Michael Hsing, Fuqiang Ban, Artem Cherkasov. Mol Inform 2020
218
4

A new coronavirus associated with human respiratory disease in China.
Fan Wu, Su Zhao, Bin Yu, Yan-Mei Chen, Wen Wang, Zhi-Gang Song, Yi Hu, Zhao-Wu Tao, Jun-Hua Tian, Yuan-Yuan Pei,[...]. Nature 2020
4

Novel method for generating structure-based pharmacophores using energetic analysis.
Noeris K Salam, Roberto Nuti, Woody Sherman. J Chem Inf Model 2009
187
4

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
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


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.