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
Times Cited: 651
Times Cited: 651
Times Cited
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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
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
51
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
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
35
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.
Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
24
CHARMM-GUI: a web-based graphical user interface for CHARMM.
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im. J Comput Chem 2008
24
CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.
Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable,[...]. J Comput Chem 2014
Emilia L Wu, Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable,[...]. J Comput Chem 2014
16
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
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
16
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
Oleg Trott, Arthur J Olson. J Comput Chem 2010
Oleg Trott, Arthur J Olson. J Comput Chem 2010
15
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
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
14
New ways to boost molecular dynamics simulations.
Elmar Krieger, Gert Vriend. J Comput Chem 2015
Elmar Krieger, Gert Vriend. J Comput Chem 2015
13
OPM database and PPM web server: resources for positioning of proteins in membranes.
Mikhail A Lomize, Irina D Pogozheva, Hyeon Joo, Henry I Mosberg, Andrei L Lomize. Nucleic Acids Res 2012
Mikhail A Lomize, Irina D Pogozheva, Hyeon Joo, Henry I Mosberg, Andrei L Lomize. Nucleic Acids Res 2012
12
CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.
Sunhwan Jo, Joseph B Lim, Jeffery B Klauda, Wonpil Im. Biophys J 2009
Sunhwan Jo, Joseph B Lim, Jeffery B Klauda, Wonpil Im. Biophys J 2009
12
Fast empirical pKa prediction by Ewald summation.
Elmar Krieger, Jens E Nielsen, Chris A E M Spronk, Gert Vriend. J Mol Graph Model 2006
Elmar Krieger, Jens E Nielsen, Chris A E M Spronk, Gert Vriend. J Mol Graph Model 2006
11
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
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
10
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
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
10
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
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
Automated builder and database of protein/membrane complexes for molecular dynamics simulations.
Sunhwan Jo, Taehoon Kim, Wonpil Im. PLoS One 2007
Sunhwan Jo, Taehoon Kim, Wonpil Im. PLoS One 2007
9
Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.
Jeffery B Klauda, Richard M Venable, J Alfredo Freites, Joseph W O'Connor, Douglas J Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D MacKerell, Richard W Pastor. J Phys Chem B 2010
Jeffery B Klauda, Richard M Venable, J Alfredo Freites, Joseph W O'Connor, Douglas J Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D MacKerell, Richard W Pastor. J Phys Chem B 2010
8
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.
In Suk Joung, Thomas E Cheatham. J Phys Chem B 2008
In Suk Joung, Thomas E Cheatham. J Phys Chem B 2008
7
Comparative protein modelling by satisfaction of spatial restraints.
A Sali, T L Blundell. J Mol Biol 1993
A Sali, T L Blundell. J Mol Biol 1993
7
H++: a server for estimating pKas and adding missing hydrogens to macromolecules.
John C Gordon, Jonathan B Myers, Timothy Folta, Valia Shoja, Lenwood S Heath, Alexey Onufriev. Nucleic Acids Res 2005
John C Gordon, Jonathan B Myers, Timothy Folta, Valia Shoja, Lenwood S Heath, Alexey Onufriev. Nucleic Acids Res 2005
7
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.
Lee, Yang, Parr. Phys Rev B Condens Matter 1988
Lee, Yang, Parr. Phys Rev B Condens Matter 1988
7
LIPID11: a modular framework for lipid simulations using amber.
Åge A Skjevik, Benjamin D Madej, Ross C Walker, Knut Teigen. J Phys Chem B 2012
Åge A Skjevik, Benjamin D Madej, Ross C Walker, Knut Teigen. J Phys Chem B 2012
7
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2.
Rajib Islam, Md Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md Sajjadur Rahman, Abdulla Al Mamun, Md Nayeem Hossain, Md Ackas Ali, Mohammad A Halim. J Biomol Struct Dyn 2021
Rajib Islam, Md Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md Sajjadur Rahman, Abdulla Al Mamun, Md Nayeem Hossain, Md Ackas Ali, Mohammad A Halim. J Biomol Struct Dyn 2021
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
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
MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.
Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, Oliver Beckstein. J Comput Chem 2011
Naveen Michaud-Agrawal, Elizabeth J Denning, Thomas B Woolf, Oliver Beckstein. J Comput Chem 2011
6
Improved side-chain torsion potentials for the Amber ff99SB protein force field.
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
Kresten Lindorff-Larsen, Stefano Piana, Kim Palmo, Paul Maragakis, John L Klepeis, Ron O Dror, David E Shaw. Proteins 2010
6
MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
6
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.
Ramu Anandakrishnan, Boris Aguilar, Alexey V Onufriev. Nucleic Acids Res 2012
Ramu Anandakrishnan, Boris Aguilar, Alexey V Onufriev. Nucleic Acids Res 2012
6
GROMACS: fast, flexible, and free.
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
David Van Der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E Mark, Herman J C Berendsen. J Comput Chem 2005
5
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
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
Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang. J Chem Inf Model 2011
Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang. J Chem Inf Model 2011
5
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
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
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
5
MCPB.py: A Python Based Metal Center Parameter Builder.
Pengfei Li, Kenneth M Merz. J Chem Inf Model 2016
Pengfei Li, Kenneth M Merz. J Chem Inf Model 2016
5
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.
Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter K Eastman, Justin A Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,[...]. J Chem Theory Comput 2016
Jumin Lee, Xi Cheng, Jason M Swails, Min Sun Yeom, Peter K Eastman, Justin A Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi,[...]. J Chem Theory Comput 2016
5
Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.
Elmar Krieger, Roland L Dunbrack, Rob W W Hooft, Barbara Krieger. Methods Mol Biol 2012
Elmar Krieger, Roland L Dunbrack, Rob W W Hooft, Barbara Krieger. Methods Mol Biol 2012
5
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
Andreas W Götz, Mark J Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2012
5
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
Araz Jakalian, David B Jack, Christopher I Bayly. J Comput Chem 2002
Araz Jakalian, David B Jack, Christopher I Bayly. J Comput Chem 2002
5
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.
Stefan Grimme, Jens Antony, Stephan Ehrlich, Helge Krieg. J Chem Phys 2010
Stefan Grimme, Jens Antony, Stephan Ehrlich, Helge Krieg. J Chem Phys 2010
5
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein-Lipid-Bilayer System Building.
Stephan Schott-Verdugo, Holger Gohlke. J Chem Inf Model 2019
Stephan Schott-Verdugo, Holger Gohlke. J Chem Inf Model 2019
13
Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.
R J Loncharich, B R Brooks, R W Pastor. Biopolymers 1992
R J Loncharich, B R Brooks, R W Pastor. Biopolymers 1992
5
Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.
Elmar Krieger, Günther Koraimann, Gert Vriend. Proteins 2002
Elmar Krieger, Günther Koraimann, Gert Vriend. Proteins 2002
5
5
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.
Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst,[...]. J Chem Theory Comput 2019
Jumin Lee, Dhilon S Patel, Jonas Ståhle, Sang-Jun Park, Nathan R Kern, Seonghoon Kim, Joonseong Lee, Xi Cheng, Miguel A Valvano, Otto Holst,[...]. J Chem Theory Comput 2019
5
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
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
4
Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation.
Md Jahirul Islam, Akib Mahmud Khan, Md Rimon Parves, Md Nayeem Hossain, Mohammad A Halim. Sci Rep 2019
Md Jahirul Islam, Akib Mahmud Khan, Md Rimon Parves, Md Nayeem Hossain, Mohammad A Halim. Sci Rep 2019
18
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
G Jones, P Willett, R C Glen, A R Leach, R Taylor. J Mol Biol 1997
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
Chaolin Huang, Yeming Wang, Xingwang Li, Lili Ren, Jianping Zhao, Yi Hu, Li Zhang, Guohui Fan, Jiuyang Xu, Xiaoying Gu,[...]. Lancet 2020
4
Making optimal use of empirical energy functions: force-field parameterization in crystal space.
Elmar Krieger, Tom Darden, Sander B Nabuurs, Alexei Finkelstein, Gert Vriend. Proteins 2004
Elmar Krieger, Tom Darden, Sander B Nabuurs, Alexei Finkelstein, Gert Vriend. Proteins 2004
4
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