Comparative study of several algorithms for flexible ligand docking
By B. Bursulaya, Maxim Totrov, Ruben Abagyan, Charles L. Brooks III. J. Comput. Aided Mol. Des., 2003
341 citations recorded by the source corpus.
Subfields: Computational Theory and Mathematics, Organic Chemistry
View Paper: https://www.semanticscholar.org/paper/e9f8c99d3a2cfc4080dbcaad8f9fba409497676d
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In Computational Theory and Mathematics
- Shengyou Huang
- Xiaoqin Zou
- Vincent Zoete
- Olivier Michielin
- Jacob D. Durrant
- James Andrew McCammon
- Aurélien Grosdidier
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In Organic Chemistry
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- Jacob D. Durrant
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- Pedro Alexandrino Fernandes
- Maria João Ramos
- Vincent Zoete
Citations in the corpus
- Advances and Challenges in Protein-Ligand Docking (2010, background): “Although many comparison studies for docking and scoring have been published [158–166], publicly available docking benchmarks such as DUD (http://dud.”
- EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization (2007, background): “38 They are presented in Table I.”
- Comparing protein–ligand docking programs is difficult (2005, background): “Similar problems can arise if the initial coordinates are modified so that the ligand center of geometry coincides with that observed in the crystal structure.(16) Also, most docking programs keep ligand valence angles fixed, which can cause problems.”
- Software for molecular docking: a review (2017, background): “FlexX, GOLD, and ICM, respectively (Bursulaya et al. 2003).”
- Protein–ligand docking: Current status and future challenges (2006, methodology): “Verdonk et al.78 have implemented a novel approach to score water mediation and displacement in the docking program GOLD.”
- Structural Basis for Ligand Recognition and Functional Selectivity at Angiotensin Receptor*♦ (2015, methodology): “rescored using the ICM binding score function (24, 25) calculated as shown in Equation 1,”
- AutoGrow: A Novel Algorithm for Protein Inhibitor Design (2009, methodology): “As ADT 1.5.2 does not assign hydrogen atoms to water molecules, the system was processed with ICM (Molsoft), which added hydrogen atoms to the protein and to the water oxygen atoms, appropriately protonated histidines, flipped certain protein amide groups, and corrected terminal phase angles.”