The "receiving" molecule, most commonly a protein or other biopolymer.
Ligand or guest or key
The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer.
Docking
Computational simulation of a candidate ligand binding to a receptor.
Binding mode
The orientation of the ligand relative to the receptor as well as the conformation of the ligand and receptor when bound to each other.
Pose
A candidate binding mode.
Scoring
The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts.
Ranking
The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding.
Docking assessment (DA)
Procedure to quantify the predictive capability of a docking protocol.
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In the fields of computational chemistry and molecular modelling, scoring functions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor.[1] Scoring functions have also been developed to predict the strength of intermolecular interactions between two proteins[2] or between protein and DNA.[3]
^Jain AN (October 2006). "Scoring functions for protein-ligand docking". Current Protein & Peptide Science. 7 (5): 407–20. doi:10.2174/138920306778559395. PMID 17073693.
^Robertson TA, Varani G (February 2007). "An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure". Proteins. 66 (2): 359–74. doi:10.1002/prot.21162. PMID 17078093. S2CID 24437518.
and 23 Related for: Scoring functions for docking information
scoringfunctions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Most...
approach fordocking. Utilizing a knowledge-based scoring scheme, it is categorized as a flexible docking method. In performance evaluations, LeDock demonstrated...
organism. Docking itself only produces plausible candidate structures. These candidates must be ranked using methods such as scoringfunctions to identify...
Lead Finder's specialization in ligand docking and binding energy estimation is a result of its advanced docking algorithm and the precision with which...
The program UCSF DOCK was created in the 1980s by Irwin "Tack" Kuntz's Group, and was the first docking program. DOCK uses geometric algorithms to predict...
case of protein docking, the search space consists of all possible orientations of the protein with respect to the ligand. Flexible docking in addition considers...
prediction, statistical potentials or knowledge-based potentials are scoringfunctions derived from an analysis of known protein structures in the Protein...
techniques include molecular docking, structure-based pharmacophore prediction, and molecular dynamics simulations. Molecular docking is the most used structure-based...
for improving enrichment and effectively mining potential candidates: Consensus scoring Selecting candidates by voting of multiple scoringfunctions May...
Maran U (January 2010). "Drug efficiency indices for improvement of molecular dockingscoringfunctions". Journal of Computational Chemistry. 31 (1): 174–84...
are compiled as high-quality data sets of protein-ligand complexes fordocking/scoring studies. Wang R, Fang X, Lu Y, Yang CY, Wang S (2005). "The PDBbind...
of drug-like molecular properties, weak scoringfunctions, or insufficient docking strategies hinder the docking process. Hence, the literature has described...
rDock (previously RiboDock) is an open-source molecular docking software that be used fordocking small molecules against proteins and nucleic acids. It...
to an hour and re-titled The Alfred Hitchcock Hour. Originally scheduled for November 22, 1963, but delayed due to the assassination of John F. Kennedy...
FlexAID is a molecular docking software that can use small molecules and peptides as ligands and proteins and nucleic acids as docking targets. As the name...
the hull, causing Janessa to die in the vacuum. A power failure with the docking door forces Brodski to go outside in an EVA suit to fix it. To distract...
Mercury. These Gemini missions went on to prove techniques for orbital rendezvous and docking crucial to a crewed lunar landing mission profile. After the...
starfighter destroyed: 100 S: For each unit of stardate that has passed: minus 1 D: Each time the player's ship is docked to a starbase for refueling and repairs:...
Nigelladine A as the most promising compound for SARS-CoV-2 inhibition with the highest dockingscoresfor the spike protein and Mpro. Thymoquinone is...
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