Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments

By M. Sastry, Jeffrey F. Lowrie, Steve Dixon, Woody Sherman. 2010

324 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Spectroscopy, Computational Chemistry & Drug Discovery

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Citations in the corpus

Molecular Docking and Structure-Based Drug Design Strategies (2015, background): “Converting the original files requires the correct assignment of stereochemistry, partial charges, and ionization states [174].”
Molecular fingerprint similarity search in virtual screening. (2015, background): “In general, fingerprints with longer bit strings have been found to perform better at similarity searching, because of increased amount of stored information (due to a reduction of bit collision for hashed fingerprints) [39].”
In silico evaluation of highly efficient organic light-emitting materials (2016, methodology): “To maximize both the model building and the analysis procedure, dendritic fingerprint [16-18] was used as a sole 2D-structure descriptor.”
Open-source platform to benchmark fingerprints for ligand-based virtual screening (2013, methodology): “One of the first collections used in multiple benchmarking studies was data for eleven targets taken from the MDL Drug Data Report (MDDR) [13,15,17-21] However, the MDDR, a commercial product, places limits on redistribution of the data, hindering the development of an open validation set.”
Comparing structural fingerprints using a literature-based similarity benchmark (2016, methodology): “Sastry et al. [18] also looked at 11 targets from the MDDR and found that a radial fingerprint (which they identify as synonymous with ECFP, although different atom types may be used) was among the top three (Molprint2D and a dendritic fingerprint were better).”
D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies (2017, background): “…of the challenge, the PDB included co-crystal structures of FXR with ligands similar to the benzimidazoles in the challenge set, as well as to ligands FXR 5 and 34 (Canvas Tanimoto coefficient of up to 0.94 [33, 34]), whereas the similarities were below 0.3 for the remaining ligands (Table S1).”
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information (2011, unknown): “outperform other fingerprinting algorithms in enrichment [61, 62].”