ArticleJournal of computer-aided molecular design2011
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Nested TMAPs to Visualize Billions of Molecules.Journal of chemical information and modeling · 2026Article
- MolCompass: multi-tool for the navigation in chemical space and visual validation of QSAR/QSPR models.Journal of cheminformatics · 2024Article
- One chiral fingerprint to find them all.Journal of cheminformatics · 2024Article
- Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization.Journal of cheminformatics · 2023Article
- AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection.Scientific reports · 2023Article
- Molecular Similarity Perception Based on Machine-Learning Models.International journal of molecular sciences · 2022Article
- Exploring the GDB-13 chemical space using deep generative models.Journal of cheminformatics · 2019Article
- Chemical space exploration guided by deep neural networks.RSC advances · 2019Article
- Getting the most out of PubChem for virtual screening.Expert opinion on drug discovery · 2016Review
- Integrated Computational Solution for Predicting Skin Sensitization Potential of Molecules.PloS one · 2016Article
- Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.Journal of cheminformatics · 2015Article
- Discovery of potent positive allosteric modulators of the α3β2 nicotinic acetylcholine receptor by a chemical space walk in ChEMBL.ACS chemical neuroscience · 2014Review
- Expanding the fragrance chemical space for virtual screening.Journal of cheminformatics · 2014Article
- Exploring chemical space for drug discovery using the chemical universe database.ACS chemical neuroscience · 2012Review
- Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments?BioEssays : news and reviews in molecular, cellular and developmental biology · 2012Article
- Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem.Journal of computer-aided molecular design · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The chemical universe database GDB-13, which enumerates 977 million organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules, represents a vast reservoir for new fragments. GDB-13 was classified using the MQN-system discussed in the preceding paper for the analysis of PubChem fragments. Two hundred and fifty-five subsets of GDB-13 were generated by the combinatorial use of eight restrictive criteria, including fragment-like ("rule of three") and scaffold-like (no acyclic carbon atoms) filters. Virtual screening for analogs of 15 commercial drugs of 13 non-hydrogen atoms or less shows that retrieving MQN-neighbors of a query molecule from GDB-13 or its subsets provides on average a 38-fold enrichment in structural analogs (Daylight-type substructure fingerprint Tanimoto T (SF) > 0.7), and a 75-fold enrichment in shape-similar analogs (ROCS TanimotoCombo score > 1.4). An MQN-searchable version of GDB-13 is provided at www.gdb.unibe.ch .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.