Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.1c01378
Abstract: The set of chemical compounds shared by two or more chemical libraries is assessed routinely as means of comparing these libraries for various applications. Traditionally this is achieved by comparing the members of the chemical… read more here.
Keywords: comparison combinatorial; fragment spaces; chemical libraries; combinatorial fragment ... See more keywords
Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries
Sign Up to like & getrecommendations! Published in 2025 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.4c01980
Abstract: The screening of chemical libraries is an essential starting point in the drug discovery process. While some researchers desire a more thorough screening of drug targets against a narrower scope of molecules, it is not… read more here.
Keywords: chemical; chemical libraries; python package; dedenser python ... See more keywords
ROSHAMBO2: Accelerating Molecular Alignment for Large Chemical Libraries with GPU Optimization and Algorithmic Advances
Sign Up to like & getrecommendations! Published in 2025 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.5c01322
Abstract: Molecular alignment and 3D similarity are crucial tasks in computational drug discovery, enabling applications such as virtual screening and pharmacophore modeling. ROSHAMBO, an open-source package for optimizing molecular alignment using Gaussian volume overlaps, demonstrated near-state-of-the-art… read more here.
Keywords: virtual screening; chemical libraries; molecular alignment; alignment ... See more keywords
On-DNA Synthesis of Functionalized 4H-Pyran Scaffolds for Focused DNA-Encoded Chemical Libraries.
Sign Up to like & getrecommendations! Published in 2022 at "Organic letters"
DOI: 10.1021/acs.orglett.2c02714
Abstract: The functionalized 4H-pyran scaffold has aroused synthetic attention because it is widely found in many interesting pharmacologically relevant compounds. We here disclose its incorporation into DNA-encoded chemical libraries, combining this scaffold with the merits of… read more here.
Keywords: encoded chemical; dna; chemical libraries; dna encoded ... See more keywords
Multicomponent DNA-Compatible Synthesis of an Annelated Benzodiazepine Scaffold for Focused Chemical Libraries.
Sign Up to like & getrecommendations! Published in 2023 at "Organic letters"
DOI: 10.1021/acs.orglett.2c04293
Abstract: Annelated benzodiazepines are attractive drug-like scaffolds with a broad spectrum of biological activities. Incorporation of this heterocyclic core into DNA-encoded chemical libraries (DELs) via multicomponent assembly is highly demanded. Herein, we developed a DNA-compatible method… read more here.
Keywords: dna; dna compatible; chemical libraries; benzodiazepine ... See more keywords
Functional Annotation of Chemical Libraries across Diverse Biological Processes
Sign Up to like & getrecommendations! Published in 2017 at "Nature chemical biology"
DOI: 10.1038/nchembio.2436
Abstract: Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells to a compound, revealing chemical-genetic interactions that can elucidate a compound’s mode of action. We developed… read more here.
Keywords: annotation chemical; functional annotation; chemical genetic; biological processes ... See more keywords
Universal encoding of next generation DNA-encoded chemical libraries
Sign Up to like & getrecommendations! Published in 2022 at "Chemical Science"
DOI: 10.1039/d1sc05721a
Abstract: DNA-encoded chemical libraries (DELs) are useful tools for the discovery of small molecule ligands to protein targets of pharmaceutical interest. Compared with single-pharmacophore DELs, dual-pharmacophore DELs simultaneously display two chemical moieties on both DNA strands,… read more here.
Keywords: encoded chemical; dna; encoding next; chemical libraries ... See more keywords
Similarity based functionalization for enumeration of synthetically plausible chemical libraries surrounding a target
Sign Up to like & getrecommendations! Published in 2024 at "Chemical Science"
DOI: 10.1039/d4sc00523f
Abstract: Functionalization of lead compounds to create analogs is a challenging step in discovering new molecules with desired properties and it is conducted throughout the chemical industry, including pharmaceuticals and agrochemicals. The process can be time-consuming… read more here.
Keywords: chemical; chemical libraries; functionalization; libraries surrounding ... See more keywords
DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking)
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab771
Abstract: SUMMARY Deep learning (DL) can significantly accelerate virtual screening of ultra-large chemical libraries, enabling the evaluation of billions of compounds at a fraction of the computational cost and time required by conventional docking. Here we… read more here.
Keywords: deep learning; chemical libraries; gui graphical; large chemical ... See more keywords
Screening of Chemical Libraries Using Xenopus Embryos and Tadpoles for Phenotypic Drug Discovery.
Sign Up to like & getrecommendations! Published in 2022 at "Cold Spring Harbor protocols"
DOI: 10.1101/pdb.prot098269
Abstract: Phenotypic drug discovery assesses the effect of small molecules on the phenotype of cells, tissues, or whole organisms without a priori knowledge of the target or pathway. Using vertebrate embryos instead of cell-based assays has… read more here.
Keywords: embryos; chemical libraries; drug; phenotypic drug ... See more keywords
Deep reinforcement learning for de novo drug design
Sign Up to like & getrecommendations! Published in 2018 at "Science Advances"
DOI: 10.1126/sciadv.aap7885
Abstract: We introduce an artificial intelligence approach to de novo design of molecules with desired physical or biological properties. We have devised and implemented a novel computational strategy for de novo design of molecules with desired… read more here.
Keywords: models trained; design; reinforcement learning; deep reinforcement ... See more keywords