Ligand-based drug design (LBDD)Vivek YadavJurnal ReangVinitaRajiv Kumar TonkComputer Aided Drug Design (CADD): From Ligand-Based Methods to Structure-Based Approaches
In our study, ligand-based drug design (LBDD) approaches aim to identify the relationship between the physiochemical characteristics of known antibiotic ligands and their antimicrobial activities. This information can then be utilized to optimize existing drugs or inform the development of new drugs wit...
Virtual screening (VS) has become an integral part of fragment-based drug discovery (FBDD). In this study we have evaluated the applicability of ligand-based virtual screening (LBVS) methods for identifying small fragment-like biologically active molecules using different similarity descriptors and di...
Deep generative models have shown the ability to devise both valid and novel chemistry, which could significantly accelerate the identification of bioactive compounds. Many current models, however, use molecular descriptors or ligand-based predictive methods to guide molecule generation towards a desirable ...
based to machine learning. In this work, we collate 13 ligand binding site predictors, spanning 30 years, focusing on the latest machine learning-based methods such as VN-EGNN, IF-SitePred, GrASP, PUResNet, and DeepPocket and compare them to the established P2Rank, PRANK and fpocket and ...
Therefore, reports of autophagosome tethering compounds (ATTECs) have received considerable attention from the drug development community. ATTECs are based on the recruitment of targets to LC3/GABARAP, a family of ubiquitin-like proteins that presumably bind to the autophagosome membrane and tether ...
Additionally, computational approaches, such as ligand- or structure-based homology modeling and docking, are gaining importance as valuable complements to experi- mental structure-function studies. These techniques, in combi- nation with modern drug screening assays, make it possible to identify ...
Sotriffer C, Klebe G: Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farm Soc Chim Ital 1989 2002, 57: 243–251. CAS Google Scholar Andricopulo AD, Salum LB, Abraham DJ: Structure-based drug design strategies in ...
Specifically, conjugative bioactive ligands to metal scaffolds is an emerging design strategy for developing metal-based drug leads [54,63]. In this study, we synthesized a series of iridium (III) and rhodium (III) bearing ligands (2-phenylquinoline, 2,9-dimethyl-1,10-phenanthroline, and ...
design of proteins that target neosurfaces, that is, surfaces arising from protein–ligand complexes. To develop this strategy, we leveraged a geometric deep learning approach based on learned molecular surface representations8,9and experimentally validated binders against three drug-bound protein ...