Despite their drawbacks, computational scaffold extraction methods have been frequently used in approximate benchmarks for scaffold hopping. In many systematic retrospective studies, connectivity-based methods were shown to be at least equally effective as 3D methods, especially when the conformations of ...
Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs with their protein targets to propose new d
Virtual screening based on molecular docking has become one of the most widely used methods of SBDD. The primary criteria for any docking method are docking accuracy, scoring accuracy, and computational efficiency, which are all strongly influenced by the conformational searching method29,30. Molecular...
1.2. Experimental methods Many different methods have been applied to investigate or model the organization of molecules in the plasma membrane of (living) cells. We can broadly group the approaches into three categories: 1.3. Why we need simulations Even though great progress has been made to me...
(2020). Plant-derived secondary metabolites as the main source of efflux pump inhibitors and methods for identification. Journal of Pharmaceutical Analysis, 10(4), 277–290. https://doi.org/10.1016/j.jpha.2019.11.002 Article PubMed Google Scholar Chauhan, S. S., Gupta, A., Srivastava, ...
Virtual screening, on the other hand, employs computational methods to evaluate compounds, effectively narrowing down the pool of candidates that require experimental screening. This approach also allows for the selection of final compound sets based on available resources for experimental assays [18]. ...
we selected the heavy atoms covalently linked with hydrogen atoms for further analysis. We then extracted the attention weights, generated in the last layer of the Distance-aware edge to node block (Methods), of the atoms involved in the formation of hydrogen bonds. The results of these operati...
de novo drug design and scaffold hopping, network-based methods and drug discovery Rational design of natural products, peptides, enzyme inhibitors, drugs for neurodegenerative disorders, anti-inflammatory therapeutics, antibacterials for multi-drug resistant infections, and antiviral and anticancer therapeuti...
Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. Generative SBDD methods leverage structural data of drugs with their protein targets to propose new d
Part of the book series: Methods in Pharmacology and Toxicology ((MIPT)) 1514 Accesses Abstract Fragment-based drug design (FBDD) is a promising approach for drug discovery. Experimental FBDD faces some intrinsic limitations and challenges such as the high requirements for the quality of target...