3D-QSAR and molecular recognition of Klebsiella pneumoniae NDM-1 inhibitors

Benzimidazole and Benzoxazole Zinc Chelators as Inhibitors of Metallo‐β‐Lactamase NDM‐1

“…Finally, every compound is docked with hydrogen bonding between the compound and Asn220 and hydrophobic interactions with Lys211, residues that are critical for substrate binding and catalysis [18] . It has been suggested that many NDM‐1‐inhibtor interactions alter the hydrogen bonding within the protein, reducing recognition of NDM‐1 for β‐lactams [15] . Our docking studies demonstrate the complementary nature of in silico molecular docking approaches with in vitro experiments to reveal structure‐activity relationships.…”

“…Methods (i), (iii), and (v) were directly compared previously in the development of AD4Zn [14] . AD4Zn has also been previously used to determine the structure‐activity relationship of propionic sulfhydryl compounds to NDM‐1 [15] …”

3D-QSAR, molecular docking, and molecular dynamics simulation study of thieno[3,2-b]pyrrole-5-carboxamide derivatives as LSD1 inhibitors

“…The energy cut-off value was set to 30 kcal mol À1 and the default value was adopted for other parameters. 34 For CoMSIA, in addition to calculating the steric eld and electrostatic eld parameters, hydrophobic eld, hydrogen bond acceptor eld and hydrogen bond donor eld parameters were also calculated. Therefore, for the probe particle, in addition to the van der Waals radius of 1.52 A and the net charge of +1.0, while hydrophobic parameters, hydrogen bond acceptor parameters and hydrogen bond donor parameters also should be set to +1 for calculating the compound characteristics.…”

Concepts and Application of DNA Origami and DNA Self-Assembly: A Systematic Review

“…Computer is one of the three major scientific revolutions in the 20th century, which has made great contributions to the development of computing theories such as graph theory and operations research [4]. In the past decade, nontraditional computing, including artificial neural network computers, quantum computers, optical computers, nanometer computers, and molecular biological computers [5][6][7], has developed rapidly and been adopted by more and more scholars. Given the advantages of ultra-large-scale parallelism and huge data storage capac-ity, natural computing based on DNA pairing has become one of the main development directions of nontraditional high-performance computing [8,9].…”