Protein Structure Similarity Clustering: Dynamic Treatment of PDB Structures Facilitates Clustering

Abstract

In der Familie: Durch das Einführen des Ligandenandockens, der Moleküldynamik und des VAST‐Algorithmus in das Bündeln von Proteinen ähnlicher Struktur wird der Prozess erheblich rationalisiert und lässt sonst unerkannte Beziehungen zu neuen Proteincluster‐Partnern sichtbar werden. VAST=Vector Alignment Search Tool.

Biology-inspired synthesis of compound libraries

“…In a recent study, an additional method that also considers protein flexibility was introduced to the PSSC procedure. Molecular dynamics calculations generated different protein conformations, which are then tested for possible binding sites; using this modified procedure the ligand binding sites previously undetected by "static" PSSC were identified [88]. Moreover, the scope of PSSC can be extended by moving beyond structural similarity between targets, e.g., by including similarities between biosynthetic enzymes and other proteins.…”