108
P. Gong et al.
Fig. 6.2 An example of reference chemical library preparation based on toxicological mode of
action (MoA) or molecular initiating event (MIE) in the framework of adverse outcome pathway
(AOP)
6.3.2 Structural Models of Biomacromolecular Targets
The 3D crystal structures of toxicity targets are first searched in RCSB’s PDB [69]
(https://www.rcsb.org/) and NCBI’s MMDB [40] (https://www.ncbi.nlm.nih.gov/
Structure/MMDB/mmdb.shtml). If the 3D structure of a biomarcomolecular target is
not yet resolved, we first retrieve its protein sequence from relevant databases, such
as UniProtKB [70] (https://www.uniprot.org). Then, using BLAST (Basic Local
Alignment Search Tool) [71] to search for homologous proteins with available 3D
structures, we choose the one with the highest similarity to the homologous template. Homology-based modeling tools, such as Modeller [72] and Swiss-Model
P. Gong et al.
Fig. 6.2 An example of reference chemical library preparation based on toxicological mode of
action (MoA) or molecular initiating event (MIE) in the framework of adverse outcome pathway
(AOP)
6.3.2 Structural Models of Biomacromolecular Targets
The 3D crystal structures of toxicity targets are first searched in RCSB’s PDB [69]
(https://www.rcsb.org/) and NCBI’s MMDB [40] (https://www.ncbi.nlm.nih.gov/
Structure/MMDB/mmdb.shtml). If the 3D structure of a biomarcomolecular target is
not yet resolved, we first retrieve its protein sequence from relevant databases, such
as UniProtKB [70] (https://www.uniprot.org). Then, using BLAST (Basic Local
Alignment Search Tool) [71] to search for homologous proteins with available 3D
structures, we choose the one with the highest similarity to the homologous template. Homology-based modeling tools, such as Modeller [72] and Swiss-Model