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Web Services Used by UCSF ChimeraX

Web services accessed by ChimeraX fall into two general categories:

Computational Services

BLAST Protein
The Blast Protein tool performs protein sequence searches using a BLAST web service hosted by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI).

BLAT Search
The alphafold match command and AlphaFold tool Fetch function perform protein sequence searches using a BLAT web service hosted by the UCSF RBVI.

Modeller
The Modeller Comparative tool performs comparative (homology) modeling with Modeller using a web service hosted by the UCSF RBVI.

SMILES Translator
The SMILES translator provided by the National Cancer Institute CADD group is used to generate 3D molecule structures specified by SMILES string with the command open or in Build Structure.

smi23d
Generates modeled organic molecule structures specified by SMILES string with the command open or in Build Structure. The smi23d web service is provided by the cheminformatics group at Indiana University and deploys the same procedure as described for Pub3D in Willighagen et al., BMC Bioinformatics 8:487 (2007).

Data Retrieval Services

Information can be retrieved from the following databases using the open command:


UCSF Resource for Biocomputing, Visualization, and Informatics / September 2021