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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).

Clustal Omega
Multiple sequence alignment with Clustal Omega can be performed using a web service hosted by the UCSF RBVI, accessed via the sequence align command or the Sequence Viewer context menu.

ESMFold
The ESM Metagenomic Atlas provides a structure prediction server used by the command esmfold predict.

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

MUSCLE
Multiple sequence alignment with MUSCLE can be performed using a web service hosted by the UCSF RBVI, accessed via the sequence align command or the Sequence Viewer context menu.

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 / November 2022