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Web Services Used by UCSF ChimeraX

Web services accessed by ChimeraX fall into two general categories:

Computational Services

AlphaFold
The AlphaFold tool Predict option and the command alphafold predict use Google Colab to run ColabFold, an open-source, optimized version of AlphaFold 2. Users will need to have a Google account and to sign into it via a browser.

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.

Fast Sequence Database Search
A K-mer sequence search service hosted by the UCSF RBVI is used by the commands alphafold match and esmfold match, as well as the AlphaFold and ESMFold Fetch capability. This search algorithm is fast but low-sensitivity, as appropriate for searching large sequence databases for matches with very high % identity.

Modeller
Two tools run 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.

Data Retrieval Services

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


UCSF Resource for Biocomputing, Visualization, and Informatics / September 2023