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PubChem Score Matrix Service Help This document describes how to use the PubChem score matrix web service, which can be found at the URL: The score matrix service computes matrices of similarity scores for PubChem compound database identifiers. This functionality is also available though PubChem's PUG service. The size of the matrix that may be computed through this service is limited, though any number of requests may be submitted. Requests are processed in the order received. All requests are kept private; without your unique 64-bit key, nobody else can see what identifiers you have submitted. Steps to computing a score matrix: 1) Choose a scoring method from those below; more choices may be added in the future.
2) Input a list of CIDs as one of the following three formats. If this is the only list supplied (step #2 below is skipped), then these CIDs are scored against themselves; the result may be a diagonal half-matrix, depending on the format.
3) Optionally input a second list of CIDs, in which case a full matrix will be returned, with list #1 scored against list #2. 4) Select a format for the matrix file. The choices are:
5) Select a compression method for the matrix file. The choices are:
6) Initiate the request:
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