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All MS/MS data were batch searched against this target/decoy database using SEQUEST algorithm contained within Bioworks v3.2 software [ 51].
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For batch searches the PubChem query upload interface is shown below [14].
The screenshot is the result from the batch search upload of 1414 SMILES via extraction of the FPO URL for US20120040982.
Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats.
The user can further direct a batch search to download selected data and metadata associated with the successfully mapped portion of the original chemical list.
It currently supports the three different search modes: simple text search mode (in the main window), structure search mode (in the main window), and batch search mode (through the Tools menu).
A batch search of the challenge MS/MS against the challenge candidate list (in the ESD) was performed on the top 500 candidates, to avoid long computational run times.
A batch search (Fig. 13) feature allows users to input lists of chemical identifiers (hundreds to thousands) to perform a customized list mapping to DSSTox content and associated data.
The concept of the release numbers was established in order to control public access and to inform SQL*LIMS™ managers if a new protein could be identified due to new batch searches using the newest database releases.
Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats and facilitates access to available structure, property, toxicity, and bioassay data for collections of thousands of chemicals at a time.
The simple text search mode and structure search mode provide the same search functionality as the NCBI's Entrez or PubChem basic structure search, while the batch search mode extends the batch Entrez in ways enabling users to run a list of queries and merge the results into a single file.
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