Automated drug discovery protocols, or partially automated protocols, in which matrices with memories serve as the platform on which all manipulations are performed or serve as the repository of information that is transferred to other memories as the synthesized compounds are processed and screened. Also provided are automated drug discovery units for use in the protocols. The units provide a means for seamless data tracking and include instrumentation and vials with memories for information transfer to other memories in a unit. The units, which are provided herein, include some or all of the following: an automated or manual sorter, microvessels, which contain memories, an automated or semi-automated synthesizer, a microvessel washer/dryer, a manual or automated cleaver for removing compounds from the matrix with memory microvessels, and associated software. The memories may be any of any type, including electromagnetically encodable memories and optical memories, or combinations thereof. The memories may be pre-encoded or may be encodabie during, after or before processing. Also provided are manual and automated methods for sorting matrices with memories.