AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

Abstract

AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.

Keywords: AutoDrug; fragment-based drug discovery; workflow automation.

Figure 1

A simplified generic AutoDrug workflow. The entire workflow is completely automated at the SSRL beamlines and runs without user interaction or supervision.

Figure 2

Diagram of an AutoDrug workflow for data processing. The workflow reflects the exact steps that a crystallographer takes when executing programs for data processing. The subworkflows RunXds, RunPointless, RunScala, RunTruncate and RunFreeR run the programs XDS, POINTLESS, SCALA, TRUNCATE and FREERFLAG for data processing. The subworkflow RunXtriage runs xtriage, a program that analyzes the data. The diagram is understood by both software programmers and scientists, and simplifies communication during workflow development. The diagram was generated by RestFlow based on the workflow specification and was rendered using GraphViz (http://www.graphviz.org).

Figure 3

Conceptual view of a simple workflow implemented with RestFlow. A workflow comprises one or more nodes connected by data inflows and outflows. Each node encapsulates either an actor or another workflow. Each data flow is associated with a universal resource identifier (URI) template that specifies where data passing across the data flow are persisted (i.e. saved as a file).

Figure 4

The role of URI templates in the management of data in a simplified RestFlow program for crystallographic data collection. Rounded boxes represent nodes carrying out tasks at the beamline and the expressions in the square boxes are URI templates that specify routes of data flow. (a) Variables are specified in the URI templates (shown in bold curly braces: {variable}). (b) The variables are expanded at run time using current values of data and metadata passing through the node to yield unique identifiers and destinations on the file system.