Scipion-Chem: An Open Platform for Virtual Drug Screening.

Virtual drug screening (VDS) tackles the problem of drug discovery by computationally reducing the number of potential pharmacological molecules that need to be tested experimentally to find a new drug. To do so, several approaches have been developed through the years, typically focusing on either the physicochemical characteristics of the receptor structure (structure-based virtual screening) or those of the potential ligands (ligand-based virtual screening). Scipion is a workflow engine well suited for structural studies of biological macromolecules. Here, we present Scipion-chem, a new branch oriented to VDS. A total of 11 plugins have already been integrated from the most common programs used in the field. They can be used through the Scipion graphical user interface to execute and analyze typical VDS tasks. In addition, we have developed several consensus protocols that combine results from the different integrated programs to generate more robust predictions. Backstage, Scipion also facilitates the interoperability of those different software packages while tracking all of the intermediate files, parameters, and user decisions. In summary, in this article, we present Scipion-chem. This accessible, interoperable, and traceable platform provides the user with all of the tools to carry out a successful VDS workflow. Scipion-chem is openly available at https://github.com/scipion-chem.

Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.