@article{KynastSchwaegerlHoecker, author = {Kynast, Josef Paul and Schw{\"a}gerl, Felix and H{\"o}cker, Birte}, title = {ATLIGATOR: editing protein interactions with an atlas-based approach}, series = {Bioinformatics}, volume = {38}, journal = {Bioinformatics}, number = {23}, editor = {Martelli, Pier Luigi}, publisher = {Oxford University Press (OUP)}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btac685}, pages = {5199 -- 5205}, abstract = {Abstract Motivation Recognition of specific molecules by proteins is a fundamental cellular mechanism and relevant for many applications. Being able to modify binding is a key interest and can be achieved by repurposing established interaction motifs. We were specifically interested in a methodology for the design of peptide binding modules. By leveraging interaction data from known protein structures, we plan to accelerate the design of novel protein or peptide binders. Results We developed ATLIGATOR—a computational method to support the analysis and design of a protein's interaction with a single side chain. Our program enables the building of interaction atlases based on structures from the PDB. From these atlases pocket definitions are extracted that can be searched for frequent interactions. These searches can reveal similarities in unrelated proteins as we show here for one example. Such frequent interactions can then be grafted onto a new protein scaffold as a starting point of the design process. The ATLIGATOR tool is made accessible through a python API as well as a CLI with python scripts. Availability and implementation Source code can be downloaded at github (https://www.github.com/Hoecker-Lab/atligator), installed from PyPI ('atligator') and is implemented in Python 3.}, language = {en} } @incollection{SchwaegerlWestfechtel, author = {Schw{\"a}gerl, Felix and Westfechtel, Bernhard}, title = {Managing Software Product Line Evolution by Filtered Editing: The SuperMod Approach}, series = {Handbook of Re-Engineering Software Intensive Systems into Software Product Lines}, booktitle = {Handbook of Re-Engineering Software Intensive Systems into Software Product Lines}, publisher = {Springer International Publishing}, isbn = {9783031116858}, doi = {10.1007/978-3-031-11686-5_17}, pages = {429 -- 451}, abstract = {This chapter introduces SuperMod, an approach and tool to support the evolution of software product lines (SPLs) by means of a filtered editing model, which is inspired by the checkout-modify-commit workflow established in version control systems. Rather than forcing the developers into editing multi-variant artifacts of an SPL, SuperMod allows them to perform modifications successively in single-variant workspaces and to integrate the changes by indicating the logical scope, i.e., the affected variants, of the change performed. The SPL itself is managed automatically in a transparent repository by the system. As a consequence, developers may re-use the same engineering tools they also used for the development of the product variants prior to the re-engineering process. SuperMod furthermore orchestrates collaborative development and provides dedicated support for (without restricting developers to) model-driven approaches to SPL engineering. We illustrate SuperMod's capabilities by the well-known graph SPL example and discuss the practical benefits of the suggested solution to SPL evolution as well as its relation to SPL re-engineering.}, language = {en} }