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Free, publicly-accessible full text available March 1, 2025
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Abstract AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/.
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Videogame designers use tips and tricks and tools of the trade to design levels. Some of these tips are based on their gut feeling and others have been known in the game industry for the last 30 years. In this work, we discuss six of common level design patterns present in 2D videogames. The patterns under discussion are the product of an exploratory analysis of over thirty 2D games. We choose to focus on patterns that are both common and impactful for the overall player experience. We discuss in detail the rationale for and advantages of each pattern, showing examples of games that make use of such. We conclude with a discussion of the usage and understanding of these patterns from the perspective of level design and how other technical approaches can benefit from them.more » « less