Publications

AlphaFind: discover structure similarity across the proteome in AlphaFold DB #

AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.

SISAP 2023 Indexing Challenge – Learned Metric Index #

This submission into the SISAP Indexing Challenge examines the experimental setup and performance of the Learned Metric Index, which uses an architecture of interconnected learned models to answer similarity queries. An inherent part of this design is a great deal of flexibility in the implementation, such as the choice of particular machine learning models, or their arrangement in the overall architecture of the index. Therefore, for the sake of transparency and reproducibility, this report thoroughly describes the details of the specific Learned Metric Index implementation used to tackle the challenge.

Organizing Similarity Spaces Using Metric Hulls #

A novel concept of a metric hull has recently been introduced to encompass a set of objects by a few selected border objects. Following one of the metric-hull computation methods that generate a hierarchy of metric hulls, we introduce a metric index structure for unstructured and complex data, a Metric Hull Tree (MH-tree). We propose a construction of MH-tree by a bulk-loading procedure and outline an insert operation. With respect to the design of the tree, we provide an implementation of an approximate kNN search operation. Finally, we utilized the Profimedia dataset to evaluate various building and ranking strategies of MH-tree and compared the results with M-tree.