Radka Svobodová Vařeková

AlphaFind v2: Similarity Search in AlphaFold DB and TED Domains across Structural Contexts

AlphaFind v2 enables fast, structure-based search across protein structures and domains, using embeddings and US-align for refinement and supporting organism and CATH-based filtering.

Per-residue optimisation of protein structures: Rapid alternative to optimisation with constrained alpha carbons

This paper introduces a method to optimise protein structures more efficiently than traditional methods, achieving results comparable to constrained alpha carbon optimisation in less time.

GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

GOLEM visualizes the distribution of cis-regulatory elements in plant promoters, focusing on male gametophyte-related motifs across multiple plant species.

Rare ring conformations in PDB: Facts or wishful thinking?

The paper analyzes ring conformations in PDB structures, finding that most are energetically favorable, while only a small fraction of unfavorable conformations are supported by experimental evidence.

AlphaFind: Discover structure similarity across the entire known proteome

AlphaFind provides a web-based tool for fast structure-based retrieval of protein structures from AlphaFold DB using 3D features and machine learning.

Uncovering of Cytochrome P450 Anatomy by SecStrAnnotator

The paper analyzes the secondary structure anatomy of cytochrome P450 proteins using a workflow that identifies equivalent SSE groups and their properties.