Related Experiment Video
Updated: Sep 13, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
ActSeek: fast and accurate search algorithm of active sites in alphafold database
Sandra Castillo1, O H Samuli Ollila1
1VTT Technical Research Centre of Finland Ltd, Espoo, Otaniemi, 02044 VTT, Finland.
Motivation:
Finding proteins with specific functions by mining modern databases can potentially lead to substantial advancements in wide range of fields, from medicine and biotechnology to material science. Currently available algorithms enable mining of proteins based on their sequence or structure. However, activities of many proteins, such as enzymes and drug targets, are dictated by active site residues and their surroundings rather than the overall structure or sequence of a protein.
Results:
We introduce ActSeek-a computer vision-inspired fast program-that searches structural databases for proteins with active sites similar to the seed protein. ActSeek is implemented to mine proteins with desired active site environments from the Alphafold database. The potential of ActSeek to find innovative solutions to the world's most pressing challenges is demonstrated by finding enzymes that may be used to produce biodegradable plastics or degrade plastics, as well as potential off-targets for common drug molecules.
Availability And Implementation:
ActSeek source code is available in https://github.com/vttresearch/ActSeek under Non-Commercial License Agreement.
Related Concept Videos
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Ligand Binding and Linkage
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Ligand Binding Sites
Protein Families

