Easy and accurate protein structure prediction using ColabFold | Nature Protocols

Oct 17, 2024

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Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological questions, by using predicted protein structures of single monomers or full complexes, a common practice. ColabFold-AF2 is an open-source Jupyter Notebook inside Google Colaboratory and a command-line tool that makes it easy to use AF2 while exposing its advanced options. ColabFold-AF2 shortens turnaround times of experiments because of its optimized usage of AF2’s models. In this protocol, we guide the reader through ColabFold best practices by using three scenarios: (i) monomer prediction, (ii) complex prediction and (iii) conformation sampling. The first two scenarios cover classic static structure prediction and are demonstrated on the human glycosylphosphatidylinositol transamidase protein. The third scenario demonstrates an alternative use case of the AF2 models by predicting two conformations of the human alanine serine transporter 2. Users can run the protocol without computational expertise via Google Colaboratory or in a command-line environment for advanced users. Using Google Colaboratory, it takes <2 h to run each procedure. The data and code for this protocol are available at https://protocol.colabfold.com.

We present an outline of how to use ColabFold to perform structure prediction of monomers, complexes and alternative conformations and guidance on interpreting the results through appropriate confidence metrics and visualizations.

Integrating MMseqs2’s quick homology search, ColabFold enables accelerated structure prediction compared with AlphaFold2 at similar accuracy, while exposing many advanced parameters. ColabFold can be accessed through a Google Colaboratory notebook for beginners and a command-line interface for advanced users.

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All sequences used in this protocol can be found in Equipment and in the PDB.

ColabFold is available at https://github.com/sokrypton/ColabFold and https://colabfold.com. The localcolabfold installer is available at https://github.com/YoshitakaMo/localcolabfold. Colab prediction notebooks based on ColabFold-AF2 v1.5.3 and local prediction scripts are available at https://github.com/steineggerlab/colabfold-protocol, which also includes all the input and output files.

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M.S. acknowledges the support by the National Research Foundation of Korea, grants 2020M3-A9G7-103933, 2021-R1C1-C102065, 2021-M3A9-I4021220 and RS-2024-00396026; the Samsung DS research fund; the Creative-Pioneering Researchers Program; and the AI-Bio Research Grant through Seoul National University. M.M. acknowledges support by the National Research Foundation of Korea (grant RS-2023-00250470). Y.M. acknowledges support from Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under grant number JP23ama121027. S.O. was supported by the National Institutes of Health (NIH) DP5OD026389 and the National Science Foundation (NSF) MCB2032259.

These authors contributed equally: Gyuri Kim, Sewon Lee, Eli Levy Karin.

Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea

Gyuri Kim, Hyunbin Kim & Martin Steinegger

School of Biological Sciences, Seoul National University, Seoul, South Korea

Sewon Lee, Martin Steinegger & Milot Mirdita

ELKMO, Copenhagen, Denmark

Eli Levy Karin

Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan

Yoshitaka Moriwaki

Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan

Yoshitaka Moriwaki

Department of Computational Drug Discovery and Design, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan

Yoshitaka Moriwaki

Massachusetts Institute of Technology, Cambridge, MA, USA

Sergey Ovchinnikov

Artificial Intelligence Institute, Seoul National University, Seoul, South Korea

Martin Steinegger

Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea

Martin Steinegger

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G.K., S.L., E.L.K. and M.S. developed the protocol. Y.M., S.O., M.S. and M.M. developed the ColabFold software and notebooks. G.K., S.L. and H.K. performed predictions and visualized the data. S.O., M.S. and M.M. supervised the monomer and complex prediction procedures. E.L.K., Y.M., M.S. and M.M. supervised the conformation prediction procedure. G.K., S.L. and E.L.K. analyzed the results and wrote the paper, with contributions from all authors.

Correspondence to Sergey Ovchinnikov, Martin Steinegger or Milot Mirdita.

The authors declare no competing interests.

Nature Protocols thanks Jianyi Yang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Key references using this protocol

Mirdita, M. et al. Nat. Methods 19, 679–682 (2022): https://doi.org/10.1038/s41592-022-01488-1

Lee, S. et al. Cold Spring Harb. Perspect. Biol. 16, a041465 (2024): https://doi.org/10.1101/cshperspect.a041465

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Kim, G., Lee, S., Levy Karin, E. et al. Easy and accurate protein structure prediction using ColabFold. Nat Protoc (2024). https://doi.org/10.1038/s41596-024-01060-5

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Received: 21 November 2023

Accepted: 07 August 2024

Published: 14 October 2024

DOI: https://doi.org/10.1038/s41596-024-01060-5

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