Phenix prediction server

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         Purpose

This server is used in PredictModel and PredictAndBuild.

         Who can use the server

This Phenix server provides access to protein structure prediction with AlphaFold for users of the Phenix software.

         How to use this server

To use the server, use the PredictModel or PredictAndBuild functions on the Phenix GUI.

         Acknowledgements

The Phenix AlphaFold server uses AlphaFold (Jumper et al., 2021), the mmseqs2 MSA server (Steinegger, and Söding, 2017, Mirdita et al., 2019), and scripts derived from ColabFold (Mirdita et al., 2022).

Literature

Making protein folding accessible to all. M. Mirdita, K. Schütze, Y. Moriwaki, L. Heo, S. Ovchinnikov, and M. Steinegger. Nature Methods 19, 679–682 (2022).

Highly accurate protein structure prediction with AlphaFold. J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Žídek, A. Potapenko, A. Bridgland, C. Meyer, S.A.A. Kohl, A.J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A.W. Senior, K. Kavukcuoglu, P. Kohli, and D. Hassabis. Nature 596, 583-589 (2021).

MMseqs2 desktop and local web server app for fast interactive sequence searches. Mirdita M, Steinegger M, Söding J. ( 2019). Bioinformatics 35:2856-2858.

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. M. Steinegger, and J. Söding. Nature biotechnology 35, 1026-1028 (2017).