@article{Mirdita2022,
author= {Mirdita, Milot and Schütze, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin },
doi = {10.1038/s41592-022-01488-1},
journal = {Nature Methods},
title = {{ColabFold: Making Protein folding accessible to all}},
year = {2022},
comment = {ColabFold including MMseqs2 MSA server}
}
@article{Evans2021,
  author   = {Evans, Richard and O'Neill, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and  Zidek, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis},
  doi    = {10.1101/2021.10.04.463034v1},
  journal  = {bioRxiv},
  title    = {{Protein complex prediction with AlphaFold-Multimer}},
  year     =  {2021},
  comment = {AlphaFold2-multimer}
}
@article{Mirdita2019,
author = {Mirdita, Milot and Steinegger, Martin and S{"{o}}ding, Johannes},
doi = {10.1093/bioinformatics/bty1057},
journal = {Bioinformatics},
number = {16},
pages = {2856--2858},
pmid = {30615063},
title = {{MMseqs2 desktop and local web server app for fast, interactive sequence searches}},
volume = {35},
year = {2019},
comment = {MMseqs2 search server}
}
@article{Mirdita2017,
author = {Mirdita, Milot and von den Driesch, Lars and Galiez, Clovis and Martin, Maria J. and S{"{o}}ding, Johannes and Steinegger, Martin},
doi = {10.1093/nar/gkw1081},
journal = {Nucleic Acids Res.},
number = {D1},
pages = {D170--D176},
pmid = {27899574},
title = {{Uniclust databases of clustered and deeply annotated protein sequences and alignments}},
volume = {45},
year = {2017},
comment = {Uniclust30/UniRef30 database},
}
@article{Mitchell2019,
author = {Mitchell, Alex L and Almeida, Alexandre and Beracochea, Martin and Boland, Miguel and Burgin, Josephine and Cochrane, Guy and Crusoe, Michael R and Kale, Varsha and Potter, Simon C and Richardson, Lorna J and Sakharova, Ekaterina and Scheremetjew, Maxim and Korobeynikov, Anton and Shlemov, Alex and Kunyavskaya, Olga and Lapidus, Alla and Finn, Robert D},
doi = {10.1093/nar/gkz1035},
journal = {Nucleic Acids Res.},
title = {{MGnify: the microbiome analysis resource in 2020}},
year = {2019},
comment = {MGnify database}
}
@article{Steinegger2019,
author = {Steinegger, Martin and Meier, Markus and Mirdita, Milot and V{"{o}}hringer, Harald and Haunsberger, Stephan J. and S{"{o}}ding, Johannes},
doi = {10.1186/s12859-019-3019-7},
journal = {BMC Bioinform.},
number = {1},
pages = {473},
pmid = {31521110},
title = {{HH-suite3 for fast remote homology detection and deep protein annotation}},
volume = {20},
year = {2019},
comment = {PDB70 database}
}
@misc{Berman2003,
author = {Berman, Helen and Henrick, Kim and Nakamura, Haruki},
booktitle = {Nat. Struct. Biol.},
doi = {10.1038/nsb1203-980},
number = {12},
pages = {980},
pmid = {14634627},
title = {{Announcing the worldwide Protein Data Bank}},
volume = {10},
year = {2003},
comment = {templates downloaded from wwPDB server}
}
@article{Eastman2017,
author = {Eastman, Peter and Swails, Jason and Chodera, John D. and McGibbon, Robert T. and Zhao, Yutong and Beauchamp, Kyle A. and Wang, Lee-Ping and Simmonett, Andrew C. and Harrigan, Matthew P. and Stern, Chaya D. and Wiewiora, Rafal P. and Brooks, Bernard R. and Pande, Vijay S.},
doi = {10.1371/journal.pcbi.1005659},
journal = {PLOS Comput. Biol.},
number = {7},
title = {{OpenMM 7: Rapid development of high performance algorithms for molecular dynamics}},
volume = {13},
year = {2017},
comment = {Amber relaxation}
}