stuff.bib

@Article{May1976,
  author   = {May, Robert M.},
  journal  = {Nature},
  title    = {Simple mathematical models with very complicated dynamics},
  year     = {1976},
  issn     = {1476-4687},
  number   = {5560},
  pages    = {459--467},
  volume   = {261},
  abstract = {First-order difference equations arise in many contexts in the biological, economic and social sciences. Such equations, even though simple and deterministic, can exhibit a surprising array of dynamical behaviour, from stable points, to a bifurcating hierarchy of stable cycles, to apparently random fluctuations. There are consequently many fascinating problems, some concerned with delicate mathematical aspects of the fine structure of the trajectories, and some concerned with the practical implications and applications. This is an interpretive review of them.},
  doi      = {10.1038/261459a0},
  file     = {:May1976 - Simple Mathematical Models with Very Complicated Dynamics.pdf:PDF},
  refid    = {May1976},
  url      = {https://doi.org/10.1038/261459a0},
}

@Article{Sehnal2021,
  author   = {Sehnal, David and Bittrich, Sebastian and Deshpande, Mandar and Svobodová, Radka and Berka, Karel and Bazgier, Václav and Velankar, Sameer and Burley, Stephen K and Koča, Jaroslav and Rose, Alexander S},
  journal  = {Nucleic Acids Research},
  title    = {{Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures}},
  year     = {2021},
  issn     = {0305-1048},
  month    = {05},
  number   = {W1},
  pages    = {W431-W437},
  volume   = {49},
  abstract = {{Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.}},
  doi      = {10.1093/nar/gkab314},
  eprint   = {https://academic.oup.com/nar/article-pdf/49/W1/W431/38842088/gkab314.pdf},
  file     = {:Sehnal2021 - Mol_ Viewer_ Modern Web App for 3D Visualization and Analysis of Large Biomolecular Structures.pdf:PDF},
  url      = {https://doi.org/10.1093/nar/gkab314},
}

@Article{Bryant2022,
  author  = {Bryant, Patrick and Pozzati, Gabriele and Elofsson, Arne},
  journal = {Nature Communications},
  title   = {Improved prediction of protein-protein interactions using AlphaFold2},
  year    = {2022},
  issn    = {2041-1723},
  number  = {1},
  pages   = {1265},
  volume  = {13},
  comment = {FoldDock},
  doi     = {10.1038/s41467-022-28865-w},
  file    = {:Bryant2022 - Improved Prediction of Protein Protein Interactions Using AlphaFold2.pdf:PDF},
  groups  = {ideas, must_cite, AF2},
  refid   = {Bryant2022},
  url     = {https://doi.org/10.1038/s41467-022-28865-w},
}

@Article{Mirdita2022,
  author   = {Mirdita, Milot and Schütze, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
  journal  = {Nature Methods},
  title    = {{ColabFold: making protein folding accessible to all}},
  year     = {2022},
  issn     = {1548-7105},
  number   = {6},
  pages    = {679--682},
  volume   = {19},
  abstract = {ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with AlphaFold2 or RoseTTAFold. ColabFold’s 40−60-fold faster search and optimized model utilization enables prediction of close to 1,000 structures per day on a server with one graphics processing unit. Coupled with Google Colaboratory, ColabFold becomes a free and accessible platform for protein folding. ColabFold is open-source software available at https://github.com/sokrypton/ColabFoldand its novel environmental databases are available at https://colabfold.mmseqs.com.},
  doi      = {10.1038/s41592-022-01488-1},
  file     = {:Mirdita2022 - ColabFold_ Making Protein Folding Accessible to All.pdf:PDF;:41592_2022_1488_MOESM1_ESM.pdf:PDF;:41592_2022_1488_MOESM3_ESM.pdf:PDF},
  groups   = {AF2, ideas, steinegger},
  refid    = {Mirdita2022},
  url      = {https://doi.org/10.1038/s41592-022-01488-1},
}

@Article{Kempen2022,
  author       = {van Kempen, Michel and Kim, Stephanie and Tumescheit, Charlotte and Mirdita, Milot and Soeding, Johannes and Steinegger, Martin},
  journal      = {bioRxiv},
  title        = {Foldseek: fast and accurate protein structure search},
  year         = {2022},
  month        = feb,
  abstract     = {Highly accurate structure prediction methods are generating an avalanche of publicly available protein structures. Searching through these structures is becoming the main bottleneck in their analysis. Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster. Foldseek is free open-source software available at foldseek.com and as a webserver at search.foldseek.com.Competing Interest StatementThe authors have declared no competing interest.},
  doi          = {10.1101/2022.02.07.479398},
  elocation-id = {2022.02.07.479398},
  eprint       = {https://www.biorxiv.org/content/early/2022/02/09/2022.02.07.479398.full.pdf},
  file         = {:Kempen2022 - Foldseek_ Fast and Accurate Protein Structure Search.pdf:PDF},
  groups       = {ideas, extra, steinegger},
  publisher    = {Cold Spring Harbor Laboratory},
  url          = {https://www.biorxiv.org/content/early/2022/02/09/2022.02.07.479398},
}

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