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README.md

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-license: cc-by-4.0
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+---
+license: cc-by-4.0
+tags:
+- structural_biology
+- PPIs
+- mass_spectrometry
+- AlphaFold
+pretty_name: >-
+  DirectContacts2: A network of direct physical protein interactions derived
+  from high throughput mass spectrometry experiments
+repo: https://github.com/KDrewLab/DirectContacts2_analysis.git
+---
+# DirectContacts2: A network of direct physical protein interactions derived from high throughput mass spectrometry experiments
+Proteins carry out cellular functions by self-assembling into functional complexes, a process that depends on direct physical interactions 
+between components. While tools like AlphaFold and RoseTTAFold have advanced structure prediction, they remain limited in scaling to the full 
+human proteome. DirectContacts2 addresses this challenge by integrating diverse large-scale datasets, including AP/MS (BioPlex1–3, Boldt et al., Hein et al.), 
+biochemical fractionation (Wan et al.), proximity labeling (Gupta et al., Youn et al.), and RNA pulldown (Treiber et al.), to predict whether ~26 million 
+human protein pairs interact directly or indirectly.
+
+## Funding
+NIH R00, NSF/BBSRC
+
+## Citation
+Erin R. Claussen, Miles D Woodcock-Girard, Samantha N Fischer, Kevin Drew
+
+## References
+Kevin Drew, Christian L. Müller , Richard Bonneau, Edward M. Marcotte (2017) Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLOS Computational Biology 13(10): e1005625. https://doi.org/10.1371/journal.pcbi.1005625
+Samantha N. Fischer, Erin R Claussen, Savvas Kourtis, Sara Sdelci, Sandra Orchard, Henning Hermjakob, Georg Kustatscher, Kevin Drew hu.MAP3.0: Atlas of human protein complexes by integration of > 25,000 proteomic experiments. Molecular Systems Biology 1–33 (2025) doi:10.1038/s44320-025-00121-5.
+Huttlin et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome Cell. 2021 May 27;184(11):3022-3040.e28. doi: 10.1016/j.cell.2021.04.011.
+Huttlin et al. Architecture of the human interactome defines protein communities and disease networks. Nature. 2017 May 25;545(7655):505-509. DOI: 10.1038/nature22366.
+Treiber et al. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis.. Mol Cell. 2017 Apr 20;66(2):270-284.e13. doi: 10.1016/j.molcel.2017.03.014.
+Boldt et al. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nat Commun. 2016 May 13;7:11491. doi: 10.1038/ncomms11491.
+Youn et al. High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Mol Cell. 2018 Feb 1;69(3):517-532.e11. doi: 10.1016/j.molcel.2017.12.020.
+Gupta et al. A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell. 2015 Dec 3;163(6):1484-99. doi: 10.1016/j.cell.2015.10.065.
+Wan, Borgeson et al. Panorama of ancient metazoan macromolecular complexes. Nature. 2015 Sep 17;525(7569):339-44. doi: 10.1038/nature14877. Epub 2015 Sep 7.
+Hein et al. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell. 2015 Oct 22;163(3):712-23. doi: 10.1016/j.cell.2015.09.053. Epub 2015 Oct 22.
+Huttlin et al. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. 2015 Jul 16;162(2):425-40. doi: 10.1016/j.cell.2015.06.043.
+Reimand et al. g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016 Jul 8;44(W1):W83-9. doi: 10.1093/nar/gkw199.
+
+## Associated code 
+
+# Usage
+
+## Accessing and using the model
+DirectContacts2 was constructed using [AutoGluon](https://auto.gluon.ai/stable/index.html) an auto-ML tool. The module [TabularPredictor](https://auto.gluon.ai/stable/api/autogluon.tabular.TabularPredictor.html)
+is used to is used train, test, and make predictions with the model.