ProteomeScout
Matlock MK, Holehouse AS, Naegle KM. ProteomeScout: a repository and analysis resource for post-translational modifications and proteins. Nucleic Acids Res. 2015;43(Database issue):D521-D530. doi: 10.1093/nar/gku1154.
Downloads
| Dataset | Description | Status |
|---|---|---|
| Protein data TSV | Primary TSV-backed protein/PTM dataset. | Available (117910586 bytes) |
| Citation TSV | Evidence and citation records linked from PTM entries. | Available (19755 bytes) |
Species Reference Datasets
| Species | Reference CSV | Size |
|---|---|---|
| . Bos Taurus Reference Dataset | ._bos_taurus_reference_dataset.csv | 4096 bytes |
| . Drosophila Melanogaster Reference Dataset | ._drosophila_melanogaster_reference_dataset.csv | 4096 bytes |
| . Homo Sapiens Reference Dataset | ._homo_sapiens_reference_dataset.csv | 4096 bytes |
| . Mus Musculus Reference Dataset | ._mus_musculus_reference_dataset.csv | 4096 bytes |
| . Rattus Norvegicus Reference Dataset | ._rattus_norvegicus_reference_dataset.csv | 4096 bytes |
| . Saccharomyces Cerevisiae Strain Atcc 204508 S288C Reference Dataset | ._saccharomyces_cerevisiae_strain_atcc_204508_s288c_reference_dataset.csv | 4096 bytes |
| Bos Taurus Reference Dataset | bos_taurus_reference_dataset.csv | 1648875 bytes |
| Drosophila Melanogaster Reference Dataset | drosophila_melanogaster_reference_dataset.csv | 470442 bytes |
| Homo Sapiens Reference Dataset | homo_sapiens_reference_dataset.csv | 38442946 bytes |
| Mus Musculus Reference Dataset | mus_musculus_reference_dataset.csv | 16897222 bytes |
| Rattus Norvegicus Reference Dataset | rattus_norvegicus_reference_dataset.csv | 5332058 bytes |
| Saccharomyces Cerevisiae Strain Atcc 204508 S288C Reference Dataset | saccharomyces_cerevisiae_strain_atcc_204508_s288c_reference_dataset.csv | 1937548 bytes |
Software
ProteomeScoutAPI
Holehouse AS, Naegle KM. Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations. PLoS One. 2015;10(12):e0144692. doi: 10.1371/journal.pone.0144692.
KSTAR
Crowl S, Jordan BT, Ahmed H, Ma CX, Naegle KM. KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data. Nat Commun. 2022;13(1):4283. doi: 10.1038/s41467-022-32017-5.
CoDIAC
Kandoor A, Martinez G, Hitchcock JM, Angel S, Campbell L, Rizvi S, Naegle KM. CoDIAC: A comprehensive approach for interaction analysis provides insights into SH2 domain function and regulation. Sci Signal. 2025;18(913):eads8396. doi: 10.1126/scisignal.ads8396.
PTM-POSE
Crowl S, Coleman MB, Chaphiv A, Jordan BT, Naegle KM. Systematic analysis of the effects of splicing on the diversity of post-translational modifications in protein isoforms using PTM-POSE. Cell Syst. 2025;16(7):101318. doi: 10.1016/j.cels.2025.101318.
DANSy
Shimpi AA, Naegle KM. Uncovering the domain language of protein functionality and cell phenotypes using DANSy. bioRxiv [Preprint]. 2025 Jul 1:2024.12.04.626803. doi: 10.1101/2024.12.04.626803.
OpenEnsembles
Ronan T, Anastasio S, Qi Z, Tavares PHS, Sloutsky R, Naegle KM. OpenEnsembles: A Python Resource for Ensemble Clustering. J Mach Learn Res. 2018;19(26):1-6.
ASPEN
Sloutsky R, Naegle KM. ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models. eLife. 2019;8:e47676. doi: 10.7554/eLife.47676.