Beyond Proteins: Modeling the Complexity of the Proteoform with π-Proteoformer

Checkpoints This directory contains pre-trained and fine-tuned model checkpoints for Proteoformer. Pre-trained Model proteoformer-base (proteoformer-base.tar.gz) The base Proteoformer model pre-trained on large-scale protein sequences and proteoform corpus. This checkpoint directory proteoformer-base.tar.gz zip serves as the foundation for all downstream fine-tuning tasks. Fine-tuned Checkpoints PTM_bench (PTM_bench.tar.gz) Fine-tuned models for PTM site prediction tasks on various modification types: Checkpoint Modification Type Target Residue acetylation_k_checkpoint_proteoformer.pt Acetylation Lysine (K) glycosylation_n_checkpoint_proteoformer.pt Glycosylation Asparagine (N) methylation_k_checkpoint_proteoformer.pt Methylation Lysine (K) methylation_r_checkpoint_proteoformer.pt Methylation Arginine (R) phosphorylation_st_checkpoint_proteoformer.pt Phosphorylation Serine/Threonine (S/T) phosphorylation_y_checkpoint_proteoformer.pt Phosphorylation Tyrosine (Y) sumoylation_k_checkpoint_proteoformer.pt SUMOylation Lysine (K) ubiquitination_k_checkpoint_proteoformer.pt Ubiquitination Lysine (K) PTM functional association prediction Fine-tuned model for predicting functional associations of PTM sites: Checkpoint Task PTM_sites_functional_association_prediction_ckpt.pt PTM Functional Association Prediction Variant_PTM_effect Fine-tuned models for predicting the effects of genetic variants on PTM sites: Checkpoint Task Direct_Variant_PTM_effect_ckpt.pt Direct variant effect on PTM sites Indirect_Variant_PTM_effect_ckpt.pt Indirect variant effect on PTM sites License These checkpoints are released under the Apache 2.0 License.