| Cryo-EM structure determination |
| From cryo-EM density map to atomic structure: CryoAtom |
| Protein structure prediction |
| Protein structure prediction by trRosetta: trRosetta |
| Deep learning-based inter-residue contact and distance prediction: MapPred |
| Protein domain boundary prediction: UniDoc |
| Assessment of predicted inter-residue distance: APD |
| Model quality assessment: QDistance |
| Threading with contacts predicted by deep learning: CATHER |
| RNA structure and function prediction |
| RNA 3D strucutre prediction: trRosettaRNA |
| RNA inter-nucleotide contact prediction: RNAcontact |
| RNA solvent accessibility prediction: RNAsol |
| RNA threading: RNAthreader |
| RNA-ligand binding site prediction: RNAsite |
| Intrinsic Disordered Protein |
| Disordered flexible linker prediction: APOD |
| Disordered linear interacting peptides: CLIP |
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| Protein structure alignment |
| Multiple protein structure alignment and structure database search: mTM-align |
| Protein-ligand interactions |
| Protein-ligand binding database: Q-BioLiP |
| Protein-ligand complex structure prediction: COACH-D |
| Protein-DNA/RNA binding site prediction: NucBind |
| Coenzyme A (CoA)-binding site prediction: CoABind |
| Peptide-binding site prediction: PepBind |
