Utilities
Search proteins against public databases
Altschul et. al
A web macromolecule viewer embedded into Tamarind (Visualize your PDB files and more!)
Sehnal et. al.
Add metal ions to protein
Durr et. al
Add waters to protein
Kuang et. al
All-atom reconstruction and refinement of reduced protein models
Rotkiewicz P. et. al
Multiple Protein Structure Alignment at Scale
Gilchrist et. al
Ultra-fast protein structure search, multimer search, and clustering
van Kempen et. al
Codon language model
Heuschkel et. al
Detect pockets on a protein
Guilloux et. al
Detect and characterize biomolecular cavities
Guerra et. al
Position-Specific Iterated BLAST for detecting distant protein homologs
Evaluate your docking interface
Basu et. al
Score and rank antibody-antigen complex models by predicted DockQ
Xu et. al
Search immune proteins against public databases using nucleotides or AA sequences as input
Ye J et. al
Clustering by MSA
Steinegger et. al
Multiple sequence alignment
Sievers F et. al
Reconstruct ancestral sequences from modern sequences
Sugihara Y et. al
Annotate immune proteins
Dunbar et. al
Prihoda D et. al
Check protein structure quality
Davis et. al
Predict DockQ score of a predicted protein structure
Bryant et. al
Align list of sequences
Eddy et. al
Predict the pKa values of ionizable groups in proteins
Olsson et. al
Search antibody sequences from patents and literature
Abanades B et. al
Align a list of PDB files
Delano et. al
Remove non-globular regions from predicted protein structures given a pdb file
Tam et. al
Calculate RMSD between two protein structures
Min distance between two sets of selected residues
Almeida DS et. al
Calculate radius of gyration of a protein structure
Structurally align proteins and nucleic acids
Chengxin Zhang et. al
Back-translation of a protein sequence
Rice P et. al
Automatic oligonucleotide design for PCR-based gene synthesis
Hoover DM et. al
Predict protein chemical shifts from PDB structures
Claes et. al
Search Observed Antibody Space (OAS) paired sequence database to find similar protein sequences
Olsen TH et. al
Convert between different file formats
Search ChemBL database to find similar molecules
Mendez D et. al
Search PubChem database to find similar molecules
Generate overview and schematic diagrams of protein chains, DNA, ligands, and metal ions
Laskowsk et. al
Cluster a list of PDB files or a trajectory
McGibbon et. al