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.
Predict zinc binding sites on protein
Lin et al.
All-atom reconstruction and refinement of reduced protein models
Rotkiewicz P. et al.
Deep learning-based kcat prediction
Li et al.
Predict paratope residues
Papadopoulos et al.
Multiple Protein Structure Alignment at Scale
Gilchrist et al.
Ultra-fast protein structure search, multimer search, and clustering
van Kempen et al.
Fix and prepare PDB structures for downstream simulation
Eastman P et al.
2D projection of protein surface features
Schweke et al.
Codon language model
Heuschkel et al.
Detect pockets on a protein
Guilloux et al.
Detect druggable ligand-binding pockets on RNA
Veenbaas 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.
Multiple sequence alignment (MSA)
Steinegger et al.
Search immune proteins against public databases using nucleotides or AA sequences as input
Ye J et al.
Clustering by MSA
Multiple sequence alignment
Sievers F et al.
Reconstruct ancestral sequences from modern sequences
Sugihara Y et al.
Statistical coupling analysis of protein sequence alignments
Rivoire O 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.
In silico protease digestion of proteins (Expasy rules).
Levitsky 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
Ensemble RMSD calculator (up to 50 conformers, autodetects multi-model or multi-file input)
Gil et al.
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.
Oligo binding free-energy scan for ASO and siRNA site ranking
Lu ZJ et al.
Predict protein chemical shifts from PDB structures
Claes et al.
Predict antibody paratopes from heavy chain structures
Chinery 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.
Identify interface residues between protein chains using Voronoi tessellation
Steven Grudman et al.
Predict conformational flexibility of antibody and TCR CDR3 loops
Spoendlin et al.
Cluster a list of PDB files or a trajectory
McGibbon et al.
End-to-end gapmer ASO designer: RNase-H cleavage PWM, off-target BLAST, cross-species homology, and SNP avoidance.
Chen et al.
RNA accessibility and secondary-structure analysis for ASO / siRNA target-site selection (ViennaRNA folding engine).
Lorenz et al.
Contact molecular surface area for protein-protein interfaces
Lawrence MC et al.