Utilities
BLAST Search
Search proteins against public databases
Altschul et al.
Molstar Viewer
A web macromolecule viewer embedded into Tamarind (Visualize your PDB files and more!)
Sehnal et al.
PPM 3.0
Predict how a protein sits in a membrane: orientation, depth and hydrophobic thickness
Andrei L. Lomize et al.
AllMetal3D
Add metal ions to protein
Durr et al.
SuperWater
Add waters to protein
Kuang et al.
SuperMetal
Predict zinc binding sites on protein
Lin et al.
PULCHRA
All-atom reconstruction and refinement of reduced protein models
Rotkiewicz P. et al.
TCRdock Analyze
Analyze TCR:pMHC complexes: parse docking geometry, docking-RMSD, TCRdist.
Bradley P.
DLKcat
Deep learning-based kcat prediction
Li et al.
ParaSurf
Predict paratope residues
Papadopoulos et al.
FoldMason
Multiple Protein Structure Alignment at Scale
Gilchrist et al.
Foldseek
Ultra-fast protein structure search, multimer search, and clustering
van Kempen et al.
PDBFixer
Fix and prepare PDB structures for downstream simulation
Eastman P et al.
SURFMAP
2D projection of protein surface features
Schweke et al.
SynCodonLM
Codon language model
Heuschkel et al.
Lacuna
Find cryptic binding pockets with conformational ensemble analysis
Moore, C.W.
zPocket
Predict ligand-binding pockets from a protein sequence
Portnoi et al.
FPocket
Detect pockets on a protein
Guilloux et al.
fpocketR
Detect druggable ligand-binding pockets on RNA
Veenbaas et al.
pyKVFinder
Detect and characterize biomolecular cavities
Guerra et al.
PSI-BLAST Search
Position-Specific Iterated BLAST for detecting distant protein homologs
Altschul et al.
PEPMatch
Match peptides against reference proteomes with mismatch/indel tolerance
Marrama D et al.
DockQ
Evaluate your docking interface
Basu et al.
FoldBench Evaluator
Score a predicted complex the way FoldBench does
Xu et al.
DeepRank-Ab
Score and rank antibody-antigen complex models by predicted DockQ
Xu et al.
Multiple Sequence Alignment
Multiple sequence alignment (MSA) using Tamarind-hosted MMSeqs2
Steinegger et al.
IgBLAST
Search immune proteins against public databases using nucleotides or AA sequences as input
Ye J et al.
UniRef90 Novelty Search
MMseqs2 search against UniRef90 for design novelty
Steinegger et al.
Binder Novelty Search
MMseqs2 search against the ProteinBase known-binder corpus for binder novelty
Steinegger et al.
MSA Clustering
Clustering by MSA
Steinegger et al.
RNA MSA
Nucleotide multiple sequence alignment for RNA
Wheeler et al.
MSA Analysis
Multiple sequence alignment
Sievers F et al.
Ancestral Sequence Reconstruction
Reconstruct ancestral sequences from modern sequences
Sugihara Y et al.
pySCA
Statistical coupling analysis of protein sequence alignments
Rivoire O et al.
ANARCI
Annotate immune proteins
Dunbar et al.
SAbR
Renumber antibody structures from their backbone coordinates
del Alamo
Antibody Annotation
Annotate immune proteins
Prihoda D et al.
MolProbity
Check protein structure quality
Davis et al.
PDockQ
Predict DockQ score of a predicted protein structure
Bryant et al.
HMMalign
Align list of sequences
Eddy et al.
HMMER Search
Homology search against SwissProt or Pfam profile HMMs
Eddy et al.
PeptideCutter (Pyteomics)
In silico protease digestion of proteins (Expasy rules).
Levitsky et al.
PROPKA
Predict the pKa values of ionizable groups in proteins
Olsson et al.
PLAbDab
Search antibody sequences from patents and literature
Abanades B et al.
Align PDBs
Align a list of PDB files
Delano et al.
AlphaCutter
Remove non-globular regions from predicted protein structures given a pdb file
Tam et al.
BindCraft2 Score
BindCraft2's structural and developability checks on one binder-target complex
RMSD Calculator
Calculate RMSD between two protein structures
Delano et al.
pyRMSD
Ensemble RMSD calculator (up to 50 conformers, autodetects multi-model or multi-file input)
Gil et al.
Min Distance Between Selected Residues
Min distance between two sets of selected residues
Almeida DS et al.
Radius of Gyration
Calculate radius of gyration of a protein structure
Delano et al.
USalign
Structurally align proteins and nucleic acids
Chengxin Zhang et al.
Emboss Backtranseq
Back-translation of a protein sequence
Rice P et al.
DNAWorks
Automatic oligonucleotide design for PCR-based gene synthesis
Hoover DM et al.
OligoWalk
Oligo binding free-energy scan for ASO and siRNA site ranking
Lu ZJ et al.
Legolas
Predict protein chemical shifts from PDB structures
Darrows et al.
Paragraph Paratope Prediction
Predict antibody paratopes from heavy chain structures
Chinery et al.
OAS Search
Search Observed Antibody Space (OAS) paired sequence database to find similar protein sequences
Olsen TH et al.
File Converter
Convert between different file formats
Similarity Search
Find compounds similar to your query, across hosted databases or your own uploaded library
Mendez D et al.
PDBsum
Generate overview and schematic diagrams of protein chains, DNA, ligands, and metal ions
Laskowsk et al.
INTERCAAT
Identify interface residues between protein chains using Voronoi tessellation
Steven Grudman et al.
ITsFlexible
Predict conformational flexibility of antibody and TCR CDR3 loops
Spoendlin et al.
Cluster PDBs
Cluster a list of PDB files or a trajectory
McGibbon et al.
ClinASO
End-to-end gapmer ASO designer: RNase-H cleavage PWM, off-target BLAST, cross-species homology, and SNP avoidance.
Chen et al.
PLIP
Exact noncovalent inter-chain interaction profiling with source residue mappings.
Adasme et al.
ViennaRNA
RNA accessibility for ASO site selection and isolated RNA/DNA secondary-structure thermodynamics.
Lorenz et al.
Contact MS
Contact molecular surface area for protein-protein interfaces
Lawrence MC et al.