Utilities
Aliphatic Index
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
AlphaFold Database Download
Download AlphaFold DB predicted structures and confidence files by UniProt accession.
Amino acid composition
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
BindingDB Download
Download BindingDB binding record files by BindingDB monomer ID.
ChEBI Download
Download ChEBI chemical entity records as JSON by ChEBI ID.
ChEMBL Download
Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.
CSV to FASTA
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
DNA mutator
Generate batches of mutated DNA variants from one or more FASTA sequences. Create substitution, insertion, deletion, or mixed variant libraries with reproducible settings.
DNA Shuffle
Shuffle DNA sequences while preserving nucleotide, dinucleotide, or k-mer composition for generating randomized control sequences
DNA to Protein Converter
Translate DNA sequences to protein sequences using genetic code
DNA to RNA converter
Convert DNA sequences to RNA (transcription) - replaces T with U
DNAGenIQ - Random DNA sequence generator
Generate random DNA sequences with customizable length, GC content, and restriction sites for molecular cloning and testing purposes.
Extinction coefficient calculator
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
FASTA splitter
Split FASTA files into record-based chunks by sequence count, target file count, maximum residues per file, or one file per sequence.
FASTA to FASTQ Converter
Convert FASTA sequence files to FASTQ format with mock quality scores
FASTQ to FASTA converter
Convert standard FASTQ reads to FASTA with validation, IUPAC nucleotide support, average-quality filtering, and downloadable summaries
Filter DNA
Clean and filter DNA sequences by removing or replacing non-standard nucleotide characters. Supports multiple filter modes including standard 4 bases, IUPAC ambiguity codes, and custom character sets.
Filter protein
Clean and filter protein sequences by removing or replacing non-standard amino acid characters. Supports multiple filter modes including standard 20 amino acids, IUPAC codes, and custom character sets.
GenBank Feature Extractor
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
GenBank to FASTA Converter
Convert GenBank files to FASTA format
Glycosylation site finder
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
GRAVY
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
InChI to SMILES
Convert InChI strings into SMILES with batch support and downloadable outputs.
Instability Index
Calculate the instability index of protein sequences. Values above 40 indicate an unstable protein with a short half-life in vitro.
InterPro Download
Download InterPro protein family and domain records as JSON by InterPro ID.
Ligand fixer
Fix ligand files that fail RDKit, Meeko, or docking preparation. Repair SDF, MOL, and MOL2 inputs, apply safe chemistry cleanup, and export docking-ready SDF files.
MOL to SMILES
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
MOL2 to SMILES
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
One-to-Three Converter
Convert single-letter amino acid codes to three-letter codes
Open Babel
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
PDB Download
Download PDB, CIF, and FASTA files from RCSB PDB by 4-character structure ID.
PDB to CIF Converter
Convert Protein Data Bank files to Crystallographic Information File format
PDB to FASTA converter
Convert Protein Data Bank files to FASTA sequence format
PDB to MOL2 Converter
Convert Protein Data Bank files to MOL2 molecular format
PDB to SDF Converter
Convert Protein Data Bank files to Structure Data Format
PDB2PQR
PDB2PQR prepares protein structures for electrostatics calculations by adding missing atoms, predicting protonation states using PROPKA, and assigning atomic charges and radii from standard force fields.
PDBe Download
Download PDBe structure files as PDB and CIF by PDB ID.
PDBFixer
PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.
pI Calculator
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Protein molecular weight calculator
Calculate protein molecular weight (MW) from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV sequence input, average or monoisotopic masses, initiator Met removal, and disulfide correction.
Protein motif scanner
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Protein to DNA converter
Reverse translate protein sequences to possible DNA sequences
ProtGenIQ - Random protein sequence generator
Generate random protein sequences with customizable length, composition, and amino acid properties
PubChem Download
Download PubChem compound records as JSON, SDF, and SMILES by CID, compound name, or InChIKey.
QuickGO Download
Download QuickGO Gene Ontology term records as JSON by GO ID.
Reverse complement generator
Generate reverse, complement, or reverse-complement of DNA/RNA sequences
Rhea Download
Download Rhea biochemical reaction records as RDF by Rhea reaction ID.
RNA to DNA converter
Convert RNA sequences to DNA (reverse transcription) - replaces U with T
RNAGenIQ - Random RNA sequence generator
Generate random RNA sequences with customizable types and structural features
SDF to PDB Converter
Convert Structure Data Format files to Protein Data Bank format
SDF to SMILES
Convert SDF ligand files, including multi-record batches, into SMILES strings.
SMILES to InChI
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
SMILES to MOL2
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
SMILES to PDB
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
SMILES to SDF
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Three-to-one converter
Convert three-letter amino acid codes to single-letter codes
TXT to FASTA converter
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
UniProt Download
Download UniProt protein sequence records as FASTA and JSON by accession.