All tools

Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.

Download AlphaFold DB predicted structures and confidence files by UniProt accession.

Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.

Download BindingDB binding record files by BindingDB monomer ID.

Download ChEBI chemical entity records as JSON by ChEBI ID.

Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.

Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection

Mutate DNA online and generate reproducible substitution, insertion, deletion, or mixed variant libraries from plain sequences or FASTA.

Shuffle DNA sequences while preserving nucleotide, dinucleotide, or k-mer composition for generating randomized control sequences

Translate DNA sequences to protein sequences using genetic code

Convert DNA sequences to RNA (transcription) - replaces T with U

Generate random DNA sequences with customizable length, GC content, and restriction sites for molecular cloning and testing purposes.

Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.

Split FASTA files into record-based chunks by sequence count, target file count, maximum residues per file, or one file per sequence.

Convert FASTA sequence files to FASTQ format with mock quality scores

Convert standard FASTQ reads to FASTA with validation, IUPAC nucleotide support, average-quality filtering, and downloadable summaries

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.

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.

Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features

Convert GenBank files to FASTA format

Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.

Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.

Convert InChI strings into SMILES with batch support and downloadable outputs.

Calculate the instability index of protein sequences. Values above 40 indicate an unstable protein with a short half-life in vitro.

Download InterPro protein family and domain records as JSON by InterPro ID.

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.

Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.

Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.

Convert single-letter amino acid codes to three-letter codes

Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.

Download PDB, CIF, and FASTA files from RCSB PDB by 4-character structure ID.

Convert Protein Data Bank files to Crystallographic Information File format

Convert Protein Data Bank files to FASTA sequence format

Convert PDB structures up to 20,000 atoms to Tripos MOL2 with Open Babel in the browser

Convert Protein Data Bank files to Structure Data Format

PDB2PQR prepares protein and nucleic-acid structures for electrostatics calculations by adding missing atoms, predicting protonation states using PROPKA, and assigning atomic charges and radii from standard or custom force fields.

Download PDBe structure files as PDB and CIF by PDB ID.

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.

Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.

Calculate protein molecular weight from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV input, average or monoisotopic masses, initiator Met removal, and disulfide correction.

Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.

Reverse translate protein sequences to possible DNA sequences

Generate random protein sequences with customizable length, composition, and amino acid properties

Download PubChem compound records as JSON, SDF, and SMILES by CID, compound name, or InChIKey.

Download QuickGO Gene Ontology term records as JSON by GO ID.

Generate reverse, complement, or reverse-complement of DNA/RNA sequences in raw, FASTA, or FASTQ format

Download Rhea biochemical reaction records as RDF by Rhea reaction ID.

Convert RNA sequences to DNA (reverse transcription) - replaces U with T

Generate random RNA sequences with customizable types and structural features

Convert Structure Data Format files to Protein Data Bank format

Convert SDF and MOL ligand structures to AutoDock PDBQT format

Convert SDF ligand files, including multi-record batches, into SMILES strings.

Convert SMILES strings into InChI strings with batch support and downloadable outputs.

Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.

Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.

Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.

Convert three-letter amino acid codes to single-letter codes

Convert TXT or pasted DNA, RNA, and protein sequences to FASTA locally in your browser, with cleanup, validation, and downloads.

Download UniProt protein sequence records as FASTA and JSON by accession.