ProteinIQ

File format

FASTQ to FASTA TXT to FASTA PDB to FASTA PDB to SDF PDB to MOL2 PDB to CIF GenBank to FASTA SDF to PDB

DNA sequence

DNA to protein Reverse complement Random DNA generator

Protein sequence

Protein parameters Protein molecular weight Amino acid composition Extinction coefficients (verify)Aliphatic index (verify)Instability index Protein pI (fix)GRAVY index (verify)Protein to DNA Random protein generator Three-to-one converter One-to-three converter

PDB to MOL2 converter

Convert PDB protein structure files to MOL2 format for molecular modeling and drug design applications. Upload a PDB file or paste the structure data below.

Input (PDB format)

PDB

Or fetch by PDB ID

Enter a 4-character PDB ID to fetch the structure from RCSB database

Click to upload or drag and drop

PDB file (.pdb, .ent)

Max size: 50MB

Advanced conversion options

Chain selection

All chainsSpecific chains

Atom inclusion options

Include hydrogen atomsInclude heteroatoms (ligands, water, etc.)

Atom typing scheme

SYBYL (C.3, N.am, O.2, etc.)Tripos force fieldSimple element types

Structure options

Separate residues into substructuresGenerate bond connectivityAdd partial charges (Gasteiger method)

Output (MOL2 format)

MOL2

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