Options for exploring, presenting, and sharing 3D macromolecular structure models (PDB files), all free:

  • Recommended*: (easiest yet powerful; work in Windows, Mac OS X, linux; nothing to install)
    • Protein Data Bank has

      • An interactive 3D view in Jmol.
      • Full names of ligands, sites, non-standard residues.
      • Color by evolutionary conservation (ConSurf) to identify functional sites.
      • Published abstract.
      • Articles explaining structural bioinformatics terms and concepts including asymmetric unit, biological unit, electron density maps, NMR, resolution, R free, R value, See list at About Macromolecular Structure.
    • FirstGlance in Jmol – FirstGlance.Jmol.Org (easiest available; used by Nature et al.)
        One-click views of major structural features including:

      • Secondary structure, N and C termini
      • Composition (protein, DNA, RNA, ligands, solvent)
      • Hydrophobic vs. polar; charge
      • Non-covalent interactions with any moiety you specify
      • Find by sequence number or name; Hide portions.
      • Salt bridges, cation-pi interactions, temperature and more.
    • Customized Molecular Scenes are created most easily, by far, in the protein structure wiki Proteopedia.Org:
      • Scene-Authoring Tools make it easy (menus, buttons, forms; no command language to learn!)
      • See scene in Jmol as you create it (WSYWIG). Undo button!
      • Videos show you how.
      • Saved scenes are immediately on-line to share with anyone.
      • Popup button enlarges molecular scenes to full screen for lecture projection.
      • Save any page for off-line display.
      • Protect pages so only you can change them.
    • Powerpoint Slides, Publication-Quality Molecules, Animations, etc.

  • Also Excellent
    • Protein Explorer in Jmol
      • A Jmol version of the original Protein Explorer (see below) ported and greatly enhanced by Bob Hanson.
      • MDL Chime has been eliminated from this version.
      • Use with some caution as it is under development (2010) and occasional bugs may remain.
  • Other free molecular visualization software packages are listed at MolVisIndex.Org.

Educational molecular visualization resources for teachers: MolviZ.Org
For high school (secondary school) biology teachers: HighSchool.MolviZ.Org (New in 2009)

*Opinions and recommendations expressed on this page are those of Eric Martz.


As life is more than 2D, Proteopedia helps to bridge the gap between 3D structure & function of biomacromolecules. Proteopedia presents this information in a user-friendly way as a collaborative & free 3D-encyclopedia of proteins & other biomolecules.

FirstGlance in Jmol: Guided macromolecular visualization with remarkable ease of use.

MolviZ “Top 5”: The “Top 5” 3D Molecular Visualization Technologies

Amino acids molecular structure

An amino acid is an organic molecule that is made up of a basic amino group (−NH2), an acidic carboxyl group (−COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for α-amino [alpha-amino] carboxylic acid. A very essential component in building muscles, and favorite of any powerlifter, check out protein recommendations.

Growth Hormone molecular structure

The major isoform of the human growth hormone is a protein of 191 amino acids and a molecular weight of 22,124 daltons. The structure includes four helices necessary for functional interaction with the GH receptor. Read more about HGH and HGH supplements.


Peptide molecules are composed of two or more amino acids joined through amide formation involving the carboxyl group of each amino acid and the amino group of the next. The chemical bond between the carbon and nitrogen atoms of each amide group is called a peptide bond. Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. A peptide is formed by joining two or more amino acids. When the number of amino acids is less than about 50 these molecules are named peptides while larger sequences are referred to as proteins. The amino acids are coupled by a peptide bond, a special linkage in which the nitrogen atom of one amino acid binds to the carboxyl carbon atom of another. Read what’s the difference between Peptides & Protein and how peptides help in bodybuilding.

Structure of amino acids, peptides and proteins