Summary: software to add Hydrogens to proteins.
Previously, I requested:
> I need to find software that will add
> hydrogens to proteins structures in
> PDB format. It must run on a PC (win95 or NT).
Here is a brief summary of the responses I received.
I downloaded MSI's WebLab viewer (option B, below) and
really like it. I still have not tried the other
Thanks again to all who responded. Your suggestions
were very helpful.
Rick Ornstein had a program called Network. It worked on Biosym car files; so
maybe you could do a translation. I don't know if it is still maintained by
his group. Also, it was written for UNIX but could probably be ported to NT.
Try WebLab Viewer 2.0 - available free from MSI at
If you have a good Kekule structure available, then PCMODEL (Serena
Software...812-3330823/Gilbert "-at-" indiana.edu) should be able to do it.
Dear Mark, Babel (freeware) can add/subtract H atoms to several types of
files, enclosed PDB files. I've not the exact address of it in mind while
I'm writing but you may find a link to it in our software page at
This is a very basic feature that probably isn't highlighted because just
about every program can do it. Chem3D, Macromodel, and Hyperchem are among
the three most-often-mentioned programs on this list, I think. All of them
can do what you describe. For more information, see (in order):
Check out the Molecular Modelling Toolkit at
It has everything you need to addd hydrogens in reasonable (but not
necessarily energy-minimized) positions to proteins. It's free and
should run on Win95 and NT (but not DOS or Win 3.1 - it needs long
file names), although I have tested it only on Unix systems.