[gmx-users] best software to design molecules

John Kerrigan kerrigje at umdnj.edu
Thu Jun 12 14:13:01 CEST 2003

Hmmm ...  Great question!  Swiss PDB viewer (aka DeepView see
http://us.expasy.org/spdbv/) is a wonderful tool for modifying protein
structure files and as an interface to SwissModel.  Here's some of what you
can do with DeepView:

1. DeepView will fix disordered residues in a structure file.  It will
rebuild missing side chains automatically for you.  Beware, the new PDB file
will tag the rebuilt side chain atoms with annoying control characters that
you must remove in a text editor.

2.  You can mutate residues with a click of the mouse.

3.  You can use DeepView to prepare input to the SwissModel server
(Homology/Comparative Modelling).  You can build homology models from a
sequence (FASTA format) and a reference structure.  DeepView can do multiple
sequence alignments.

DeepView is a nice robust little freebie application for working with
proteins.  I highly recommend it.

A handy cost-effective tool for building things is MOE (Molecular Operating
Environment) available from Chemical Computing Group
(http://www.chemcomp.com).  You can build polypeptides from scratch in
various secondary structure forms (you can't fold them, of course), nucleic
acid chains (DNA only, single strand and duplexes), and small molecules.  We
also use Sybyl (Tripos) and InsightII (Accelrys) for building things.

Hope this is helpful.



John E. Kerrigan, Ph.D.
Computational Biologist

Adjunct Associate Professor
Dept. of Pharmacology

Academic Computing Services
RWJMS-Univ. of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08854

(732) 235-4473  phone
(732) 235-5252  fax


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