[Chimera-users] some CADD tools released

gentamicin5 gentamicin5 at yahoo.com.tw
Wed Nov 19 04:38:11 PST 2003

Dear all,

I have written some CADD tools, and the details are
described below.
All of these programs are released under GNU/GPL.
You can download them from:

CADD tools (linux & irix)
PSCAN is a small but a practical tool for finding any
potential binding site of a protein. It can picture
the size and appearance of a binding site, and point
out the possible pharmacophore.Thus it is helpful for
drug design. While running DOCK, QCPE_MS is necessary
for autoMS and even the next step sphgen. QCPE_MS,
however, is a commercial package. Now, PSCAN and
SPHBOX can do the same job. After removing all dots
outside of the target binding site by SPDBV (or
others), and choosing several positions you are
interesting, run SPHBOX to generate sph and box files.

PMOL2Q is a specific file format converter for protein
pdb file to mol2 file with adding hydrogens and
partial charges. From v2.1.1, PMOL2Q can also output
pdbq and pdbqs format. (The pdbqs format is added
solvation data according with ADDSOL in AutoDock) It
can recognize each amino acid and reconstruct the
coordination precisely. The bond length of 109 pm for
C-H, 101 pm for N-H, 96 pm for O-H and 134 pm for S-H
are used for adding hydrogens.You can choose to add
global hydrogens or only polar hydrogens. KOLL and
AMBER95 partial charges are available in PMOL2Q.
PMOL2Q can also check probabel error of protein
coordination, including incomplete atom_missing
residues and atom bumps. Hydrogens will not be added
on incomplete residues if they exist. You need to fix
it by other program before converting file format.
(ex. SPDBV can fix the incomplete residues by mutate

DBFILTER can check the mol2 format database, and pick
out any problematic structure which results in
"segmentation fault" of DOCK during flexible docking.
(for example, salt or structure which contains
multi-molecular built in....) And DBFILTER will output
a new database which you want. There are also 12 kinds
of filters for spotlighting drug-like properties.
Including: Common_atoms_only, Molecular_weight, LogP,
H_bond_donors, H_bond_acceptors, Sum_of_N+O, Halogens,
Rings, Big_ring_members, Rotatable_bonds, CH3(CH2)n- , CF3(CF2)n-.

每天都 Yahoo!奇摩

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