---------------------------------------
FRESNO: FRee Energy Scoring at NOvartis

(c) Dr. Didier ROGNAN
Bioinformatics Group
UMR CNRS 7081 
74 route du Rhin, B.P.24
F-67400 Ilkirch
France
_____________________________________

You can use Fresno either as a stand-alone program or as an interface to the SYBYL modelling package




A) Fresno as a standalone programme,

1) define a sybyl mol2 file in which ccordinates of your protein-ligand complex have been stored. 
2) at the unix prompt type

fresno -a n <input.mol2   (n= number of the first ligand atom)



Example: a mol2 file of a receptor-ligand complex is given in this distribution (test.mol2

The following command: fresno -a 4666 <test.mol2

should give you the following output:


 4703    atoms found
(  38    ligand atoms)
        Tot.     HB     Lipo      Rot.
Scores            1.0   218.4     1.6
Energy  -30.4    -3.3   -25.6     4.0

P(Ki)     5.3

Special:
                Lennard-Jones interaction:
                Tot.     rep.   att.
                -154.8   59.2   -213.9

                Buried polar score:     176.2
                Rot. Bonds (froz.):         2(2)
                H-Bonds/buried:           1.0


The PKi value gives you an idea of the affinity of the compound for your target.

B) Fresno interfaced to SYBYL

Two files (fresno.col, fresno.menubar) are provided with the distribution. Please locate both files under 
$TA_ROOT/sybylbase/tables/addons/ . Then, edit the file $TA_ROOT/tables/menubars/sybyl/menubar.spl
and place the following line :
"FRESNO..."              "$RUN fresno_score" \

just before the line starting with "BOSS..." (line 1005 in my SYBYL distribution) 

Restart SYBYL and execute Fresno at the menu:
Compute >> Interfaces >> Fresno
The interface requires that the protein and the ligand are stored in separate molecule areas (e.g. M1 and M2) 
