Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
HI - try the program contact from the ccp4 suite. http://www.ccp4.ac.uk/html/contact.html J Eleanor Dodson <[EMAIL PROTECTED]> wrote:> > mathias wrote: >> Dear all, >> >> Can anyone of you guys recommend free software, or any open access >> internet server, to calculate VDW interactions of small molecules >> binding to protein. The only information I need is an output file >> which lists all amino acids of the target protein which make VDW >> interactions with the binding small molecule. >> Thank you very much for your help and recommendations, >> >> Mathias >> >> > Have you tried the MSD Pisa server at the EBI ? It lists all sorts of > information? > > Eleanor -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
mathias wrote: Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias Have you tried the MSD Pisa server at the EBI ? It lists all sorts of information? Eleanor
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
CONTACT from the CCP4 suite can do this - have a look at the documentation and examples. Tadeusz "mathias" <[EMAIL PROTECTED]> Sent by: "CCP4 bulletin board" 27-Feb-2007 18:43 Please respond to "mathias" <[EMAIL PROTECTED]> To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] software to calculate VDW interactions between small molecule and protein Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
Hi Mattias, CCP4mg will list contact areas in the form of the attached file. This is evaluating the buried area (ie difference is solvent accessible area with and without the ligand bound). It ought to be possible to run a script if you have a significant number of structures - contact me for help there. Liz On Tuesday 27 February 2007 18:43, mathias wrote: > Dear all, > > Can anyone of you guys recommend free software, or any open access > internet server, to calculate VDW interactions of small molecules > binding to protein. The only information I need is an output file > which lists all amino acids of the target protein which make VDW > interactions with the binding small molecule. > Thank you very much for your help and recommendations, > > Mathias Residue contact area for:/home/lizp/ccp4mg_tutorial/1df7.pdb :: All peptide Full selection command: amino_acid Solvent Accessible area by residue -- A/5(ILE) 8.89 A/6(TRP) 5.08 A/7(ALA) 0.61 A/20(ILE) 22.14 A/25(PRO) 10.42 A/27(ASP) 12.92 A/28(GLN) 67.26 A/29(ALA) 12.42 A/30(HIS) 0.73 A/31(PHE) 45.34 A/32(ARG) 28.13 A/46(THR) 3.44 A/49(SER) 15.28 A/50(LEU) 20.84 A/51(PRO) 19.36 A/53(LYS) 5.19 A/54(VAL) 24.08 A/57(LEU) 13.83 A/58(PRO) 1.87 A/60(ARG) 5.47 A/94(ILE) 6.73 A/111(GLU) 0.13 A/113(THR) 1.07 //500(NDP) 22.55 //502(GOL) 13.01 Solvent Accessible area by atom --- A/5(ILE)/C 0.15 A/5(ILE)/O 2.49 A/5(ILE)/CG1 5.57 A/5(ILE)/CD1 0.69 A/6(TRP)/CA1.89 A/6(TRP)/C 2.64 A/6(TRP)/O 0.56 A/7(ALA)/N 0.18 A/7(ALA)/CB0.43 A/20(ILE)/CG1 0.73 A/20(ILE)/CD1 21.40 A/25(PRO)/CA 0.03 A/25(PRO)/O5.61 A/25(PRO)/CB 4.78 A/27(ASP)/OD1 4.42 A/27(ASP)/OD2 8.50 A/28(GLN)/CA 0.40 A/28(GLN)/C1.30 A/28(GLN)/O4.55 A/28(GLN)/CB 6.98 A/28(GLN)/CG 8.79 A/28(GLN)/CD 4.61 A/28(GLN)/OE1 26.03 A/28(GLN)/NE2 14.61 A/29(ALA)/N0.91 A/29(ALA)/CA 5.76 A/29(ALA)/CB 5.75 A/30(HIS)/CD2 0.73 A/31(PHE)/CA 0.00 A/31(PHE)/CB 5.01 A/31(PHE)/CG 2.65 A/31(PHE)/CD1 10.20 A/31(PHE)/CD2 10.49 A/31(PHE)/CE1 5.70 A/31(PHE)/CE2 7.06 A/31(PHE)/CZ 4.23 A/32(ARG)/CB 5.64 A/32(ARG)/CG 0.34 A/32(ARG)/CD 14.03 A/32(ARG)/NH1 8.12 A/46(THR)/CG2 3.44 A/49(SER)/O6.04 A/49(SER)/CB 0.40 A/49(SER)/OG 8.84 A/50(LEU)/CA 0.29 A/50(LEU)/CD2 20.55 A/51(PRO)/CG 7.12 A/51(PRO)/CD 12.24 A/53(LYS)/NZ 5.19 A/54(VAL)/CG1 14.02 A/54(VAL)/CG2 10.06 A/57(LEU)/CD1 0.44 A/57(LEU)/CD2 13.39 A/58(PRO)/CG 1.31 A/58(PRO)/CD 0.56 A/60(ARG)/NH1 1.44 A/60(ARG)/NH2 4.03 A/94(ILE)/O3.57 A/94(ILE)/CD1 3.16 A/111(GLU)/O 0.13 A/113(THR)/OG1 1.07 //500(NDP)/NO2*1.04 //500(NDP)/NC7 0.02 //500(NDP)/NO7 8.52 //500(NDP)/NC4 8.04 //500(NDP)/NC5 4.12 //500(NDP)/NC6 0.81 //502(GOL)/C1 4.27 //502(GOL)/O2 8.73 Total solvent accessible area: 366.79Angstoem*2
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
Molprobity has a great tool for this under the section Visualize interface contacts. One caveat though, if the small molecule isn't already in ligand depot you have to provide your own PDB format description. On 2/27/07, mathias <[EMAIL PROTECTED]> wrote: Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
Dear Mathias,
In the old days, I used a program called "ligplot", which gives you
a .ps output file with the interactions involved, and the distances.
I'm using PyMol as well, but things might not be exactly what you
want. Here, I'm just looking at residues 4.2 angstrom away in the
interacting pocket between my protein and my ligand. It's very fast
to do, and you can even have an output picture. Following is a fast
script where protein.pdb and ligand.pdb are the required files.
Please note that in addition to the picture generated, the script
will also generate two files with interacting residues in one, and
interacting atoms in the other. Again, I'm not sure that it will be
of any use still...
#Run this under PyMol#
delete all
## settings for the final picture ##
set depth_cue=1
set ray_trace_fog=1
set cartoon_discrete_colors, 1
set dot_solvent, 1
set dot_density, 3
set dot_color, white
space cmyk
set sphere_scale, 0.25
## load your 2 pdbs ##
load protein.pdb, my protein
load ligand.pdb, my_ligand
## look at the interacting residues ##
h_add
flag ignore, none
from pymol import cmd
ligand_area=cmd.get_area("my_ligand")
protein_area=cmd.get_area("my_protein")
create my_complex, my_ligand|my_protein
complex_area=cmd.get_area("my_complex")
from pymol import stored
## interacting residues set at 4.2 angstrom distance ##
cmd.select("interacting_atoms", "* w. 4.2 of my_ligand")
stored.list=[]
cmd.iterate("interacting_atoms", "stored.list.append((resi, resn))")
select interacting_residues, br. interacting_atoms
disable interacting_residues
## generate the picture ##
color white, my_protein
color yellow, my_ligand
color blue, e. n
color red, e. o
color forest, e. s
color orange, e. p
hide
show spheres, interacting_atoms&!e. h
show sticks, interacting_residues&!e. h
label (name ca+C1*+C1'&(br.(interacting_residues))),"%s-%s"%(resn,resi)
save interacting_residues.pdb, interacting_residues, quiet=0
save interacting_atoms.pdb, interacting_atoms, quiet=0
orient
zoom interacting_residues
## numerical values of surface interactions ##
print ligand_area
print protein_area
print complex_area
print (ligand_area + protein_area) - complex_area
#
All the best.
Leo
On Feb 28, 2007, at 3:43 AM, mathias wrote:
Dear all,
Can anyone of you guys recommend free software, or any open access
internet server, to calculate VDW interactions of small molecules
binding to protein. The only information I need is an output file
which lists all amino acids of the target protein which make VDW
interactions with the binding small molecule.
Thank you very much for your help and recommendations,
Mathias
==
Chavas Leonard M.G., Ph.D.
Structural Research Center
KEK,PF. 1-1 Oho
Tuskuba, Ibaraki - Japan
-
PHS: +81(0)29-864-5200 (ext: 2682)
e-mail: [EMAIL PROTECTED]
URL: http://pfweis.kek.jp/~leo
==
Re: [ccp4bb] software to calculate VDW interactions between small molecule and protein
I have a perl script to do this job. The pdb file should contain your ligand. Simplest way to run it is "lig_contact file.pdb" If the script does not find the ligand, you can switch to command line options. The script prepares a pymol input file and fires it up to display the interactions. After you close the pymol window you can see the pymol script file. The list of interactions is listed as "distance .?? = (ligand atom), (protein atom)." in this file. The '??' could be cc (hydrophobic interaction) or hb (hydrogen bond). Thanks Abhinav -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of mathias Sent: Tuesday, February 27, 2007 10:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] software to calculate VDW interactions between small molecule and protein Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias lig_contact Description: lig_contact
[ccp4bb] software to calculate VDW interactions between small molecule and protein
Dear all, Can anyone of you guys recommend free software, or any open access internet server, to calculate VDW interactions of small molecules binding to protein. The only information I need is an output file which lists all amino acids of the target protein which make VDW interactions with the binding small molecule. Thank you very much for your help and recommendations, Mathias
