Huey, Ruth, Garrett M. Morris, Arthur J. Olson, and David S. Goodsell. 2007. “A Semiempirical Free Energy Force Field with Charge-Based Desolvation.” Journal of Computational Chemistry 28 (6): 1145–52. doi:10.1002/jcc.20634.
输出例子:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Total Intermolecular Interaction Energy = -3.1862 kcal/mol
Total Intermolecular vdW + Hbond + desolv Energy = -0.2499 kcal/mol
Total Intermolecular Electrostatic Energy = -2.9362 kcal/mol
Total Intermolecular + Intramolecular Energy = -5.6314 kcal/mol
epdb: USER Estimated Free Energy of Binding = -1.40 kcal/mol [=(1)+(2)+(3)-(4)]
epdb: USER Estimated Inhibition Constant, Ki = 94.72 mM (millimolar) [Temperature = 298.15 K]
epdb: USER
epdb: USER (1) Final Intermolecular Energy = -3.19 kcal/mol
epdb: USER vdW + Hbond + desolv Energy = -0.25 kcal/mol
epdb: USER Electrostatic Energy = -2.94 kcal/mol
epdb: USER (2) Final Total Internal Energy = -2.45 kcal/mol
epdb: USER (3) Torsional Free Energy = +1.79 kcal/mol
epdb: USER (4) Unbound System's Energy [=(2)] = -2.45 kcal/mol
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461
重新打分用法:
1
vina --config config.txt --score_only
config.txt的例子如下:
1
2
3
4
5
6
7
8
receptor = protein.pdbqt
ligand = ligand.pdbqt
center_x = -2.491 # Center of Grid points X
center_y = 30.038 # Center of Grid points Y
center_z = -10.765 # Center of Grid points Z
size_x = 25 # Number of Grid points in X direction
size_y = 25 # Number of Grid points in Y Direction
size_z = 25 # Number of Grid points in Z Direction
版本:
1
2
vina --version
AutoDock Vina 1.1.2 (May 11, 2011)
DrugScoreX
License: free without any limitations (redistribution requires permission)
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes Gerd Neudert and Gerhard Klebe Journal of Chemical Information and Modeling 2011 51 (10), 2731-2745
用法:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
dsx_mac_64.mac -h
...
pro_file : A pdb or mol2 file of your protein.
In pdb format metals in this file will be treated as part
of the protein. => Be sure to delete metals in the pdb file
if you want to supply some metals seperately (-M met_file)!
All other HETATMs will be ignored!
In mol2 format everything will be taken as part of the
protein. => Be sure to delete molecules you want to supply
seperately (-C, -W, -M) from the protein-mol2-file!
lig_file : A mol2- or autodock dlg-file containing all molecules that
O’Boyle, Noel M., Michael Banck, Craig A. James, Chris Morley, Tim Vandermeersch, and Geoffrey R. Hutchison. “Open Babel: An Open Chemical Toolbox.” J Cheminf 3 (2011): 33.
使用:
1
2
3
4
babel -H
Open Babel converts chemical structures from one file format to another
一个LC/MS数据管理和分析C++工具包 网站:http://open-ms.sourceforge.net/ Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. “OpenMS – an Open-Source Software Framework for Mass Spectrometry” BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.
