非常有用的蛋白质科学工具与项目

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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:

vina --version
AutoDock Vina 1.1.2 (May 11, 2011)

DrugScoreX

License: free without any limitations (redistribution requires permission)

DrugScoreX是一个较新的，对于蛋白配体打分具有比DrugScore更高精度的软件，其打分功能是基于统计势能？(statistical potentials)

网址:http://pc1664.pharmazie.uni-marburg.de/drugscore/

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:

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
              should be scored.

...

译者注:其可以对金属离子进行打分

例子:

译者注:个人觉得作者下载的是mac版本

dsx_mac_64.mac -P protein.pdb -L ligand.mol2 -D pdb_pot_0511

其中pdb_pot_0511在下载文件中:

dsx/
    ACC_DON_AnD_HYD_ARO_map.def    
    mac64/               # directory that contains the binaries
    README.txt            
    pdb_pot_0511/     # potentials

LigScore

License: free, open-source (GNU GPL)

与DrugScore的算法类似,提供本地(IMP 工具包)以及在线服务。
其得分功能具有两种”口味”, RankScore ，推荐被用于不同配体在蛋白结合界面的评分(例如虚拟筛选); PoseScore ，在设置的一系列配体叠代中寻找优化的结合构象(例如相同的具有不同方向或者构象的配体)

网址:http://salilab.org/imp/
在线网址:http://modbase.compbio.ucsf.edu/ligscore/

Fan H, Schneidman-Duhovny D, Irwin J, Dong GQ, Shoichet B, Sali A. Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions. J Chem Inf Model. 2011, 51:3078-92.

使用:

ligand_score -h
Usage: ligand_score file.mol2 file.pdb [libfile]

其中 protein_ligand_pose_score.lib 用来 PoseScore 打分， protein_ligand_rank_score.lib 用来 RankScore 打分。

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