'Web Server'button in the top navigation, and next you will be lead to one certain calculator.
'Get Smiles/Smarts'button to copy the SMILES to clipboard.
Paste the SMILES in the
'Text Box' and choose
'view molecular structure' or
Note: 'view molecular structure' is the function of JSDraw.
If calculating descriptors of a number of molecules at one time, click the
'browse' button and select your file (*.smi or *.sdf) , then click
Note:The file should be well checked and prepared before using. You can use 'ChemCONV' or other related software to prepare. The input format must be standard
After the completion of calculation, the browser will redirect users to the result page, In which you will get your result showing and download the result by certain format.
The whole process of calculating 3D molecular descriptors is nearly the same with that of Calculating 1D/2D molecular descriptors.
After selecting descriptors, a kind of forcefield for MOPAC optimization is needed and must be chosen from the drop-down menu. For more information please refer ChemMOP.
Note: Limited by the system resources, we set a maximum number of batch computing for each calculator. As the calculation of 3D descriptors includes an optimizing process, the time for calculating should be much longer. Users should wait a bit longer if suspended animation happens.
refer the process of calculating 1D/2D molecular descriptors
Note: Because of the different definitions of the 42 kinds of fingerprints, the ways to display the results are not the same. The result provides the bits-on and bits-off with 1 and 0.The default is bits-on. At the same time, several kinds of output formats are available for users.
|Calculator||Supported input format||3D information|
|CDK||*.smi, *.sdf||selectable(contained in the file)|
|RDKit||*.smi, *.sdf||not required|
|Pybel||*.smi, *.sdf||not required|
|Calculator||Supported output format|
*.csvformat. Four kinds of other formats, namely,
'WEKA_HASHED' , 'LIBSVM_MATRIX' , 'LIBSVM_SPARSE','FULL_TAB_UNFOLDED'will be provided when calculating the fingerprints from jCompoundMapper.
1. Why does the error message pop up: Sorry! the program based on RDKit can not identify!The loop will break by this smile,We will show results calculated before this?
As the pictures above show, the data file is invalid for requirement of RDKit. It may be caused by the reason that one of the smiles is not correct. You can use "view your molecule" function to check your smiles. Or you can drop the one and continue calculating it.
2. Why does the suspended animation happen when calculating 3D molecular descriptors?
It is well known to all that 3D optimization of drug molecules is quite a time-consuming process, such as the pseudo diagonalization, full diagonalization, and density matrix assembling in MOPAC. So we suggest that users should not submit a job containing number of molecules more than 100 when calculating 3D molecular descriptors, especially including someone with large molecular weight.
3. Why does the blank result page appear when using the file of correct format ?
This situation is not commonly encountered. If it happens, please check your file. ave you ever edited the file via other editors that add some special style for the content,for example, colored the string inside? The built-in module requires the plain text without any style.
4. Why does the error message pop up when use the correct
It is related with the
*.sdf file format.The M CHG and M RAD lines are used for connection tables that ‘overflow’ the allowed atom block limits.By now the M CHG and M RAD lines can not be handled correctly in some cases.
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