May 17 2013
[ MolCart License | Connect to MolCart | MolCart Compounds | MolCart SDF | Chemical Search | Molcart New Database | Molecular Editor | convert to 3D | Grid View | Convert Chemical | convert to 3D and preserve | Add Property Column | Extract Ligand | Druglikeness | Chemical Monitor | Faq molcart text search | SMILES | APF Model | Chemical Rotate | Remove salt ]Frequently asked questions regarding small molecules, ICM-Chemistry tools and MolCart
When you unpack the MolCart distribution from www.molsoft.com/support you will be given a unique number (which you need to send to email@example.com to get a MolCart license) along with MolCart login details such as Server Name, UserName and Password.
Once you have the MolCart distribution loaded you can connect to MolCart by going to Tools/Chemistry/Connect to Molcart
MolCart Compound Database is an up-to-date collection of vendor compound databases. This database is divided into three collections:
Each collection consists of two components:
The MolCart compounds can be downloaded from http://www.molsoft.com/screening.html then to unpack them type:
zcat vendor.gz | mysql -h<hostname> -u<user> -p<password> molcart_database_name
In the terminal window type:
write molcart table="molcart_table_name" "name_of_sdf"
You can search MolCart or Chemical Tables using the ICM Chemical Search Window. This window can be displayed by going to:
To write the data from a query to a new MolCart database table use the Add to DB option in the Chemical Search window.
Use the molecule editor
or look for the ICM molecular editor button at the top of the graphical user interface.
To change the layout of a chemical table (eg converting a table to grid view).
To do this:
To read a chemical table into ICM:
To add a chemical property to the table.
You can extract a ligand from an ICM object or PDB file by:
When building a molecule in the ICM Molecular Editor (Tools/Chemistry) properties such as druglikeness are calculated on the fly. The properties can also be added by inserting a column into a chemical table (right click on column header/ insert column/ Function = Chemical). These values should be used as a guide and druglikeness is a prediction based on drug-like properties. A druglikeness value less than zero indicates that the compound may have some non-drug-like properties.
If you do not see the chemical monitor in the ICM Molecule Editor - Go to:
To perform a text search an index needs to be made on the field you wish to search. To do this:
See How To section.
_setAPFparams is in the distribution since 3.6-0;
icm _apf3Dqsar train=trainingSet.sdf activity=LogIC50 table=testSet.sdf
Training and test set compounds should be all pre-aligned, for example by aligning training set actives using APF multiple chemical alignment, and then superimposing the test compounds onto aligned actives using APF superposition. Any external alignment method can be used as well. The field containing activity data in the training set SDF is specified by activity= argument.
The script also can take alignments in icm multiple object format *.ob, in which case SDFs are only used for input/output of activity data and can be just 2D:
icm _apf3Dqsar train=trainingSet.sdf align=trainingSet3Daligned.ob activity=LogIC50 predict=testSet3Daligned.ob table=testSet.sdf
The results are written to testSet_predict.sdf output file. Some statistics is reported along the way. If testSet.sdf contains activity (i.e. LogIC50) column like the training set, RMSD and R2 will be reported as well.
See this description in the command line manual:
You can do this in the menu option Chemistry/Standardize and check the remove salt option.
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