SPCI

Automatic tool for mining structure-property relationships from chemical data sets

Description

Retrieves structure-property relationship from data sets in a chemically meaningful way.
Returns estimated contributions of fragments to the investigated property of compounds from a data set and can estimate contribution of different physicochemical factors as well.

Features

1. Easy to use straightforward workflow with GUI.
2. Automatic model building and cross-validation.
3. Build models for imbalanced data set using the multiple oversampling approach.
4. Prediction with built models.
5. Several fragmentation schemes to compute fragment contributions of:

• common functional groups and rings;
• Murcko scaffolds;
• user-defined fragments;
• automatically generated fragments (based on SMARTS pattern matched broken bonds);
• per atom fragmentation.

Visualization of results

1. Built-in visualization.
2. rspci - R package for custom visualization (https://github.com/DrrDom/rspci)
3. Online tool for visualization, plot customization and figure downloading (http://158.194.101.252:3838/spci-vis/). Demo version is here (http://158.194.101.252:3838/spci-vis-demo/)
4. Per atom contributions can be visualized with RDKit similarity maps.

Manual

Short manual is included.

Publications

Structural interpretation was published in the paper http://dx.doi.org/10.1002/minf.201300029 Integrated structural and physicochemical interpretation was published in the paper http://dx.doi.org/10.1021/acs.jcim.6b00371

Citation

1. Polishchuk, P. G.; Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N., Universal Approach for Structural Interpretation of Qsar/Qspr Models. Mol. Inf. 2013, 32, 843-853 - http://dx.doi.org/10.1002/minf.201300029.
2. Polishchuk, P.; Tinkov, O.; Khristova, T.; Ognichenko, L.; Kosinskaya, A.; Varnek, A.; Kuz’min, V., Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. J. Chem. Inf. Model. 2016, 56, 1455-1469 - http://dx.doi.org/10.1021/acs.jcim.6b00371.

Home page

http://qsar4u.com/pages/sirms_qsar.php

License

GPLv3

What's new

1.0.0

• RDKit is used as a backend instead of Indigo
• multiple undersampling was implemented
• changed default descriptors, that make this version incompatible with previous models and vice versa.
• updated sirms descriptors
• many small fixes and improvements

1.1.0 (07.02.2021)

• added support of RDKit descriptors
• added per atom fragmentation
• reorganized as a Python package