Applications and Web Service Mash-ups
Among other things, on this page are included those IU-developed web services that have web clients available.Combinatorial Library Generation
Combinatorial Library Generation - Ugi Reaction (Although this is for the Ugi reaction, it can easily be extended to arbitrary reaction schemes since it is based on a web service to generate reagent fragments which are then combinatorially combined to give the final library.)
Molecular Similarity
Molecular Similarity (Returns the Tanimoto similarity between two SMILES strings; 3D similarity can also be calculated (though there is no web client)) (Usage)Mutagenicity Predictions
Ames Mutagenicity Predictions - Random Forest Ames Mutagenicity Predictions - Random Forest (Uses random forest model to predict whether a structure specified in SMILES format is mutagenic or not according to the Ames test; based on 166 bit MACCS fingerprints. The model uses a 4337 compound dataset studied by Kazius et al. (J. Med. Chem, 2005, 48(1), 312-320), which was divided approximately equally (1.2:1) between mutagens and nonmutagens. OOB error was 15.39% and test set error was 15.32%. (Usage)pkCell
Pharmacokinetic Calculator (pkCell) (Makes a connection to the Rserve process, using a fixed value of the Rserve host. Calculator evaluates pharmacokinetic parameters pKa and logP.) Developed in collaboration with Dr. Gus Rosania (University of Michigan Alliance for Cheminformatic Exploration) UsagePubChemSR (Search and Retrieve) Tool
Developed by Junguk Hur for the Windows environment. Features:- Text (keyword) search against any of the three PubChem databases (PubChem Compound, PubChem Substance, and PubChem Bioassay)
- Spelling correction for mis-spelled search terms
- Bulk-download of data from PubChem
- Two different display options (DocSummary and Tab-delimited)
- Direct data export to MS Excel
- Automatic/Manual data field list update
- Link to PubChem Web page for search results
- User-friendly GUI
Structure Diagrams
Structure Diagrams (Gets the 2D structure diagram of a SMILES string) (Usage)Toxicity Predictions - Random Forest
Toxicity Predictions - Random Forest (Uses a 10-model ensemble of random forests to predict whether a structure (specified in SMILES format) is toxic or not, based on 1052 bit BCI fingerprints. Each model is based on a dataset about 4600 structures, equally split between toxic and non-toxic compounds.Note, this page is a proof-of-concept of model deployment using R web services coupled to a remote R engine. The model still requires more validation.) (Usage)
ToxTree
ToxTree Server (Estimates toxic hazard from a SMILES string by applying a decision tree approach) (Usage)Utility Methods
Utility Methods (MW, Molecular formula, Fingerprints, PDB) (Usage)-
Web Clients:
Zhou Lab Services
- SPEM (Prediction/analysis tools for sequences)
- TUPS (Prediction/analysis tools for secondary structures)
- SPINE (Structural properties of proteins by integrated nerual networks)
- SPARKS, SCUD, DDOMAIN (Prediction/analysis tools for tertiary structures)
- DFIRE (Prediction analysis tools for interactions)
- DOGMA (Prediction/analysis tools for network graph)
- Prediction/analysis tools for folding kinetics