CHEMBIOGRID: Projects > All Cheminformatics Web Services

All Cheminformatics Web Services

A list of all web services developed by CICC personnel. In some
cases, the services were developed in conjunction with
organizations outside Indiana University. In a few cases, WSDLs of
others are included.

Web Service Clients and Downloadable Programs

RSS feed for this page

CMLRSSServer (Generates a CMLRSS feed of Chemical Markup
Language data from input molecules in CML format)

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.

Digital Chemistry web services (Various clustering services to classify
chemical structures in a dataset on the basis of similarities between
them; These services are private, but are available on request to licensed
Digital Chemistry users.) (Usage)

makebitsGenerate: Generate fingerprints from a SMILES structure depiction
divkmGenerate: Cluster fingerprints with Divkmeans
smile2dkm: Generate a clustered hierarchy from a SMILES structure
optclusGenerate: Generate the best levels in a hierarchy with Kelley scoring method
rnnclusGenerate: Extract individual cluster partitions from a cluster hierarchy (optclus included)
smile2ClusterPartitioned: Generate a new SMILES structure with an extra cluster column that is an individual cluster partition

Drug Likeness Returns the number of failures for Lipinski's Rule of Five. A value of 0 would indicate that it is drug-like; increasing values indicate that it is more nondrug-like. (Usage)

InChIGoogle (Input an InChI and search Google) (Usage)

InChiServer (Generates an InChI from various chemical structure file formats) (Usage)

getBasic: Gets an InChI basic depiction
insert2CML: Inserts an InChI string to a CML molecule
generateMasterEntry: Generates a master entry for a molecule which will be recorded in the InChI index database

Molecular Descriptors (TPSA, XLogP, Surface area, etc.) (Usage)

Molecular Similarity (Returns the Tanimoto similarity between two SMILES strings) (Usage)

Pair wise similarity
Similarity matrix
3D similarity
Distance moments for use in 3D similarity calculations

Fingerprint Similarity

NIH DTP Similarity Search on Developmental Therapeutics Program Data (For a given SMILES string, provides exact search, similarity search, or filtering based on a given value for the Tanimoto coefficient; uses gNova cartridge for canonical SMILES)

NIH DTP Cancer Cell Line Activity Predictions

Open Babel (Transform a chemical structure file format to another format; Current stable version 1.0.0 is used.) (Usage)

OpenEye web services (FRED Docking, FILTER Property Calculation and Filtering, OMEGA 2D-3D Conversion; These services are private, but are available on request to licensed OpenEye users.)

OptiCat Web service (a user-friendly toolbox for building genetic algorithms dedicated to chemistry, in particular catalysis. Developed by Dr. Frédéric Clerc) Download Opticat and the source code

OSCAR3 URL Service (A joint project with the University of Cambridge Unilever Centre for Molecular Science Informatics to enable web services for their OSCAR software that scans text to identify chemical compounds by name) (Usage)

oscar3Lite: Invokes OSCAR3 with the Lite option that provides named entities like chemicals
oscar3Full: Invokes OSCAR3 with the Full option that provides markup experimental data as well as named entities like chemicals
oscar3SAF: Invokes OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words
oscar3SAF2URL: Invokes OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words; The result is denoted in a URL format that is accessible through the Internet.)
oscar3URL2SAF2URL: Invokes OSCAR3 with the standoff(SAF) document option that looks for references to markup chemical words; Both the input and the result is denoted in an URL format that is accessible through the Internet.)
oscar3URLParseInto2URL: Invokes OSCAR3 with the ParseInto option that enables multiple resource processing and looks for references to markup chemical words; Both the input and the result are denoted in an URL format that is accessible through the Internet.)

PubChem Database (local IU version) Rajarshi Guha. These services are essentially wrapped queries for the local version of the PubChem database.

Structure (Provides methods to get Pubchem Compound information) (Usage)
Synonym (Provides methods to get synonyms given a compound or substance ID. SMILES support coming) (Usage)
Derived properties (Get calculated properties (SLogP and SMRef) given a compound ID. Can also search via exact values and ranges (but this is very slow at the moment). (Usage)
Docking results (Provides methods to get the docked structures (for a given target) for PubChem compounds based on CID, sorted score values or by SMARTS patterns. Ligands are returned in SDF format. Currently only the ligand structures are accessible and the actual score values are coming soon.) (Usage)
3D structures (This service provides access to MMFF94 optimized 3D structures for PubChem compounds. Structures are returned in SD format and can be accessed by CID or by SMARTS patterns.) (Usage)

PubDock web services

R and R-based web services Rajarshi Guha. If there are algorithms or features you'd like to see or if you find bugs go to the Sourceforge page and submit a feature request or bug report

Sampling distributions (Usage)
Linear Regression (Usage)
CNN Regression (Usage)
RF Regression (Usage)
LDA Classification (Usage)
K-means Clustering (Usage)
t-Test (Usage)
XY Plots (Usage)
Histogram Plots (Usage)
Feature selection (Stepwise and exhaustive feature selection) (Usage)
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) Usage

Web client for pkCell

Toxicity Predictions - Random Forest Ensemble (Usage)

Web client for Toxicity Predictions

Ames Mutagenicity Predictions - Random Forest (Usage)

Web Client for Ames Mutagenicity Predictions

NIH DTP Cancer Cell Line Activity Predictions

Structure Diagrams (Gets the 2D structure diagram of a SMILES string) (Usage)

2D Structure Diagrams

3D Coordinate Generation (Generates 3D coordinates from a SMILES string using either MM2 or MMF94 forcefields; Does a reasonable job for most molecules with output as an SDF file) [Service Code] [ client code] (Usage)

ToxTree Server (Estimates toxic hazard from a SMILES string by applying a decision tree approach) (Usage)

ToxTree

Utility Methods (MW, Molecular formula, Fingerprints, PDB) (Usage)

VOTables--The VOTable format is an XML representation of the tabular data (data coming from applications such as the Digital Chemistry suite and NIH online screening centers). The XML format of tabular data can be used for creating web services infrastructure and can potentially be used as a replacement/supplement for CML tables. With the use of JAVA Parser API for VOTables, one can build spreadsheet or plotter applications.

Convert tab file to VOTables
VotableToTabbedFileService (Converts votable.xml file to tabbed file)
VOTable Formatter (Retrieves all header information from votable.xml files)
Convert votable.xml file to Excel spreadsheet
Spreadsheet to VOTable
Output Spreadsheet
Cluster output to VoTables for use with parsing Digital Chemistry's clustering output

Generic SOAPClient (allows you to access web services using a web browser. It performs dynamic bindings and executes methods at remote web services.)

chemical informatics & cyberinfrastructure collaboratory

All Cheminformatics Web Services

Menu