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  1. Seminar at MSBoston 2014:  Phase 2 results of the RADIANCE trial...
  2. MS Drug Discovered at TSRI Is Safe and Effective in Phase II Study   
  3. Scripps Research Institute Scientists Identify First Potentially Effective Therapy for Human Prion Disease   
  4. Probe from SRIMSC Enters Phase II/III Clinical trials.   
  5. The Scripps Molecular Screening Center becomes the first to have 1000 AIDs in PubChem!   
  6. Receptos Scientists Publish Determination of a High Resolution S1P1 Structure in Science   
  7. NIH Common Fund researchers uncover structure of important target for drug design   
  8. NIH Research Matters: Designing New Diabetes Drugs   
  9. Discovery of a treatable mechanism for avoiding the deadly response to flu: North County Times, Eurekalert [1, 2]    
  10. Nature: Suppression of TH17 differentiation and autoimmunity by a synthetic ROR ligand   
  11. Scripps Research and MIT scientists discover class of potent anti-cancer compounds    
  12. MLP Probe Project Leads to First in Human Studies    
  13. Business Wire:   Receptos Initiates Clinical Trials for S1P1 Agonist Program, Aimed at Multiple Sclerosis   
  14. Nature:   Quantitative reactivity profiling predicts functional cysteines in proteomes.

  15. Nature:   Anti-diabetic drugs inhibit obesity-linked phosphorylation of PPARc by Cdk5.
  16. Discovery and optimization of chemical probes to define important molecular signals in medicine.
  17. Nature Reviews Drug Discovery article:   Chemical modulators of S1P receptors as barrier-oriented therapeutic molecules.
  18. Nature Chemical Biology article: S1P1 signaling just keeps going and going and going…
  19. Nature Biotechnology article:   Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes.
Home » Available Software
Available Software

Descriptors App

This tool allows live sketching of compounds and calculation of chemical descriptors. Previous calculations are stored in a table for comparison. The new functionality incorporates substructure filters for detection of Pan Assay Interference (PAINS) compounds (Baell and Holloway, 2010) and medicinal chemistry scoring rules from Eli Lilly (Bruns and Watson, 2012). The latter in particular is important as it establishes what a major pharmaceutical company considers clean compounds.

Disclaimer: there is another tool that wraps the Lilly software available from the NCGC center.

Access here.


BioAssayOntology Template



Entrez Excel Addin

An Excel Add-in that links to NCBI Entrez EUtilities web services and create tables from any Entrez database (e.g. Protein, Gene etc). Entrez query syntax is supported and summaries and links between databases (e.g. Protein -> Gene) can be displayed. Download here.


BioAssayOntology Template



Pilot PAINS Generator

Performs SMARTS searching for Pan Assay Interference Compounds (PAINS) as described in Baell and Holloway 2010. SMARTS searching is via the JoeLib cheminformatics library and the PAINS SMARTS were provided by Rajarshi Guha of the NCGC center. Download here.


Molecular Image Excel Writer for Pipeline Pilot

Generates a column of chemical images and property fields in an Excel workbook. It will handle tens of thousands of compounds. Download here.


Molecular Scaffold Generator for Pipeline Pilot

Extracts predefined scaffolds from compounds as described by the Strip-It tool from Silicos Inc. Covers Murcko and Rings-with-Linkers type scaffolds. Download here. template

We have introduced a template for annotations in PubChem BioAssays. At the MLPCN face to face in July 2011 there was a consensus within the Informatics Working Group that the centers should start to include annotations in their BioAssay submissions.

Continuing from our existing work with the PubChem Deposition System, we have made a new Excel template to be used for PubChem BioAssay deposition. The categorized comments tab of this template includes BioAssayOntology annotations with drop down lists for controlled vocabulary values. The template can be directly used with the PubChem Deposition System Tool from which a description xml can be created and subsequently uploaded into PubChem. The BAO categorized comments, once filled in, can also be copied and pasted in the PubChem BioAssay Upload Excel template for direct upload into PubChem.

BioAssays from PubChem that include the annotations can be found with this link:[categorizedcommenttitle]


BioAssayOntology Template



PubChem Promiscuity

Go to PubChem Promiscuity website. 

Updated: October 2011

This tool gathers promiscuity data for a list of PubChem Compound or Substance identifiers (CIDs or SIDs). There are two choices for output format: per compound or per compound and protein. The tool provides the following data:

  • Active and total assay counts
  • Active and total assay counts for:
    • Molecular Libraries Program assays
    • ChEMBL assays
    • "Projects" (sets of assays connected to a Summary AID)
    • Moleular Libraries Program "Projects"
    • Assays with no protein targets (e.g. cytotoxicity assays)
    • Luciferase assays
    • Beta-lactamase assays
    • Fluorescence assays
  • Active and total protein counts
  • Chemical smiles
  • Lipinski 'rule of 5' violation count
  • Functional Group Detection (PAINS groups) 
  • Full set of chemical descriptors available from Entrez ESummary

PubChem Promiscuity



CARS CSV Creator

Posted: February 2011

The Common Assay Reporting System (CARS) allows the MLPCN center investigators and NIH program managers to track and share the status of assay screening campaigns and related issues. The MLPCN centers must enter metrics of their progress into CARS. Such metrics include PubChem BioAssay AIDs, counts of synthesized and purchased compounds, count of substances screened and hits. It is up to each individual center to provide their metrics to CARS and these are entered via web page or CSV file. 

This application partially automates the creation of CARS CSV files by gathering relevant information from PubChem for a given AID. On-hold assay information can be obtained by using the PubChem Deposition Login.

Database queries are required to separate purchased, synthesized and MLSMR substances for CARS stages 4 and 5.




CARS CSV Creator war file can be downloaded here

Installation directions can be downloaded here.


PubChem Curve Fit

A new way for public users and assay providers to view doseresponse datasets from PubChem. At this time, PubChem does not have the abilityto display curve fits, only straight line plots. Nor is there a view where it candisplay more than one of these at a time. Using the relational PubChem mirror (described below), we have extended the NCGC Curve Fit tool to enable loading of dose response datasets directly from PubChem. A PubChem query (using Entrez indexes and filters) is specified manually, or using a graphical interface where it is possible to specify such a query as “show me the top 1000 compounds within Assay A, subtracting out those that are active in counter-target Assay B”. The raw data is then downloaded from PubChem,including assay results and compounds, assembled in the relational mirror and loadedinto the Curve Fit tool.

A Java WebStartTM version of the tool can be run from here.


PubChem Curve Fit


PubChem Deposition System Excel Tool

Updated 8th November 2012.

This original tool existed for six months before the requisite functionality was found in PubChem. It was promoted and presented to PubChem staff so we can hope that we had influence in effecting the change.

We now present a formatted, vocabulary controlled Excel Workbook based on our original work that can be the front end to the new Deposition System upload. By using formatting and controlling the vocabulary of terms it becomes a true user interface and very much easier to use. It can be downloaded here


PubChem XML Tool


Orignal PubChem Deposition Excel Tool 

The aim of this tool is to make it easier to interact with the PubChem Deposition System. The tool will read and write PubChem XML Description files into Excel Workbooks. The XML files can then be processed via web based or FTP based deposition. In particular it is easier to perform list based operations, copy and paste, drag down column completion and making subtle changes from existing depositions in Excel, something that is hard to do on a web page where each data item is in it's own separate form field and where individual changes require a round-trip to the server.

A Java WebStartTM version of the tool can be run from here and the software source code can be found here. A new Excel template that includes BAO categorized comments tag names and drop down lists for values has been created and is available here.


Relational database mirror of PubChem BioAssay

This is a software library that can use NCBI EUtilities and PubChem's PUG and FTP site to populate a local relational database of BioAssays and their associated compounds. Features include integrated chemical structure processing via JChem from Chemaxon and curve fitting via the Curve Fit library described on this page.

The source project can be found here


Standalone Curve Fitting and Plotting Java Library.

Curves can be plotted via JFreeChart and the Google Chart API.

This project incorporates code from NCGC CurveFit, a "United States Government Work" which as such is in the Public Domain. Specifically it derives from and makes use of classes within the gov.nih.ncgc.batch package. A binary jar file containing the incorporated code is included with this project.



An example of the Google Chart output can be seen here. Source project can be found here.


Chemistry Addin for Excel (ChemXL)

This tool has 2 major functions;

1) insert images of chemical structures from PubChem CIDs, SIDs or Smiles that exist in the worksheet. These images sort and filter correctly.

2) open a SDF file into the worksheet. 


Chemistry Tool for Excel

This work makes use of Chemaxon JChem technology. Kudos also given to PCExcel which inspired this work. Download ChemXL here.  


Images Addin for Excel

This tool can import image files into Excel cells. Images can be imported into a column or a row or from filenames that exist in the worksheet. Additionally, images already in the worksheet can be 'fixed' into a cell. The images will sort and filter correctly.


Images Addin for Excel

Download here


CDK Chemical Image Generator and Customizer

Export molecules in image and document formats using the Chemistry Development Kit (CDK). Currently the following types are supported: jpeg, png, bmp, wbmp, gif, emf, pdf, svg, swf, ps, mol, smi, sdf. Source code for the project can be found here. For a demo click here.



Google Scholar Citations for PubMed

This tool will take a PubMed PMID and run a Google search to obtain the number of times it has been cited. The resulting Google Scholar link is inserted into the PubMed page as shown in the picture.

To use this tool you will need to be using the Firefox browser with the Greasemonkey extension installed. You can then install the tool here.




ExcelTableModel Java Library

Uses the Apache POI library to read/write Excel Worksheets via a javax.swing.table.TableModel implementation. Additional code to insert images into worksheet cells. Source project can be found here.


MS Drug Discovered at TSRI is Safe and Effective in Phase II Study


A compound discovered and synthesized in The Scripps Research Institute (TSRI) labs of Professors Hugh Rosen and Edward Roberts has provided positive results for safety and efficacy in Phase 2 clinical trials for relapsing multiple sclerosis, according to Receptos, the biopharmaceutical company developing the drug for approval by the US Food and Drug Administration.

“The Rosen and Roberts laboratories are very gratified to see these direct improvements in the lives of patients and families dealing with this debilitating illness,” said Rosen. “These data support our labs' approach at TSRI—that discovery of fundamental mechanisms in chemical biology provides the foundation for intelligent intervention in disease processes. Meeting the needs of patients and their families is our high calling in biomedical science.”

The drug candidate, RPC1063, was first discovered at TSRI from work in the National Institutes of Health (NIH) Molecular Libraries Initiative. The randomized, double-blind Phase 2 study assessed the efficacy, safety and tolerability of two orally administered doses of RPC1063 against placebo in 258 patients with relapsing multiple sclerosis across 77 sites in 13 countries. There was a highly statistically significant 86 percent reduction in MRI measures of disease activity.

A Phase 3 trial—a randomized, double-blind study involving 1,200 patients with relapsing multiple sclerosis—was launched in December 2013.

The detailed clinical abstract can be found  here.

Copyright (c) 2008-2011 TSRI.