SeaChange in silico adverse event predictions highlighted in Genetic Engineering & Biotechnology News

Nov. 17, 2014 by Site Administrator

Excerpt from "Weaving a Stronger Drug Safety Net" article in Genetic Engineering & Biotechnology News

San Jose, November  17th,  2014 — SeaChange Pharmaceuticals in silico adverse predictions were recently highlighted in well-writen Genetic Engineering & Biotechnology News article by MaryAnn Labant.

» View the full article here

Here is the relevant section excerpted from the GEN article*: 

In Silico Predictions

Inspired by the ligand-based organization of targets in classical pharmacology, the Similarity Ensemble Approach (SEA) is a rapid, broad-scale, and model-free chemoinformatic computational method that operates on hundreds of thousands of ligands organized by their molecular targets.

“SEA allows us to ask and quantify whether any given drug or drug-like molecule is more similar to a target’s ligands than would be expected by random chance alone. A strong significance score is a prediction of possible off-target activity for that drug,” explained Michael Keiser, Ph.D., founder and chairman of SeaChange Pharmaceuticals and assistant professor at the University of California San Francisco School of Medicine.

“In collaboration with Novartis, we were able to determine that some off-targets were antitargets, which we found to be associated with adverse drug reactions (ADRs) via a guilt-by-association enrichment factor metric,” added Dr. Keiser. “Correspondingly, we were able to show that these antitargets were often better explanations of the drug’s known adverse reactions than any of its previously reported targets.” Off- and antitarget predictions are intended to prioritize, not to replace, the use of screening and experimental safety assays. Calculations are run rapidly on tens or hundreds of thousands of drug-like molecules to determine areas of potential liability for compounds.

Typical positive predictive values (PPVs) are 48–52%, even among known drugs, where one might have expected previously unreported antitargets to be sparse. These PPVs are approximately an order of magnitude better than those achieved in most virtual-screening campaigns.

The approach can be used for drugs and small molecules in development or on the market with known structures, and focuses on predicting ADRs that are mediated by specific antitargets.

The future goal is direct prediction of entire multitarget combinations. The increasing availability of big data may one day allow linking a drug’s full on- and off-target profile with a patient’s unique genomic profile and electronic medical records for use in the emerging field of systems pharmacology.

* MaryAnn Labant. "Weaving a Stronger Drug Safety Net." Genetic Engineering & Biotechnology News. Nov. 15, 2014 (Vol. 34, No. 20). http://www.genengnews.com/gen-articles/weaving-a-stronger-drug-safety-net/5355/

 

keywords: #SaferPharmaFaster, SEAware™, adverse events, press

 

Please Vote for SeaChange!

Oct. 7, 2014 by Michael Boyd

 

Help us make drugs safer and more effective by voting for us here:

Vote Now!

Voting is now over. We came within 10% of our goal, so thank you for all the support!

#SaferPharmaFaster

 

keywords: #SaferPharmaFaster, SEAware™, press

 

SeaChange releases updated SEAware™ version, now easier to use than ever

April 22, 2014 by Site Administrator

Announcing SEAware™ Version 1.7.0
A prediction engine for drug mechanism and toxicity

Major changes:

  • ChEMBL17 based default libraries include more and more accurate target annotations
  • Input molecule normalization gives more consistent predictions
  • Shorter RDKPath fingerprints reduce bit collisions and increase predictitivity
  • Streamlined file reading code with better error handling
  • More consistent command line parameters for the fingerprint subcommand

Highlighted new features:

  • Main viewer ease of use features (column sorting, color coding, tooltips)
  • Right-click context menus allow for extras like copying smiles
  • Improved unicode support for filenames

 

About SEAware™

The SEAware™ software package harnesses the power of our Similarity Ensemble Approach (SEA) to offer unprecedented utility for predicting drug effects [1]. It enables exploration of new therapeutic uses for known drugs [2]; mechanism of drug action [3]; causes of side effects and adverse drug reactions [4]; and multi-target activity and polypharmacology [5].

Use SEAware™ Primary to query your individual small molecules against the public ChEMBL database in our easy-to-use graphical interface. Leverage target predictions across an entire screening campaign using SEAware™ Professional, featuring a full command line interface for pipeline integration. Harness the true power of the Similarity Ensemble Approach (SEA) by tuning the statistics to your chemical matter and predicting against your own target library annotations with SEAware™ Designer.

Contact Information 
C. Nicholas Hodge
sales@seachangepharma.com
(415) 937-1732
3031 Tisch Way, Suite 711, San Jose, CA 95128

References
1. Keiser and Roth, et al. Nat Biotechnol, 2007 (2):197-206
2. Keiser et al., Nature, 2009, 462: 173-181
3. Laggner et al., Nat Chem Biol, 2011 18;8(2):144-6
4. Lounkine and Keiser et al.,  Nature, 2012 486: 361–367 
5. Keiser, Irwin, and Shoichet, Biochemistry, 2010 49(48): 10267-10726

 

keywords: SEAware™, technology

 

Sales Opportunity

Dec. 2, 2013 by Nicole Norton

This sales position is now filled, look for more oportunities in the future.


Sales Opportunity at SeaChange

About SeaChange

SeaChange Pharmaceuticals, Inc. develops new chemoinformatic and statistical methods to uncover links between drug molecules and the biological targets responsible for disease and adverse effects.  Our technology is now available to the scientific community as the SEAware™ software package.

SEAware™ harnesses the power of our Similarity Ensemble Approach (SEA) to offer unprecedented utility for predicting drug effects. It uncovers new therapeutic uses for known drugs; mechanism of drug action; causes of side effects and adverse drug reaction; and multi-target activity and polypharmacology.

Job Description

We are looking for a salesperson to join our team of scientists and software developers. The ideal candidate resides in the SF Bay area and works with the team at Santana Row, Campbell/San Jose, CA. Remote candidates considered if located in a drug discovery ‘hot spot’, such as San Diego, Boston, or New Jersey/Philadelphia corridor.

Key responsibilities:

a.      Driving sales.

b.      Reporting client needs, priorities, and feedback in our CRM.

Successful Candidate

Must Haves:

1.       Bachelor’s degree or 3+ successful years in sales.

2.       ‘Can do’, positive, energetic attitude (with realistic expectations).

3.       Team player, who wants to work with a group that likes, trusts and supports each other, and brings a friendly, pleasant attitude to both clients and coworkers.

4.       Experience in sales. A sales sheet would be helpful to establish this.

5.       Attention to detail and the ability to build meaningful CRM entries.

You Also Have:

6.       Experience selling high-end software.

7.       Knowledge of pharmaceutical research community.

8.       Knowledge of computational chemistry and associated methods and tools.

9.       Knowledge of drug discovery or programming.

We will consider candidates without skills #6-9, as long as intellect and ‘quick-study’ ability to understand the issues and concerns are clearly demonstrated.

Compensation

For simplicity for both parties, the initial period will be a contract (1099) position. After the initial period, full-time W-2 employment can be discussed.

We offer a base salary commensurate with experience, and a commission for every sale made. We have set a conservative sales target for next year; if met, this represents an attractive package.

Next Steps

Please direct all inquiries to apply@seachangepharma.com

This sales position is now filled, look for more oportunities in the future.

 

keywords: careers

 

SeaChange releases SEAware™, software for predictive matching of drugs with disease and toxicity targets

Sept. 11, 2013 by Site Administrator

New Similarity Ensemble Approach software is now commercially available, offering enhanced security, speed, and the ability to leverage both proprietary and public scientific data.

San Francisco, September  11th,  2013 — SeaChange Pharmaceuticals Inc., a privately held platform and products pharmaceuticals company, is pleased to announce the immediate availability of SEAware™, its proprietary Similarity Ensemble Approach (SEA) software, that allows analysis and visualization tools for prediction of drug and other small molecule activity and toxicity against biological targets. Three levels of software are available directly from the SeaChange website.

“Our pharma, academic, and government partners have found SEA most valuable in-house, where it’s fast, easy, and secure,” said Michael Keiser, Founder and COO. “We’ve had many requests to make SEA  available and we’re excited to respond today with SEAware™. It’s a turn-key package that has 10x the calculation speed and a new, intuitive interface—a ‘google for drug targets.’ In the most extensive suite, users can leverage their own proprietary data or modify available public libraries. These advances let our clients explore what-if questions about drug off-target effects at the press of a button.”

Nicholas Hodge, Chief Scientific Officer, pointed out that “preclinical in vitro and in vivo testing of drug candidates against the increasing number of biological targets remains cost-prohibitive. One of the best uses of SEAware™ is as a predictive ‘filter’ to reduce the testing of molecules for activity or toxicity to a manageable number of targets. As clients become familiar with the method, and build curated reference libraries, the predictive accuracy – already high – will continue to improve. Over time, SEA will become the method of choice for target, mechanism and adverse effect identification of drugs and leads. With a preclinical opportunity cost of a million dollars a day added to random screening costs, successful application of the method can repay the cost of software rapidly.”

About SEAware™

The SEAware™ software package harnesses the power of our Similarity Ensemble Approach (SEA) to offer unprecedented utility for predicting drug effects [1]. It enables exploration of new therapeutic uses for known drugs [2]; mechanism of drug action [3]; causes of side effects and adverse drug reactions [4]; and multi-target activity and polypharmacology [5].

Use SEAware™ Primary to query your individual small molecules against the public ChEMBL database in our easy-to-use graphical interface. Leverage target predictions across an entire screening campaign using SEAware™ Professional, featuring a full command line interface for pipeline integration. Harness the true power of the Similarity Ensemble Approach (SEA) by tuning the statistics to your chemical matter and predicting against your own target library annotations with SEAware™ Designer.

About SeaChange Pharmaceuticals, Inc.

  • SeaChange develops chemoinformatic and statistical methods to uncover links between drug molecules and the biological targets responsible for disease and adverse effects.</li>
  • Our focus is software development, sales and  support to pharmaceutical clients and finding new uses for known drugs


SeaChange was founded in 2009 by John Irwin, Michael Keiser, and Brian Shoichet at UCSF. Commercial development began in 2010 with Nicholas Hodge, who brings an extensive background in drug discovery and small-company building. The company continues to be supported by government and private grants, paid project and technology access contracts with pharmaceutical companies, and, recently, by software sales. Our Director of Operations is Nicole Norton, and our Lead Software Developer is Michael Mysinger. The company is located in the Mission Bay region of San Francisco, within walking distance to the UCSF campus. 

Our emphasis is on improving and disseminating cheminformatic technologies supported by sales, consulting projects, and government grants. We thereby also increase our understanding of client needs and typical uses, enabling simpler and more powerful software in future releases. SeaChange also maintains an internal research program that applies SEA to the known pharmacopeia with the objective of identifying known drugs with unexpected and beneficial activity as well as commercial potential. 

Contact Information
C. Nicholas Hodge
sales@seachangepharma.com
(415) 937-1732
409 Illinois St., San Francisco, CA 94158

References
1. Keiser and Roth, et al. Nat Biotechnol, 2007 (2):197-206
2. Keiser et al., Nature, 2009, 462: 173-181
3. Laggner et al., Nat Chem Biol, 2011 18;8(2):144-6
4. Lounkine and Keiser et al.,  Nature, 2012 486: 361–367
5. Keiser, Irwin, and Shoichet, Biochemistry, 2010 49(48): 10267-10726

» Read the full news release on BusinessWire.com

keywords: SEAware™, press, technology

 

New computational platform predicts side effects

June 11, 2012 by Site Administrator

SeaChange recently reported a joint study in Nature with UC San Francisco and the Novartis Institutes for BioMedical Research that demonstrates the fully-automated application of a core technology to predict the side effect liabilities of drugs and preclinical compounds on an unprecedented scale. The platform's predictions were tested experimentally in 694 prospective lab assays and also against 348 proprietary data-points, yielding a success rate over twenty times higher than existing broad-scale computational approaches.

Companies or investors interested in learning more about SeaChange and our ability to find new uses for existing drugs and their side effects may contact us.

Read the UCSF press release »

keywords: paper, side effects, technology

 

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