The BioSciences Group of Fujitsu Offers ‘High Throughput Docking’ to Overcome Challenges of High Throughput Screening

Bio-IT World Expo – Boston, Massachusetts
May 18 , 2005

At Bio-IT World Expo in Boston, The BioSciences Group of Fujitsu Computer Systems demonstrated its offerings in “High Throughput Docking,” (HT Docking) as a means to make High Throughput Screening (HTS) more productive and effective in drug discovery.

One of the basic challenges of High Throughput Screening is that it can sometimes be inefficient, as the process requires the high-volume use of inexpensive assays to filter results. This leads to potential “false negative” results that can cause promising leads to be missed – in turn leading to lost discovery opportunities and wasted resources. Fujitsu technology and methods demonstrate how this can be overcome by in silico “High Throughput Docking” as a complement to traditional High Throughput Screening.

HT Docking is an in silico technique that allows researchers to dock entire libraries of compounds against a potentially large number of target proteins via computer modeling – prior to, or in parallel with, conventional screening – to eliminate the need for performing assays on the vast bulk of unlikely leads. As a result, researchers will be able to use better, more reliable assays on a smaller number of more promising leads. In turn, this will help reduce the problem of “lost opportunities,” by reducing false negatives that make finding the best candidates for drug development even more challenging.

Fujitsu offers HT Docking hardware and software solutions in support of its method, which entails progressive in silico validation of leads through a variety of algorithms. The Fujitsu process is as follows:

  1. ShapeDock – a fast search algorithm that quickly filters millions of possible leads down to tens of thousands
  2. FastDock™ – a slower, more precise automated docking process that further prioritizes leads down to hundreds
  3. Precise free energy of binding calculations using GROMACS, a molecular dynamics simulation which models in detail the binding energy of protein ligand interactions, including accurately modeling hydration effects on binding energetics. This technique is designed for generating tens of validated leads
  4. The validated leads are then subjected to high-quality screening assays

“The concept of ‘High Throughput Docking’ is not a new one,” said Takahiro Tsunekawa, vice president of the BioIT Solutions Group. “It is a well-known idea that, due to past technology limitations, was considered impractical for use on a scale comparable to that of High Throughput Screening.”

According to Dr. Michael McManus, vice president of the BioSciences Group, “The Fujitsu philosophy is to save the HTS component until later in the process – after the majority of unpromising leads have been winnowed by High Throughput Docking.”

He added, “After making a careful study of how to make the technique practical and affordable for researchers, Fujitsu technology and methods are now in a position to enable HT Docking as a viable complement to HTS, to make this process more efficient and cost-effective.”

About The BioSciences Group of Fujitsu Computer Systems

The BioSciences Group, a division of Fujitsu Computer Systems Corporation, capitalizes on Fujitsu Limited’s over 20 years of leadership in creating innovative and reliable solutions for helping experimental scientists overcome the challenges in their laboratory workflow. BioSciences Group solutions provide a framework for researchers to make in silico predictions about leads, targets, and interactions, and to validate these hypotheses experimentally.

BioSciences Group offerings include the CAChe® suite of life sciences predictive modeling tools, the ActiveSite™ module for drug discovery lead-generation, and the BioServer™ massively parallel simulation server for genomics-based drug design. For more information, please see:

About Fujitsu Computer Systems

Headquartered in Sunnyvale, Calif., Fujitsu Computer Systems is a wholly owned subsidiary of Fujitsu Limited (TSE:6702) committed to the design, development and delivery of advanced computer systems and managed services for the business enterprise. The company offers a complete line of high-performance mobile computers, scalable and reliable servers, storage, and middleware as well as managed and professional services. Fujitsu Computer Systems emphasizes leading-edge technology, exceptional product quality and user comfort and productivity, as well as outstanding customer service. More information on Fujitsu Computer Systems is available at:

About Fujitsu

Fujitsu is a leading provider of customer-focused IT and communications solutions for the global marketplace. Pace-setting device technologies, highly reliable computing and communications platforms, and a worldwide corps of systems and services experts uniquely position Fujitsu to deliver comprehensive solutions that open up infinite possibilities for its customers’ success. Headquartered in Tokyo, Fujitsu Limited (TSE:6702) reported consolidated revenues of 4.7 trillion yen (US$44.5 billion) for the fiscal year ended March 31, 2005. For more information, please see:

Fujitsu, the Fujitsu logo, BioServer, BioMedCAChe, CAChe, and PRIMEQUEST are registered trademarks or trademarks of Fujitsu Limited in the United States and other countries. LisH is a trademark of Celestar-Lexico Sciences in the United States and other countries. All other trademarks and product names are the property of their respective owners.

The statements provided herein are for informational purposes only and may be amended or altered by Fujitsu Computer Systems Corporation without notice or liability. Product description data represents Fujitsu design objectives and is provided for comparative purposes; actual results may vary based on a variety of factors. Specifications are subject to change without notice.

Copyright 2005 Fujitsu Computer Systems Corporation. All rights reserved.