Dr. Carlos L. Simmerling

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  www.supercomputingonline.com/article.php?sid=13513 - [Cached Version]
  Published on: 4/21/2007    Last Visited: 4/21/2007  

  Dr. Carlos Simmerling at Stony Brook University in New York won $50,000 and top honors for his breakthrough medical research, while the University of California-Riverside (UCR) earned Honorable Mention and $5,000.
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  Working on an SGI Altix system located at the National Center for Supercomputing Applications (NCSA), Simmerling and his team have developed simulation methods that can explore the molecular basis for diseases such as AIDS, cancer and tuberculosis.The team recently achieved the most extensive computer simulations ever done on HIV protease, a molecule that slices a pre-HIV protein chain into the pieces that ultimately assemble into a mature and infectious virus.The simulations modeled how the viral protease changes structure over time, revealing for the first time how it transiently opens during its function, allowing drugs to gain access to the interior and inactivate it.The results provide vital data in the effort to develop new treatments for the 40 million people currently living with AIDS.
  
  "This is a tremendous honor - one that recognizes what human effort and technological advances can achieve when brought to bear on a problem that had previously proved insurmountable," said Simmerling, an associate professor in Stony Brook's Department of Chemistry and director of Computational Biology for Stony Brook's Institute for Chemical Biology and Drug Discovery.
  
  Simmerling has concluded that using NCSA's powerful Altix system has made a dramatic difference in his research."The Altix allows us to obtain new medical advances in months, rather than in years," he said.

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  www.acscomp.org/Meetings/pastprograms/2004/Fall_Abstrac - [Cached Version]
  Published on: 10/1/2004    Last Visited: 6/6/2008  

  Raphaël Geney and Carlos L. Simmerling, Department of Chemistry, Stony Brook University, State of University of New York, Stony Brook, NY 11794-3400, Fax: 631-632-7942, rgeney@ic.sunysb.edu
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  Melinda M. Layten, Molecular and Cellular Biology Program, Stony Brook University, Life Sciences Building, Stony Brook, NY 11794, mlayten@csb.sunysb.edu, Bentley A. Strockbine, Department of Pharmacology, Stony Brook University, Niels H. Andersen, Department of Chemistry, University of Washington, and Carlos L. Simmerling, Department of Chemistry, Stony Brook University

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  amber.ch.ic.ac.uk/Questions/mail/299.html - [Cached Version]
  Published on: 10/23/2003    Last Visited: 8/15/2008  

  Carlos said it mostly well (except suggestions that I somehow know thisbetter).
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  > [mailto:owner-amber@scripps.edu] On Behalf Of Carlos Simmerling
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  > > From: owner-amber@scripps.edu on behalf of Carlos Simmerling

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  www.acscomp.org/Division/officers/index.html - [Cached Version]
  Published on: 6/6/2008    Last Visited: 6/6/2008  

  Dr. Carlos Simmerling Councilor (2007-2009):Stony Brook University Tel: (631) 632-1336

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  blog.stranova.com/?p=113 - [Cached Version]
  Published on: 5/30/2007    Last Visited: 3/18/2008  

  The winner of the Humanitarian Impact Innovation award was Dr. Carlos Simmerling of Stony Brook University in New York.In my interview with Dr. Simmerling, you'll learn about his team's breakthrough computer modeling supporting advanced HIV and AIDS research using the latest supercomputer technologies, and utilizing capabilities unique to the Itanium2 processor.

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  www.metanexus.org/lectures/winners/stony_bios.asp - [Cached Version]
  Published on: 10/7/2008    Last Visited: 7/19/2008  

  R. David Bynum | William C. Chittick | Robert P. Crease | Alfred Scharff Goldhaber | David Hanson | Sr. Margaret Ann Landry, RSHM | Gary Mar | Michael Marx | Eduardo Mendieta | Carol Ochs | Robert Pollack | Sheldon J. Reaven | John D. Ryan | Carlos L. Simmerling | Peter Steinfels | Clifford Swartz | Peter C. Williams
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  Carlos L. Simmerling (Ph.D., U of Illinois, Chicago) is Assistant Professor of Chemistry at Stony Brook and a member of the Center for Structural Biology.His research interests focus on the structural dynamics of complex biomolecular systems such as proteins and nucleic acids.He uses computer simulation methods and jointly develops one of the most widely used programs for molecular simulation.In 2002, Simmerling became the first researcher to use computational methods to successfully predict the atomic-level structure of a protein and subsequently received international recognition, with profiles of the work in journals and newspapers in more than 10 different languages.Simmerling's research also uses computer-generated graphical representations to visualize nano-scale biological processes.He developed a popular molecular graphics program, and his images have been featured in many publications such as Radiology Today, Reader's Digest and the US Department of Health and Human Services newsletter.The National Institutes of Health chose Simmerling's work for the sole graphic to accompany their 2003 press release, "Research of the Year."Professor Simmerling was the 2003 Stony Brook recipient of the SUNY Chancellor's "Excellence in the Pursuit of Knowledge" award.

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  www.itaniumsolutions.org/community/blog/the_power_of_pa - [Cached Version]
  Published on: 10/7/2008    Last Visited: 8/31/2008  

  Dr. Carlos Simmerling of Stony Brook University, the winner of the Alliance's Humanitarian award in 2007, discussed that a key reason why his biomedical research modeling performed so well was due to hands-on application and integration support from Alliance Founder SGI.SGI's team offered valuable insight which helped his application run as quickly as possible.Thanks to the collaboration between SGI and Dr. Simmerling's team's efforts in the modeling area, we may be significantly closer to a cure for HIV.

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  www.prnewswire.com/cgi-bin/stories.pl?ACCT=109&STORY=/w - [Cached Version]
  Published on: 4/17/2007    Last Visited: 4/17/2007  

  Dr. Carlos Simmerling at Stony Brook University in New York won $50,000 and top honors for his breakthrough medical research, while the University
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  Stony Brook's Simmerling won the top award in the Humanitarian Impact Innovation category.Working on an SGI Altix system located at the National Center for Supercomputing Applications (NCSA), Simmerling and his team have
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  that had previously proved insurmountable," said Simmerling, an associate professor in Stony Brook's Department of Chemistry and director of Computational Biology for Stony Brook's Institute for Chemical Biology and Drug Discovery. Simmerling has concluded that using NCSA's powerful Altix system has made a dramatic difference in his research."The Altix allows us to obtain new medical advances in months, rather than in years," he said.

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  www.metanexus.org/lectures/winners/stony.asp - [Cached Version]
  Published on: 1/1/2006    Last Visited: 7/19/2008  

  Carlos L. Simmerling is Assistant Professor of Chemistry at Stony Brook and a member of the Center for Structural Biology.

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  www.unixformula.com/new_york_research_breakthrough_on_n - [Cached Version]
  Published on: 10/7/2008    Last Visited: 11/21/2007  

  Dr. Carlos Simmerling, associate professor at Stony Brook's Center for Structural Biology, guided the research team, which successfully simulated how the HIV protease changes between two forms that already have been determined through experiments.
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  "We determined that if we knew how HIV protease opened, we could better identify a new and potentially more sensitive drug target," said Dr. Simmerling.
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  Individual simulations modeled only 50 nanoseconds of behavior -- less time than it takes a beam of light to travel 50 feet -- but they still last long enough for Dr. Simmerling and his colleagues to model HIV protease in unprecedented detail.
  
  "We can model the full change between the known structures with very high accuracy," Dr. Simmerling explained."We can also see how it opens, and where a drug molecule binds to the protease and causes it to close.And then we can reverse that process, and the protease opens again.These are all things that experiments have not been able to show us."
  
  Such reliability suggests the simulation will prove helpful in testing the potential efficacy of new drugs, and in understanding how variations of HIV seen between different patients can change a drug's behavior."HIV is a very adaptive virus that mutates easily, which can reduce the benefit of a drug," Dr. Simmerling said.
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  Dr. Simmerling's group developed the simulations using AMBER, a molecular dynamics application developed in part by Simmerling's lab.
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  "Roberto's contributions made the simulations a lot faster," said Dr. Simmerling.
  
  For the researchers, achieving such a detailed picture of HIV protease dynamics was a milestone that was a long time coming, and the broad availability of SGI Altix systems made it easier."I don't know that I would have tried this a couple of years ago," said Dr. Simmerling.
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  For instance, in tests designed to assess the viability of the project, SGI's Dr. Gomperts and Dr. Simmerling's team determined that the same AMBER simulation running on a 128- processor Xeon cluster at NCSA and on 128 processors of an Altix Bx2 system would take more than three times longer to complete on the cluster.

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