eHiTS v6.2:

eHiTS is probably the most accurate docking program currently available, with many outstanding features. Ease of use is just one of them. eHiTS continues to have the only truly exhaustive docking algorithm and one of the most accurate scoring functions available. The latest release of eHiTS offers a new, more flexible, licensing mechanism to suit the needs of any organization. Add eHiTS to your drug discovery pipeline today and start finding new drugs right away.

Apply today to join the rapidly growing eHiTS docking community. eHiTS is free for academic institutions.

eHiTS LASSO:

The newest member of the eHiTS product line is the ligand based screening  tool: eHiTS LASSO (Ligand Activity by Surface Similarity Order). eHiTS LASSO is a pharmacophore like screening tool that uses data fusion techniques combined with our ISPT (interacting surface point types) descriptor to rapidly screen databases for actives.  This new tool will allow you to find new lead compounds with novel scaffolds.

eHiTS LASSO also provides the user with a set of predefined filters that can be used to screen databases with no training needed by the user. The predefined filters were created using 97 different families of pharmaceutical interest. For each family, actives obtained from various public sources were used to create filters that can identify ligands that are likely to show activity for that family.

Improved quality and speed of docking screens:

eHiTS LASSO  is now available as a stand alone product, but can still be combined with eHiTS to provide a seamless integration of ligand screening with receptor-ligand docking.  Combining the speed and high quality enrichment from eHiTS LASSO with the excellent binding pose prediction of eHiTS docking gives you the best of both worlds - fast screening results with accurate binding poses for the most interesting compounds.

Through the Sun Grid Utility at Network.com, customers of SimBioSys Inc. have immediate access to the eHiTS virtual screening application, significantly expediting results. "Providing eHiTS in the Application Catalog on Network.com will allow us to service customers that did not previously have access to the IT infrastructure needed to use eHiTS for computationally demanding projects." says Aniko Simon, vice president of business development at SimBioSys Inc. Customers who have tapped eHiTS for cycles on the Sun Grid include Brian Bennion from the Lawrence Livermore National Labs and Michael-Rock Goldsmith, Ph.D., from the US Environmental Protection Agency.

See Sun's press release and the featured story of the day on Sun.com

Dr. Nouri Neamati Group, USC

"We found eHiTS to be easy to use and a very powerful ligand docking software package." said Dr. Nancy Deng from USC, who has been working with Dr. Nouri Neamati, an internationally known expert in the field of antiviral and anticancer drug design and discovery.

In our HIV-1 integrase drug design project, we found that eHiTS performed better in duplicating the experimentally observed conformation of a ligand observed in the co-crystal of integrase complex (1QS4) than other docking tools used. Integrase is one of the three essential enzymes important for viral replication. However, integrase has proven to be a challenging target for structure-based drug design partially due to its shallow surface in its substrate binding site. Figure 1 shows that one of the top-ranked conformations generated from eHiTS docking studies overlaps well with the experimental observation. Further application of the program indicated that enriched eHiTS scores performed exceptionally well in correctly ranking and identifying active integrase inhibitors (manuscript in press, 2007). "We will be sure to utilize eHiTS scores in our future drug design endeavors" added Dr. Deng. Figure 2 shows the possible binding mode of a potential integrase inhibitor that was selected from our database screening.

Figure 1. Comparison of experimentally observed conformation (cyan, 1QS4) and one of the eHiTS predicted (pink)

Figure 2. Possible binding mode of a selected integrase inhibitor from database mining

Dr. Pascal Muller, AliX, France

In evaluating the performance of eHiTS and FlexX Dr. Muller used the vitamin D receptor. A set of public vitamin D active ligands (28) with 1246 molecules from the Asinex Gold Update Collection acting as inactives was used. "eHiTS is much better on this case than FlexX," said Dr. Pascal Muller, Molecular Modeler at AliX, a structural genomics company in France "in addition to reproducing the X-ray binding pose, eHiTS was also able to correctly rank 15 of the 28 actives in the top 34 structures, while FlexX did not place any actives in the top 200 structures."

SimBioSys would like to invite you to visit our booth at the March ACS National Meeting.

At the 233rd  ACS national meeting, Chicago, IL, March 25-29th,
meet our representatives Dr. Zsolt Zsoldos (CEO), Dr Aniko Simon (VP) and
and Darryl Reid (Computational Scientist) at booth # 454 & 456  while exhibiting in partnership with Sun Microsystems. or come to our presentations at various sessions:

1. COMP 37: SynSPROUT and SPROUT-LeadOpt: on Sunday, 25 March 2007  at 3:35 pm,
   Section C Hyatt Regency McCormick -- 12 A
   SynSPROUT and SPROUT-LeadOpt: De novo ligand design and optimization guided by virtual synthesis
   
   
2. COMP 38: De novo eHiTS: on Sunday, 25 March 2007  at 4:10 pm
   Section C Hyatt Regency McCormick -- 12 A
   Fragment based docking combined with synthetic planning: De novo eHiTS
   
   
3. CINF 68: eHiTS Filter, a.k.a. eHiTS LASSO, on Tuesday., 27 March,  at 3:00 PM,
   Section B Hyatt Regency McCormick -- 12 B
   Surface interaction property based similarity searching with the eHiTS Filter
   
   
4. COMP 300: eHiTS and the Sun Grid Compute Utility, Thursday, 29 March 2007
   Section A McCormick Place North -- Room N136, Level 1
   eHiTS and the Sun Grid Compute Utility: Using massively parallel computation for docking

SimBioSys will also be participating in these other events:

SABPA Advances in Structure-based Drug Design Symposium, La Jolla, CA,
Saturday, March 17th, Darryl Reid, will be presenting:
Fragment based flexible ligand docking and screening with eHiTS

The 5th Intl. Workshop on New Approaches in Drug Design & Discovery
Marburg, Germany, March, 26-29  2007
Thursday, March 29, 2007, Prof. Peter Johnson, Univ. of Leeds, UK, will be presenting: "De Novo Design: Theory and Practice"

The 11th Electronic Computational Chemistry Conference (ECCC11)
SimBioSys is a proud sponsor of the 11th Electronic Computational Chemistry Conference (ECCC11), which will take place entirely on the Internet in April.

"The ECCC is the longest-running peer-reviewed online research conference in the natural sciences. Its virtual nature and free registration provide an opportunity for scientists from all countries - including developing countries - to present their papers for peer review and online discussion, and it brings important work to scientists' attention that they otherwise might not have known about." says Robert Q. Topper, an associate professor and chair of Monmouth University's Department of Chemistry, Medical Technology, and Physics, host of the conference.

The founders of SimBioSys, Zsolt Zsoldos et.al., presented their early work at the very first such conference in 1995, see SPROUT paper @ 1st ECCC.

eHiTS-to-VMD Interface Application. The Search for Tyrosine-tRNA Ligase
Inhibitors,
Krystian Eitner, Tomasz Gawda, Marcin Hoffmann, Mirosawa Jura, Leszek Rychlewski, and Jan Barciszewski; 
J. Chem. Inf. Model., Web Release Date: January 18, 2007

The authors present an interface between eHiTS and VMD to visualize calculation results for virtual high-throughput screening. This interface is freely downloadable from:  http://eitner.bioinfo.pl/bioinfo/ehits2vmd.sh

The authors  conclude that eHiTS is indeed useful in virtual high-throughput screening tasks, because in their test cases the ligand was found as one of the compounds with the highest differences in affinity to the staphylococcal protein and the human protein. They also concluded that eHiTS is a practical and comparatively fast method for the docking of ligand molecules to the receptor molecule.
Link to article: DOI: 10.1021/ci600392r

Phosphinate Inhibitors of UDP-N-Acetylmuramoyl-L-Alanyl-D-Glutamate:
L-Lysine Ligase (MurE)
Katja Strancar, Audrey Boniface, Didier Blanot, and Stanislav Gobec
Arch. Pharm. Chem. Life Sci. Volume 340, Issue 3, Date: March 2007, Pages: 127-134

The authors in this paper focus on MurD and MurE ligases, which catalyze the early steps of bacterial peptidoglycan biosynthesis and represent under-exploited targets for antibacterial drug design. They show new phosphinate inhibitors of UDP-N-acetylmuramoyl-L-alanyl:D-glutamate ligase (MurD) also inhibit UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:L-lysine ligase (MurE). They used eHiTS to investigate the possible binding mode of their new inhibitors.
Link to the article

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