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Can we trust docking results?
Sept 2010

IBM Systems and Technology Group releases a white paper with eHiTS and Cell
Oct 2008

EPA's ToxCastTM project will use SimBioSys' eHiTS as docking engine
Nov, 2007

[Events]

243rd ACS
Mar 25-29, 2012
San Diego, CA
see >> more

Index


Publications / Posters on eHiTS and other SimBioSys Products by Independent Scientists

 

Most recent
2009 and beyond user publication are listed here

.

User Publications up to 2008:

Proteins: Structure, Function, and Bioinformatics
Volume 73, Issue 4, Date: December 2008, Pages: 889-901
Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure–activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function
N. Schormann, O. Senkovich, K. Walker, D.L. Wright, A.C. Anderson, A. Rosowsky, S. Ananthan, B. Shinkre, S. Velu, D. Chattopadhyay
DOI: 10.1002/prot.22115

Mol Cell Endocrinol. 2008 Aug 14. [Epub ahead of print]
Discovery of new inhibitors of aldo-keto reductase 1C1 by structure-based virtual screening.
Brožič P, Turk S, Lanišnik Rižner T, Gobec S.

Online ISSN
0973-2063;

Print ISSN 0973-8894
Bioinformation, 2008 May 13;2(8):325-9.
Virtual screening for novel COX-2 inhibitors using the ZINC database.
Sudha KN, Shakira M, Prasanthi P, Sarika N, Kumar ChN, Babu PA.

Bioorganic & Medicinal Chemistry Letters, Volume 18 (2008), Issues 11, June 1 2008 pp.  3152–3157
"Structure-based prediction of Mycobacterium tuberculosis shikimate kinase
inhibitors by high-throughput virtual screening"
Aldo Segura-Cabrera, Mario A. Rodriguez-Perez
view Article: doi:10.1016/j.bmcl.2008.05.003 

Current Pharmaceutical Analysis, Volume 4, Number 1, February 2008, ISSN: 1573-4129
Protein-ligand Docking: A Review of Recent Advances and Future Perspectives
Montserrat Vaque, Anna Ardevol, Cinta Blade, M. Josepa Salvado, Mayte Blay, Juan Fernandez-Larrea, Lluis Arola and Gerard Pujadas
View: abstract

PLoS Computational Biology. 2008 Jan; [Open Access Reserach Article]
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators
Lei Xie, Jian Wang, Philip E. Bourne
View
Article: DOI: 10.1371

Nature / British Journal of Pharmacology (2008) 153, S7–S26; doi:10.1038/sj.bjp.0707515; published online 26 November 2007
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
N Moitessier, P Englebienne, D Lee, J Lawandi and C R Corbeil

J Chem Inf Model. 2007 Oct 18; [Epub ahead of print]
Impact of Ligand Protonation on Virtual Screening against beta-Secretase (BACE1).
Polgar T, Magyar C, Simon I, Keseru GM.
View
Article: DOI: 10.1021/ci700223p
SimBioSys: discussion

Proteins. 2007 Oct 1;69(1):160-76.
Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.
Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N.
View Article:
SimBioSys: discussion

Jul 2007, Bioorganic & Medicinal Chemistry Volume 15, Issue 14, 15 July 2007, Pages 4985-5002:
Discovery of structurally diverse HIV-1 integrase inhibitors based on a chalcone pharmacophore
Jinxia Deng, Tino Sanchez, Laith Q. Al-Mawsawi, Raveendra Dayam, Rosendo A. Yunes, Antonio Garofalo, Michael B. Bolgerd and Nouri Neamati
View: article doi:10.1016/j.bmc.2007.04.041
 
Jun 2007, Frontiers in Drug Design and Discovery,
ISBN: 90-77527-03-6, Volume 3, 2007, Pp. 477-502:
Structure-Based Virtual Screening
T. Polg�r and G.M. Keseru
View: chapter
 
Jan 2007, Journal of Chemical Information and Modeling, Web Edition January 18, 2007:
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; 
View: article

March 2006,:   Bioorganic & Medicinal Chemistry Letters Volume 16, Issue 6 , Pages 1610-1615:  gives a user's perspective on eHiTS:
Darrell E. Hurt et al: Brequinar derivatives and species-specific drug design for dihydroorotate dehydrogenase; 
View: article doi:10.1016/j.bmcl.2005.12.029


June 2005, J. Am. Chem. Soc.:
Kerwin, S. M.: Computer Software Review of: eHiTS 5.1.6, SimBioSys Inc.; 
View : article

Scientific Presentations and Posters

2006 - 2008


"Effects of initial conformations of small ligands on computational
docking accuracies"

Akifumi Oda1, Ohgi Takahashi1, Noriyuki Yamaotsu2, Shuichi Hirono2

(1)Tohoku Pharmaceutical University, 4-4-1, Komatsushima, Aoba-ku, Sendai,  Miyagi, 981-8558, Japan, http://www.tohoku-pharm.ac.jp/

(2)Kitasato University, 5-9-1, Sirokane, Minato-ku, Tokyo, 108-8641, Japan,

Presented at the IUCr 2008 Osaka, Japan conference,
XXI Congress and General Assembly of the International Union of Crystallography, 23-31 August, 2008

Site now: http://www.iucr2008.jp/

new site after Dec 25th 2008: http://www.crsj.jp/IUCr2008/

see poster abstract on our site.



"Elucidation of Mechanisms of Action of Molecules with Anti-Cancer Activity Using Molecular Docking"
Ines Sousa, Visvaldas Kairys, Jose M. Padron, Miguel X. Fernandes
2nd Meeting YBIM (Young Biomedical Investigators of the Macaronesia), held on November 10-13, 2007 at Lanzarote, Spain.
see presentation (pdf)




Structure-based Drug Design: Molecular Docking Studies
Jinxia (Nancy) Deng, PhD, Postdoctoral Research Associate
University of South California, School of Pharmacy
Sept 25,  2007  see presentation (PDF)



Digging Deeper into Deep Data: Molecular Docking as a Hypothesis-driven Biophysical Interrogation System in Computational
Toxicology (PDF, 15KB, 1pp)
Contact: Michael Goldsmith, U.S. EPA/Office of Research and
Development (ORD)/National Center for Computational Toxicology (NCCT)
See poster (PDF, 245KB, 1pp)



Preoxisome-Proliferation Activated Receptors as a Macromolecular Target for Chemical Toxicity: Models of the Interactions of PPARs with Perfluorinated Organic Compounds
Contact: Michael Goldsmith, U.S. EPA/Office of Research and
Development (ORD)/National Center for Computational Toxicology (NCCT)
See poster (PDF)


Identification of a novel BACE1 inhibitor scaffold via an in silico screening approach
James Chadwick, Kathrine A.B. Davery, N. Yi Mok, Nigel M.Hooper, A. Peter Johnson and Colin W.G. Fishwick
School of Chemistry and Institute of Moelcular and Cellular Biology, Universirty of Leeds, Leeds, UK, LS2 9JT, UK
see presentation



Presented at the 5th Joint Meeting on Medicinal Chemistry, Portoroz, Slovenia, June 17 - 21, 2007 :
Novel Inhibitors Novel Inhibitors of Isoleucyl-tRNA Synthetase as Potential Antibacterial Drugs
Nicola J. Potter, Ian Chopra, Julian G. Hurdle, A. Peter Johnson & Colin W.G. Fishwick
School of Chemistry & bInstitute of Molecular & Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K.
see presentation



STRUCTURE-BASED DESIGN OF INHIBITORS OF CLASS 2 DIHYDROOROTATE DEHYDROGENASES
Heikkila TJ, Davies M, Parsons MR, Johnson AP
MR, Johnson AP
see presentation



Design and Synthesis of New Dihydroorotate Dehydrogenase Inhibitors as Potent Antimalarials
Matthew Daviesa, Timo Heikkil�b, Dr. C. W. G. Fishwicka* and Prof. A. P.
Johnsona
School of Chemistry, University of Leeds, UK, LS2 9JT and bSchool of Biochemistry and Microbiology, University of Leeds, UK, LS2 9JT
see presentation


July 15-19, 2007, Montreal, Canada
ICTXI\u2013Eleventh International Congress of Toxicology: "Discovery Serving Society"
a poster presentation on:  "Peroxisome-Proliferator Activated Receptors as a Macromolecular Target for Chemical Toxicity: Models of the Interactions of PPARs with Perfluorinated Organic Compounds"
by  Michael-Rock Goldsmith, James Rabinowitz U.S EPA, ORD, Computational Toxicology Research Program
see presentation


De Novo Design & Synthesis of Novel RNA Polymerase Inhibitors as Potential
Anti-Tuberculosis Agents
Anil K. Agarwal, Julian Hurdle, Amer I. AlOmar, Ian Chopra, A. Peter Johnson & Colin W. G. Fishwick
see presentation
 




November 12-15, 2006, San Paolo, Brasil
The 3rd Brazilian Symposium on Medicinal Chemistry; " Recent Advances in Drug Discovery and Development",
a poster presentation on:  "Structures of the Pteridine Reductase (PTR1) from Trypanosoma brucei Complexed with Folate Analog Inhibitors."
by  Viviane Paula Martini (a), Jorge Iulek (a), William Nigel Hunter (b), Lindsay Brian Tulloch (b)
a) Department of Chemistry, Biotechnology Center, State University of Ponta Grossa - PR, Brazil. b) Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, UK.; e-mail: w.n.hunter@dundee.ac.uk, iulek@uepg.br
see presentation




SimBioSys would like to recognize the efforts of those using our products by
including them on this website.  If you have given a presentation or written
a publication using results obtained from eHiTS, please contact us so we can
acknowledge your work.




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