[Product Releases]
|
|
|
|
|
[Blog]
|
|
Most
recent post
|
[News]
|
|
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
|
|
|
|
|
|
 |
Publications
/ Posters on
eHiTS and other SimBioSys Products by Independent Scientists
|
 |
European Journal of Medicinal Chemistry Sept 22 2011 (Web)
E. Sala, et al.: Identification of human IKK-2 inhibitors of natural origin (Part
II): In Silico prediction of IKK-2 inhibitors in natural extracts with
known anti-inflammatory activity
DOI:10.1016/j.ejmech.2011.09.022
|
 |
J.Med.Chem. 2011 Aug 16 (Web)
Inhibitors of androgen receptor activation function-2 (AF2) site identified through virtual screening.
Axerio-Cilies, P.; Lack, N.A.; Nayana, R.S.; Chan, K.H.; Yeung, A.; LeBlanc, E.; Guns, E.; Rennie, P. & Cherkasov, A.
DOI: 10.1021/jm200532b
|
|
J Comput Aided Mol Des. 2011 May;25 (5):477-89.
Docking glycosaminoglycans to proteins: analysis of solvent inclusion.
Samsonov SA, Teyra J, Pisabarro MT.
DOI: 10.1007/s10822-011-9433-1.
|
 |
Biochem Pharmacol 2011 May
1;81(9):1098-105. Epub 2011 Feb 26.
Small molecule inhibitors of peptidoglycan synthesis
targeting the lipid II precursor.
Derouaux
A, Turk S, Olrichs NK, Gobec S, Breukink E, Amoroso A, Offant J,
Bostock J, Mariner K, Chopra I, Vernet T, Zervosen A, Joris B, Frère
JM, Nguyen-Distèche M, Terrak M.
DOI: 10.1016/j.bcp.2011.02.008
|
|
J Chem Inf Model.
2011 Feb 28;51(2):408-19.
Epub 2011 Feb 3.
A machine learning-based method to improve docking scoring functions
and its application to drug repurposing.
Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE.
DOI:
10.1021/ci100369f
J Chem Inf Model.
2011 Apr 28
Correction to: A machine
learning-based method to improve docking scoring functions and its
application to drug repurposing.
Kinnings SL, Liu N, Tonge PJ, Jackson RM, Xie L, Bourne PE.
DOI: 10.1021/ci2001346
|
 |
February 24, 2011: PLoS ONE 6(2): e16903.
Identification of
Human IKK-2 Inhibitors of Natural Origin (Part I): Modeling of the
IKK-2 Kinase Domain, Virtual Screening and Activity Assays.
Sala E, Guasch L, Iwaszkiewicz J, Mulero M,
Salvado M-J, et al. (2011)
DOI:10.1371/journal.pone.0016903
|
|
January 5, 2011; J. Chem. Inf. Model.
Virtual
Decoy Sets for Molecular Docking Benchmarks
Izhar Wallach and Ryan
Lilien
|
 |
Sept 2010, J
Comput Chem
Can we trust docking
results? Evaluation of seven commonly used
programs on PDBbind database
Dariusz Plewczynski, Michał Łaźniewski, Rafał Augustyniak, Krzysztof
Ginalski
View: DOI:
10.1002/jcc.21643
|
|
Mar 2010,
Drug Discovery Today
volume 15, issue 5-6, year 2010, pp. 186 - 197
Therapeutic
strategies underpinning the development of novel techniques for the
treatment of HIV infection
Tan, J.J., Cong, X.J., Hu, L.M., Wang, C.X., Jia, L., Liang, X.-J.
View: doi:10.1016/j.drudis.2010.01.004
|
|
Dec 2009,
Bioorganic & Medicinal Chemistry Letters, Volume 19, Issue 23, 1
December 2009, Pages 6770-6774
Discovery of novel
non-peptide inhibitors of BACE-1 using virtual high-throughput screening
N. Yi Mok, James Chadwick, Katherine A.B. Kellett, Nigel M. Hooper, A.
Peter Johnson, Colin W.G. Fishwick
View: doi:10.1016/j.bmcl.2009.09.103
|
|
August 31, 2009;
Chem.Res.Toxicol. 2009, 22, 1594-1602
Molecular
Modeling for Screening Environmental Chemicals for Estrogenicity: Use
of the Toxicant-Target Approach
James R. Rabinowitz, Stephen B. Little, Susan C. Laws and Michael-Rock
Goldsmith
View article: doi:
10.1021/tx900135x
|
|
April 7, 2009;
J. Med. Chem. 2009, 52, 2683 - 2693
Structure-Based
Design, Synthesis, and Characterization of Inhibitors of Human and
Plasmodium falciparum Dihydroorotate Dehydrogenases
Matthew Davies,Timo Heikkila, Glenn A. McConkey, Colin W. G. Fishwick,
Mark R. Parsons, and A. Peter Johnson
View article: doi:
10.1021/jm800963t
|
|
May 2009,
Journal of Chemical Information and Modeling,
J Chem Inf Model.; Publication Date (Web): May 15, 2009
Docking Ligands
into Flexible and Solvated Macromolecules. 4. Are Popular Scoring
Functions Accurate for this Class of Proteins?
Englebienne P, Moitessier N
DOI: 10.1021/ci8004308
|
|
May 2009,
PLoS Comput Biol. 2009 May; 5(5): e1000387.
Published online 2009 May 15.
Drug
Discovery Using Chemical Systems Biology: Identification of the
Protein-Ligand Binding Network To Explain the Side Effects of CETP
Inhibitors
Li Xie, Jerry Li, Lei Xie, and Philip E. Bourne
View Article: doi:
10.1371/journal.pcbi.1000387.
|
|
Mar 2009,
Bioorganic & Medicinal Chemistry
Volume 17, Issue 5, 1 March 2009, Pages 1884-1889; Epub 2009 Jan 29.
Discovery
of new inhibitors of the bacterial peptidoglycan biosynthesis enzymes
MurD and MurF by structure-based virtual screening.
Turk S, Kovac A, Boniface A, Bostock JM, Chopra I, Blanot D, Gobec S.
View: doi:10.1016/j.bmc.2009.01.052
|
Bioinformation
(Online ISSN 0973-2063;
Print ISSN 0973-8894) |
Docking
study of triphenylphosphonium cations as estrogen receptor alpha
modulators.
Salisbury JP, Williams JC Jr.
Bioinformation. 2009;3(7):303-7. Epub 2009 Feb 28.
PMID: 19293997, PDF
version
|
|
CoMFA,
LeapFrog and blind docking studies on sulfonanilide derivatives acting
as selective aromatase expression regulators.
Gueto C, Torres J, Vivas-Reyes R.
Eur J Med Chem. 2009 Feb 15.
|
|
Bioorg Med
Chem Lett. (Web): 2009 Jan 19.
"Design
and synthesis of new hydroxyethylamines as inhibitors of
d-alanyl-d-lactate ligase (VanA) and d-alanyl-d-alanine ligase (DdlB)"
Sova
M, Cadež G, Turk S, Majce V, Polanc S, Batson S, Lloyd AJ, Roper DI,
Fishwick CW, Gobec S., Faculty of Pharmacy, University of Ljubljana,
Askerceva 7, 1000 Ljubljana, Slovenia.
view article: http://dx.doi.org/10.1016/j.ejmech.2006.08.007
|
 |
Proteins: Structure, Function, and
Bioinformatics,
Published Online: 23 Jan 2009
"De
novo identification of binding sequences for antibody replacement
molecules"
Stephen Quirk(1), Shi Zhong(2), Rigoberto
Hernandez(2)
(1)Kimberly-Clark Corporation, Roswell,
Georgia 30076
(2)Center for Computational Molecular
Science and Technology, School of Chemistry and Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332-0400
view article: DOI:
10.1002/prot.22382
|
|
J. Med. Chem.,
2009, 52 (1), pp
20–32,
Publication Date (Web): December 10, 2008
"Pharmacophore Guided Discovery of Small-Molecule Human
Apurinic/Apyrimidinic Endonuclease 1 Inhibitors"
Zahrah Zawahir, Raveendra Dayam, Jinxia Deng, Cherelene Pereira and
Nouri Neamati
Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy,
University of Southern California, 1985 Zonal Avenue, Los
Angeles, California, 90033
view Article: doi:10.1021/jm800739m
|
|
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
view Article: DOI:
10.1002/prot.22115
|
|
Mol Cell
Endocrinol. 2009 Mar 25;301(1-2):245-50. Epub 2008 Aug 14.
Discovery of new
inhibitors of aldo-keto
reductase 1C1 by structure-based virtual screening.
Brožič
P, Turk
S, Lanišnik
Rižner T, Gobec
S.
|
Bioinformation
(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 - 2009
|
|
|
 Computer Science
Department, Trinity College, Dublin, Ireland 
|
|
"gLite Porting to the PS3 using ETICS for
electronic High Throughput Screening (eHiTS)"
by: E. Kenny, P. Lavin, J. Walch, B. Coghlan
EGEE '09
Conference, September 21-25, 2009 in Barcelona, Spain, EU
see poster as: png,
PDF
|
|
"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.
Back to the Top.
|
|
|
