CSA Trust Grant 2013 - call for application

February 8th, 2013

As SimBioSys employees were proud recipients of the Chemical Structure Association (CSA) Trust Grant in the past, we are now pleased to post this year’s invitation to apply. The due date for receipt of proposals is March 14, 2013.

Applications Invited for CSA Trust Jacques-Émile Dubois Grants for 2013.CSA Trust LogoThe Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research. In support of its charter, the Trust has created a unique Grant Program, renamed in honor of Professor Jacques-Émile Dubois who made significant contributions to the field of cheminformatics. The Trust is currently inviting the submission of grant applications for 2013.Purpose of the GrantsThe Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds. A Grant will be awarded annually up to a maximum of five thousand U.S. dollars ($3,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support.

Who is Eligible?

Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria.

Which Activities are Eligible?

Grants may be awarded to acquire the experience and education necessary to support research activities; e.g. for travel to collaborate with research groups, to attend a conference relevant to one’s area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of one’s research.

Application Requirements

Applications must include the following documentation:

1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant;
2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s objectives and the clarity of this statement are essential in the evaluation of the application);
3. A brief biographical sketch, including a statement of academic qualifications;

4. Two reference letters in support of the application. Additional  materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-4. Three copies of the complete application document must be supplied for distribution to the Grants Committee.

Deadline for Applications

Applications must be received no later than March 14, 2013. Successful applicants will be notified no later than May 2, 2013.

Address for Submission of Applications

Three copies of the application documentation should be forwarded to: Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA. If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor@nfais.org prior to submission so that she can contact you if the e-mail does not arrive.


Chemical Structure Association Trust: Recent Jacques-Emile Dubois Grant Awardees
Tu C. Le: CSIRO Division of Materials Science & Engineering, Clayton, VIV, Australia. Tu V. was awarded the Grant for travel to attend a Cheminformatics course at Sheffield University and to visit the Membrane Biophysics group of the Department of Chemistry at imperial College London.
J. B. Brown: Kyoto University, Kyoto, Japan. J.B. was awarded the Grant for travel to work with Professor Ernst Walter-Knappat the Freie University of Berlin and Professor Jean-Phillipe Vert of the Paris MinesTech to continue his work on the development of atomic partial charge kernels
J. B. Brown: Kyoto University, Kyoto, Japan. J.B. was awarded the Grant for travel to work with Professor Ernst Walter-Knappat the Freie University of Berlin and Professor Jean-Phillipe Vert of the Paris MinesTech to continue his work on the development of atomic partial charge kernels
Laura Guasch Pamies: University Rovira & Virgili, Catalonia, Spain. Laura was awarded the Grant to do three months of research at the University of Innsbruck, Austria.
Maciej Haranczyk: University of Gdansk, Poland. Maciej was awarded the Grant to travel to Sheffield University, Sheffield, UK, for a 6-week visit for research purposes.
Rajarshi Guha: Indiana University, Bloomington, IN, USA. Rajarshi was awarded the Grant to attend the Gordon Research Conference on Computer Aided Design in August 2007.
Krisztina Boda, University of Erlangen, Erlangen, Germany. Krisztina was awarded the Grant to attend the 2006 spring National Meeting of the American Chemical Society in Atlanta, GA, USA.

eHiTS v12 is released

July 2nd, 2012

Cross posting from CCL:

Simulated Biomolecular Systems Inc. (SimBioSys) is happy to announce the release of eHiTS 12. eHiTS is a fragment-based molecular docking application that employs a statistically derived scoring function, and includes family-based enhancements for pose generation and scoring.

New improvements and features in eHiTS’ 12 include:

  • A new, rigorous protonation state handling mechanism that employs hydrogen bond network optimization and on-the-fly evaluation states. Output structures now include explicit hydrogens.
  • A more accurate algorithm for classification of targets to protein-families, considering both geometric and sequence criteria.
  • Family-based detection of hot-spots in binding sites, and utilization of those as attraction points during docking.
  • Docking constraints can be defined by users by fixing ligand fragments to specified locations, or by requiring specified receptor-ligand interactions to be satisfied.
  • A newly trained scoring function using an extended and highly curated knowledgebase of ligand-receptor complexes.

eHiTS’ approach to the docking problem has been unique in various aspects. It divides the ligand to fragments that are docked independently everywhere in the binding pocket, identifies compatible sets of fragment poses that reconstruct full ligand poses, and then optimizes the poses within the binding site. This algorithmic approach guarantees a comprehensive and unbiased sampling of the conformations space. An on-the-fly assessment of protonation states further alleviates potential biases, and reduces the burden on users of structure preparation. The use of protein family knowledge in eHiTS has been shown to improve pose prediction and virtual screening performance. Emphasis is given in eHiTS to ease of use, and optional automated assignment of hydrogens and charges is available.

A major advancement in the technology in the new version is the introduction of target-sites. Prior to docking, local minima are detected by probing the binding pocket thoroughly. Those local minima, along with optional user constraints and automated constraints are used as target-sites – hot-spots that are targeted during pose generation and are promoted by scoring. The use of target-sites gives rise to greater accuracy, and reduced dependence on initial conditions.

Evaluation copies of eHiTS 12 can be obtained by submitting a demo request on our website:

About SimBioSys

SimBioSys Inc. is a Toronto based company dedicated to development of scientific tools for drug discovery and organic synthesis planning. It retains a constant focus on the innovation of algorithms to provide improved throughput and accuracy in the fields of flexible docking and virtual screening. SimBioSys is also a pioneer in the field of computer-aided retrosynthetic analysis where it supports chemists through the challenges of organic synthesis. With attention to detail, ease-of-use and improved productivity, SimBioSys has built a strong reputation of delivering state-of-the-art scientific solutions to biotechnology, pharmaceutical and other companies in the chemical industry.

For additional information please contact:
Orr Ravitz, PhD
Chief Operating Officer
(416) 741-4263
ravitz (_) simbiosys.com

Happy Canada Day with eHiTS v12

July 1st, 2012

As you might know, SimBioSys headquarter is located in Toronto, Ontario, Canada, and while our team consists of exceptionally talented scientist from many different ethnic backgrounds, we all celebrate Canada Day on July 1st. This year we made a special tribute – with releasing eHiTS v12 and celebrating it as expected with a red and white cake as the picture demonstrates below.

eHiTS v12 cake

The cake was excellent, just like the release of eHiTS v12! It’s faster, more accurate and more convenient to use than the previous release eHiTS Lightning was – it is now up to you to test if it is surpassing the competitors!

Happy Canada Day and happy docking to all our users.

The SimBioSys team.

ARChem is making a leap forward by including Stereochemistry in its retrosynthetic analysis engine

May 10th, 2012

Our understanding of the role chirality plays in the activity of drugs has been steadily growing in recent decades. Although we cannot always explain mechanistically why different enantiomers can manifest strikingly diverging  pharmacological behaviors, we can often measure significant differences in their binding affinity, selectivity and ADME properties. Even for drugs that are currently marketed in racemic mixtures there is often evidence that one of the  enantiomers dominates the pharmacology of the drug. It is not surprising therefore, that stereo-selective methods and chiral starting materials have become pivotal to synthesis in this domain.

Including stereochemistry into our synthesis planning tool, ARChem, has been a major undertaking at SimBioSys. The development encompassed many layers, from algorithmic perception of the full spectrum of stereogenic types, through representation of stereochemical reactions, to the proper depiction of molecules. We are very excited to release the first version of ARChem to address stereochemistry. It offers the following capabilities:

  1. Full perception of stereochemistry in the target molecule.

  2. Matching of literature precedents with proper chirality during the retrosynthetic analysis.

  3. Matching proper enantiomers from the collection of starting materials.

The synthesis for Azalanstat below demonstrates the utility of these features. The synthetic route suggested by ARChem, generates one of the chiral centers of the target molecule using an enantioselective reaction step taken from a specific literature example, whereas the other chiral center is introduced using a chiral starting material.


All steps in the plan are supported by literature examples, and all starting materials are found in catalogs of commercial suppliers.

While we hope you share our satisfaction with this accomplishment, our work on stereochemistry is far from complete. The next few months will be dedicated to developing the capability of generating enantioselective reaction rules. This will allow ARChem to provide the novelty and robustness it achieves in the synthesis design of achiral compounds, and will further enhance its usefulness as a synthetic idea generator.

Stereochemistry in ARChem, and the state of CADD during the ACS meeting in San Diego

March 7th, 2012

We would like to invite you to two events that will take place during the ACS national meeting in San Diego later this month. The first is a talk describing a significant and highly anticipated development in our retrosynthetic analysis project, ARChem, and the second is a special symposium, cosponsored by SimBioSys and co-organized by one of us, reviewing the state of the art and the future of computer-aided drug design.

The introduction of stereochemistry capabilities in ARChem is very significant. Most of the other synthesis design tools, and until recently, our own automated retrosynthetic analysis system ignored any stereochemistry in the target molecule, and likewise, the reaction rules in ARChem did not include any stereochemical information, yet most of the molecules in the pharma industry today include at least one stereocenter. In a CINF symposium, Professor A. Peter Johnson will expose, for the first time, the various facets of stereochemistry in ARChem, including: representation and perception of stereogenic types, representation of streochemical reaction rules and strategies, stereochemical reaction searching and example extraction, and enantioselective rule application. Examples of the retrosynthetic analysis of stereochemically complex targets will be given to demonstrate the new capabilities of the system:

Title: Advanced reaction searching: A comprehensive treatment of stereoselctivity in reactions
Date/Time: Tuesday, March 27, 2012 - 03:45 PM
Location: San Diego Convention Center, room 27A

SimBioSys is also a proud sponsor of a special session that will bring together thought leaders from the industry and the academia who are at the forefront of drug discovery to discuss the role computational methods have been playing in the field and the expectations for the future. 8 talks will feature opinionated accounts of the state-of-the-art in different sub-disciplines (e.g. QM methods, docking, MD simulations etc), and will describe the strengths and shortcomings of the methods in real life scenarios. The session is organized by our own, Orr Ravitz with Chris Corbeil from CCG and Jason Cross from Cubist, and is guaranteed to be a fascinating event.
Title: Computer-Aided Drug Design: Hopes, Reality and Prospects
Date/Time: Monday, March 26, 2012; 8:15 - 11:35 am & 1:00 - 4:30 pm
Location: San Diego Convention Center, room 27A

If you would like to meet Orr Ravitz and/or Peter Johnson and discuss our tools, learn about our research projects, pursue collaborations or simply say hi or get to know us, please contact us in advance or during the meeting by email or by phone.

Have a wonderful spring meeting in sunny California!

SimBioSys to present at the upcoming BAGIM meeting

January 12th, 2012

We are pleased to announce that Drs. Zsolt Zsoldos and Orr Ravitz from SimBioSys will be presenting at the upcoming BAGIM (Boston Area Group for Informatics and Modeling) meeting, on Thurs., Jan 19 2012.

Title: Family based scoring and docking constraints in eHiTS

Abstract: eHiTS uses a novel, statistical knowledge-based scoring method consisting of interacting surface points and physical terms combined with an adaptive parameter scheme. This approach offers users the capability to fine-tune the scoring function using their data and thus incorporate their full body of knowledge in a systematic and automatic fashion. (See recent paper: “Improving molecular docking through eHiTS’ tunable scoring function”, O. Ravitz, Z. Zsoldos, and A. Simon, Journal of Computer-Aided Molecular Design, 25(11), 1033-1051 (2011) DOI: 10.1007/s10822-011-9482-5).

Prior to the talk, a short overview of the CLiDE program will be given. CLiDE is a tool for extraction of chemical structures from documents and images. The program is capable of transforming 2D molecular depictions into standard chemical file formats, and it interfaces with the major chemical editors. The technical and scientific challenges of perceiving chemistry from images of varied qualities and representation conventions will be discussed, and examples for how those issues are addressed by CLiDE will be given. We will show how the different versions of CLiDE meet the different needs of chemists, as well as of IT and IP professionals constructing chemical databases from publications, patents, and reports.

More info on the event at the BAGIM page: http://bagim.org/next_meeting.html

If you are in the Boston area and would like to meet with us prior or after the event please let us know, just leave a comment on this post or send us an e-mail.

Holiday Greetings from the SimBioSys Team

December 15th, 2011

Thank you for your support and best wishes for the year ahead.

The SimBioSys Team

Happy Holidays

Movie on: ARChem in a nutshell

November 28th, 2011

One of our customers recently asked us to provide him with a short presentation explaining our retrosynthetic analysis software, ARChem, so that he would be able to advertise it to potential users within his organization. Since, to paraphrase the old adage, a clip is worth a thousand slides, we opted for a 5 minutes video.

It’s not easy to squeeze the essence of a product like ARChem into a short video, since it has so many facets: the search engine, the solutions display, solutions filtering, interfacing with reaction databases not to mention all the science that is at work under the hood. So we decided to focus on the core value of ARChem: the ability to harvest knowledge from experimental data, and to convert the knowledge to ideas. In 5 minutes we show, without discussing the fascinating underlying technology, the available search strategies, solutions viewing and construction, sharing ideas with your fellow researchers, and viewing literature examples. Please see the movie at:

ARChem movie http://www.simbiosys.com/archem/video/

We hope you will find it interesting.

eHiST Tune and Score methods are published with validation results

November 16th, 2011

Our article on eHiTS Tune and Score is now available online:

Improving molecular docking through eHiTS’ tunable scoring function
Journal of Computer-Aided Molecular Design
DOI: 10.1007/s10822-011-9482-5

The article contains lots of useful information about eHiTS Score and Tune algorithms, as well as it gives validation of the same using a number of test sets, including CDK2 and BACE1 for pose prediction, DUD for virtual screening and PDBBind for affinity prediction. eHiTS results are compared with other programs’ published results where such data were available. For example enrichment results on the DUD set were compared using results from Cross et.al (DOI: 10.1021/ci900056c)

eHiTS comparision on DUD

In conclusion, the article states that knowledge-based approaches are mainstream methods today, because they benefit from the ever expanding base of experimental data and from continuous progress in computational methods, and that score tuning is a natural extension of that concept. The authors also hope to solicit for wider use of the score tuning methodology and creation of test sets in the user community.

See the full article here

Zsolt Zsoldos from SimBioSys to present at the MCADD Fall 2011 Seminar on Oct 5th

September 14th, 2011

MCADD announcement:


The Montreal Computer-Aided Drug Design (MCADD) organizing committee is annoucing the Fall 2011 seminar will feature Zsolt Zsoldos of SimBioSys Inc. (http://www.simbiosys.ca/) . He will be presenting his talk entitled “Automated tuning of eHiTS scoring weights specific to protein families”. The seminar will be October 5th at 3pm in room 501 of the Goodman Cancer Center of McGill University. This seminar will be followed by a wine and cheese reception afterwards. We look forward to seeing you there and please feel free to forward this email to anyone interested in attending the seminar and/or joining the MCADD Group (students and post-docs are welcome).

Additionally we invite you to follow and receive announcements from the MCADD community on linkedin. Just ask to join the Montreal Computer-Aided Drug Design group
( http://www.linkedin.com/groups?gid=2983304&trk=myg_ugrp_ovr ).

Christopher Corbeil
Chair, 4th MCADD Organizing Committee

Organizing Committee members:
Pierre Bonneau, Boehringer Ingelheim (Canada) Ltd.
Araz Jakalian, Boehringer Ingelheim (Canada) Ltd.
Enrico O. Purisima, NRC-BRI
Constatin Yannopolous, Vertex Canada

MCADD Seminar

Date: October 5th, 2011

Location:    Room 501 (Karp Conference Room) Goodman Cancer Center, McGill University, 1160 Pine Ave. West, Montreal, Quebec

Time:     3:00pm - Seminar: /Automated tuning of eHiTS scoring weights specific to protein families/, Zsolt Zsoldos,  SimBioSys Inc. Toronto, Canada

4:00pm - Cocktail/Wine


The molecular docking paradigm, has thus far failed to produce a generic approach that would deliver accurate pose prediction capabilities, and reliable rank-ordering of conformations and ligands consistently for any biological system of interest. This reality, which has been addressed by numerous methodology papers and comparative studies, has been largely attributed to the inability of scoring functions to capture different chemical interaction types at a uniform level of accuracy. Several studies attempted to develop guidelines for choosing the most suitable docking and scoring method for a specific problem based on protein family classification of the target, dominant interactions, and other properties of the studied system. Consensus techniques, on the other hand, try to synergistically integrate information from multiple sources  assuming agreement between different methods is indicative of more accurate values. Both approaches, however, have shown only limited success in improving binding mode and activity prediction capabilities.

An alternative solution, and arguably a more rigorous one, would be to tailor the scoring function for the system of interest. eHiTS uses a novel scoring method consisting of a statistical knowledge base focused  on interacting surface points and physical terms combined with an adaptive parameter scheme. This  approach offers users the capability to fine-tune the scoring function using their data and thus incorporate  their full body of knowledge in a systematic and automatic fashion. In many realistic drug discovery  scenarios, structural and ligand-activity information is sufficient in a statistical sense to adjust a limited set  of parameters representing the relative weights of the various terms in the eHiTS scoring function. During tuning, receptor targets are clustered according to the chemical and shape similarity of the active site, and weight sets are optimized for each family. Pharmacophore constraint descriptions are thus generated automatically from the recurring interaction patterns observed in a specific active set profile. These constraints can be used for constrained docking or pharmacophore-enhanced scoring schemes.

In this talk, an overview of the eHiTS’ tuning utility will be given, outlining the underlying methodology. Results will be presented showing the enhancements achieved by the tuning process on docking and scoring performance.