SimBioSys Blog

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.

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:

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

We hope you will find it interesting.

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)

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
http://www.springerlink.com/content/r1t66167718h5110/

MCADD announcement:

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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

===============================================
Abstract

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.

Whether you are at work, at home or on a trip this summer, you can stay informed about the latest software tools of SimBioSys. Three of our products: CLiDE, eHiTS and ARChem, will be showcased in rotation on our weekly seminar series. Join us for these one hour online sessions given every Thursday at noon, EDT.

Starting July 14th we presented CLiDE (Chemical Literature Data Extraction) office tool - which can extract chemical structures embedded in PDF files, Word documents, JPEG and TIFF files, and other document and picture formats. CLiDE is a productivity and convenience tool, it saves the time and trouble of copying useful, and often complex structures from an image into a chemical editor or an e-lab notebook. It is useful for your everyday work, as well as for creating chemical knowledge-bases from journal articles, patents, and web content. (http://pubs.acs.org/doi/abs/10.1021/ci800449t)

There will be two more sessions for CLiDE:
* Thurs., Aug 4, 12 noon EDT
* Thurs., Aug 25., 12 noon EDT

On July 21st we presented eHiTS and its utilities (LASSO, CheVi, Score and Tune) for molecular docking and virtual screening. With its exhaustive conformational search, automated protonation state handling mechanism, and a tunable scoring function eHiTS provides one of the top-performing algorithms in the field: “the fastest” [1], “the most accurate” [2], and “the easiest to use with automated protonation/tatutomerization assigments” [3].

There will be two more sessions for eHiTS
* Thurs., Aug 11, 12 noon EDT
* Thurs., Sep 1., 12 noon EDT

On July 28th we presented ARChem, the newest tool to help organic chemist with synthesis planning.  Synthetic chemists in industry nowadays face an enormous challenge: to develop novel  chemicals, faster, safer, greener and cheaper. In order to solve this multi-dimensional problem most chemists make some use of reaction databases but these are most helpful when the synthesis of the target entity has already appeared in the literature.

ARChem Route Designer is a tool which goes well beyond this and is a computer system designed to support the organic synthetic chemist in the planning the synthesis of novel as well as known compounds. Its features include:

* reaction rules generated by automated mining of large reaction databases
* application of those rules on-the-fly in a retrosynthetic fashion to convert a novel chemical target all the way to readily available starting materials
* display of information from multiple resources (such as literature reactions from Reaxys (*), and starting materials from multiple vendors) in the system
* scoring the many alternatives based on various criteria (shortest path, highest yield, lowest material cost and other options)

There will be two more sessions for ARChem
* Thurs., Aug 18, 12 noon EDT
* Thurs., Sep 8., 12 noon EDT

The webinar sessions are live, and they provide you an opportunity to ask questions and receive  immediate feedback. In case you missed the session you can always view its recording, or join us during the next session on the product of your interest.

Don’t miss out this opportunity, register now at:
http://www.simbiosys.com/products/webinar_request.html
We are looking forward to seeing you at our summer webinars!

posted by: Aniko

References:
[1]: Quote from Dr. Katie Simmons, University of Leeds, UK
[2]: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21643/abstract
[3]: Quote from Dr. Mihaly Mezei, Mount Sinai School of Medicine, NY, USA

Notes:

(*) Reaxys and Reaxys Data represented in ARChem Webinar is used with kind permission of the copyright owner Elsevier Properties SA.
Copyright 2010-2011 (c), Elsevier Properties SA, All rights reserved. Authorized use only.  Reaxys(r) is a trademark owned and  protected by Elsevier Properties SA and used under license.

You may have come across a recent paper by a group of researchers from UCSD, Leeds and Stony Brook that utilized eHiTS for identifying targets for drug repurposing. The paper “A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing” (http://pubs.acs.org/doi/abs/10.1021/ci100369f) introduces an “inverse screening” scenario in which one searches for receptors that may bind a compound, in this case a known drug, and will suggest new therapeutic benefits for the molecule. The authors demonstrate experimentally and using benchmarks, how customizing the score to the receptors of interest improves the ability to identify active compounds, and to give a rough estimate for their relative activity.

The authors chose to use eHiTS not only because of its good performance as a docking tool, but also because it facilitates the score tuning exercise. eHiTS reports to the user not only a single score value, but also the individual terms, 20 in total, that build-up this value. The study examined various ways to recombine some of the score terms such that receptor-specific properties can be reproduced with improved accuracy.

An erratum for the paper was published yesterday (http://pubs.acs.org/doi/abs/10.1021/ci2001346), revising all the “native” eHiTS results, i.e. the out-of-the-box results without additional tuning. The original paper displayed results that were not in line with results obtained by us and others (see, for example: http://pubs.acs.org/doi/abs/10.1021/ci100374f), which prompted us to contact the authors. A few good words about the authors are in place. Once they heard our concerns, they acted swiftly and with full transparency to elucidate the problems, and once the source of the error was identified, they moved rapidly to publish the correction. This level of openness, integrity and cooperation should not be taken for granted, and we salute the team of researchers for their approach.

The root of the error was in the misidentification of the relevant scoring value in the eHiTS output. As stated in the erratum, eHiTS’ output includes an Energy value and a Score value. The Score value is the term that should be used in pose prediction and virtual screening scenarios. It is a scoring scheme that is trained on PDB complexes and is designed to reproduce crystallographic poses with high fidelity. In the scoring function training, many ligand poses are generated for each PDB complex, and the scoring functions is optimized to generate good score-RMSD correlation. Implicitly this process involves positive and negative data – the correct poses which are the objective and are to be promoted vs unrealistic poses which are rejected and suppressed. The eHiTS-Energy, on the other hand, is a scoring scheme that is designed to rank-order known active molecules. It is trained to produce score-binding affinity correlation, and therefore it is trained on positive data only. Hence, the eHiTS-Energy prospects of differentiating between actives and inactives are slim, which is demonstrated in the ROC charts of the original paper. eHiTS-Score, as shown in the erratum, strongly outperforms the energy in almost all cases, and generally shows good screening capabilities in most cases.

The main two conclusions of the paper are that (i) score tuning is a powerful approach to improve docking results, specifically in screening, and that (ii) non-linear methods for combining the scoring terms are superior to linear methods in this respect. We strongly support both observations. In fact, we have learned those lessons during the development of eHiTS’ scoring function, and therefore eHiTS adopted these principles a couple of years ago. Family-based scoring is available for many cases, and non-linear methods are central in its implementation. For dozens of protein-families, for which several complexes are available in the PDB, eHiTS provides a customized scoring which is invoked automatically by analyzing the geometry of any receptor provided by the user. When the user’s target is not matched to any family in eHiTS’ knowledge-base, a default scoring scheme is used. More about the tuning approaches in eHiTS can be found in this presentation:

http://www.simbiosys.com/science/presentations/2010-03-acs/eHiTS_239_ACS_website.pdf

We are pleased to see that score customization is growingly recognized as a promising path for improving the molecular docking paradigm. The new upcoming version of eHiTS will include even more sophisticated methods of utilizing experimental data. More about this in future posts.

Posted by Orr

We, at SimBioSys, are honoured to present at the upcoming Spring 2011 ACS meeting in a full day session devoted computer-aided organic synthesis design. The session will be this Sunday, Mar 27, titled:  “50 Years of Computers in  Organic Chemistry: Symposium in Honor of James B. Hendrickson”. Please visit this session (Location: Anaheim Convention Center, Room 213C) and our talk (at 10:40 am). It should be a great and rare event.

Dr. Rachelle Bienstock,  ACS CINF Chair, Program Committee wrote
( at http://www.acscinf.org/meetings/241/highlights241.php ):

Dr. Martin Walker has organized a very special symposium for this Spring Anaheim meeting in honor of his mentor, Dr. James Hendrickson, “Fifty Years of Computers in Organic Chemistry: A Symposium in Honor of James B. Hendrickson”. Dr. Hendrikson, Professor Emeritus of Chemistry, Brandeis University, was a pioneer in the field of computer-aided organic synthesis design and was one of the early visionaries in this field. The designer of the programs SYNGEN and WebReactions, much current work in the field is built on the early work of his research group. Many of the successful students who trained with Dr. Hendrickson over his long career, or those whose work was built on ideas and concepts originating from Dr. Hendrickson’s work, will be speaking in this symposium including Dr. Paul A. Wender, Bergstom Professor in Chemistry, Stanford University; Dr. Phil S. Baran, Professor, Scripps Research Institute; Dr. Valentina Eigner-Pitto, InfoChem GmbH and Dr. Orr Ravitz, SimBioSys Inc.

To see more on the SimBioSys’ upcoming ACS presentation in this session visit:
http://www.simbiosys.com/science/presentations/2011-03-acs/abstract1.htm)

We have just discovered some great eHiTS results in the e-mail notification from ACS publishing, titled: “Most Read Articles in January from the Journal of Chemical Information and Modeling”. In the list of papers that received the highest exposure in January is:

Virtual Decoy Sets for Molecular Docking Benchmarks
Izhar Wallach and Ryan Lilien
DOI:  http://c.acs.org/ceyra/321469/70/350639/6508/0/S/0/0/tvma.html

The paper demonstrates how the composition of a screening benchmark (the DUD set in this case), and particularly the physical properties of the decoy set affects the enrichment outcome. This is a valuable insight for us as software developers, and an important one for comp.chems at large. The paper presents the screening performance of eHiTS, as well as of Glide’s on the Dud targets, and although the paper is not attempting to compare the programs, they seem to be on a par with each other in retrieving active molecules in virtual screening.

Another publication with eHiTS, presenting a successful virtual screening workflow for Human IKK-2 Inhibitors was also brought to my attention in the last few days:
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
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0016903

Both of these were added to our list of user papers with SimBioSys tools:
http://www.simbiosys.com/science/presentations/2011-03-acs/index.html 
We are looking forward to your paper with eHiTS results, please let us know about it, as soon as published, so that your work is added to our ever growing list of user publications.

To learn more about eHiTS, please contacts us by e-mail or join our docking talk at the upcoming ACS 2011 Spring meeting, in Anaheim, California:

COMP: 59
(http://abstracts.acs.org/chem/241nm/program/view.php?obj_id=63915&terms=)
“Recent developments in the eHiTS ligand docking and scoring software”
Zsolt Zsoldos, Orr Ravitz,  SimBioSys Inc., Toronto, Ontario, Canada
Session: Docking and Scoring: A Review of Docking Programs
Time: Monday, Mar 28, 2011 10:20 AM
Location: Anaheim Convention Center, Room 213 B

see more details at:
http://www.simbiosys.com/science/presentations/2011-03-acs/index.html

By now most of you are back from the holidays and the off-work relaxation. Hopefully re-energized, ready to tackle new challenges and to pursue new opportunities. At least we feel so at SimBioSys. Hence we have just released the great new ARChem 2011!

This major release includes all the concepts covered by the recent beta version, plus more:

- Better chemistry: refinements in the treatment of halogens and carbonyl groups to present more accurate chemistry.

- New solution viewing concept: the user is in control of selecting the best solution(s). The display is a hybrid between step-by-step solution construction and full synthetic route presentation, and solutions browsing is dramatically faster and more accessible.

- User can add or edit the price of any starting material or intermediate, and modify the yield of any step in the solution tree.

- The PDF export utility has been revised, and full solutions, including starting materials details, can be presented in a concise document.

- Additional updates include:
* The Marvin editor inside ARChem, as a result we now support Mac and Windows 64-bit platforms.
* Starting material catalogues, including Acros and AlfaAesar’s latest 2010 listings, and the eMolecules catalogue.
* ChemInform reaction database with latest 2010 version, introducing 80,000 new reactions.

For more details, please see the “Version info” link under the Miscellaneous menu item in the new system.

All the existing user accounts have been migrated to the new address:
https://archemdemo.simbiosys.com/ARChem
Thus you can login using your old account, if you forgot your username and password, you can reset it using the “Forgot your username/password?” link,  and if you do not have an account, you can submit a request for one at: http://www.simbiosys.com/products/demo_request.html

Many of the new features and improvements are the result of feedback that we get from users. This is the best way for us as developers to navigate our work toward a product that genuinely addresses your needs. Please send us your comments, big or small, on any aspect of your experience with ARChem. We are looking forward to your suggestions (via the feedback or bug report link in the system, or simply directly to us via email) as to what you would like to see improved in ARChem in 2011.

We appreciate your business and support for SimBioSys, and we look forward to working with you this year again.

HAPPY NEW YEAR!
from all of us at SimBioSys, Inc.

CLiDE is a sophisticated chemical OCR application, that can extract molecular structures from images or PDF files, and can save them in several chemical file formats like: MOL, SDF and XML, or transfer them seamlessly to various chemical editors.  CLiDE is available in three packages: Standard, Professional or Batch. Each of them is serving a slightly different need at different prices.  CLiDE-Standard and CLiDE-Professional offer a contemporary graphical user interface, with all the recognition features embedded in a user-friendly document/image viewer,  for more info see: http://www.simbiosys.com/products/leaflets/CLiDE_folder.pdf

Release 4 contained major improvements to the product including:

• improved recognition accuracy
• improved input & output file format handling: introduced support for several new raster image file formats (GIF, JPEG, PBM, PGM, PNG, PNM, PPM, XBM, XPM); and introduced XML output file format that can be loaded for later editing
• introduced capability to extract chemical structures from tables
• saving molecules with super atoms in expanded or contracted form

Complete listing of changes is available upon request.

Feel free to contact me if you have any questions about this new CLiDE release, or sign up for a no-fee evaluation of CLiDE on our website: http://www.simbiosys.com/products/demo_request.html

posted by Aniko