BioSolveIT News all news concerning BioSolveIT Mon, 21 Nov 2016 18:47:30 +0000 en BioSolveIT News hourly 1 Deadline for Winter Challenge 2016: Nov 24! Mon, 21 Nov 2016 18:47:30 +0000 If you are an academic or independent researcher you may submit your proposal for our Winter Challenge 2016 until Thursday, November 24. Each submission gets the chance to win a EUR 1,000 travel grant to a high profile conference.

More information, terms and conditions and how to submit your proposal can be found here:

FTrees 3. Now parallelized, much improved, and on the Mac. Fri, 16 Sep 2016 14:23:52 +0000 Continue reading FTrees 3. Now parallelized, much improved, and on the Mac.]]> FTrees Fuzzy Similarities are now available in an almost entirely re-written version that runs better and much faster. It uses all your CPUs, has an improved chemistry model behind, for example realizing different tautomers as multiple faces of the same molecule. Also you can use it in a single line with an infinitely large number of molecules in your input file. Oh, and it creates beautiful graphics of your matches, so that we can all understand WHY two molecules are seen similar or not — and the best of it all: It runs on a Mac.
Get it!]]>
New SeeSAR is out (v5.2), feat. new surfaces, magic rescaffolding and more. Fri, 22 Jul 2016 12:39:21 +0000 Continue reading New SeeSAR is out (v5.2), feat. new surfaces, magic rescaffolding and more.]]> What is SeeSAR? It is every chemist's 3D SAR & ADME dashboard and design tool

Besides a ΔG estimation, torsional analyses, a wealth of Optibrium®-powered ADME estimations, it lets you design and assess your ideas on-the-fly.

The new version will delight you with an unseen rescaffolding engine inspired by our blockbuster tool ReCore, you can enjoy new, colored surfaces, get your binding site visualization crystal clear using intelligent residue selections and a few more goodies.

The full list of novelties is described here.

Download your copy from our download page.

new SeeSAR v5.1 hops scaffolds: the first ReCore functions are online! Mon, 04 Jul 2016 16:31:13 +0000 Continue reading new SeeSAR v5.1 hops scaffolds: the first ReCore functions are online!]]>
  • ReCore Instant Rescaffolding — early integration
    Many of you will already know our award winning software ReCore. This release includes a sneak preview of the upcoming ReCore integration into SeeSAR. As this is only a preview release, you will need to carry out a few steps of preparation to discover its benefits: Ludicrously fast proposals from gigantic fragment libraries.
  • Now it is simple to rename your molecules
    Double-click on the molecule to type in a new name — this is particularly useful for putting names to results of your molecule editing.
  • Access your files and download history more easily with the centralized loader
  • Molecule annotation now only one click away
    The molecule annotation is now directly accessible with one click on the triangle mark to the left of the table rows. Mouse-over shows you your annotations while a click opens a small editor to edit them.
  • More about SeeeSAR:

    Download your copy here:

    SeeSAR 5 is out, includes visual editing of covalent ligands Wed, 01 Jun 2016 08:06:40 +0000 As of this night, SeeSAR v5 is out for your 2016 style Lead Optimization!

    A selection of improvements and novelties:

    • 10 times speed-up in browsing ligands.
    • Visual editing of covalent binders
    • Project recovery feature to support older project files.

    Download your package here. Includes a free 7 days license!

    webinar: Bruton’s Tyrosine Kinase – the story of two inhibitors Tue, 31 May 2016 17:00:33 +0000 Continue reading webinar: Bruton’s Tyrosine Kinase – the story of two inhibitors]]> Our June webinar will be touching on two recently published stories on Btk: one by Takeda and one by Genentech. Both came up with different strategies to develop a lower molecule weight inhibitor than ibrutinib. We will showcase both strategies in SeeSAR and show how SeeSAR can be used to come up with the right compound.

    The registration for the webinar is now open!

    BioSolveIT wins Evotec to search the molecular universe for better drug candidates Tue, 17 May 2016 15:00:36 +0000 St. Augustin, Germany, May 17th 2016 – Today, we announce a strategic partnership with Evotec AG ("Evotec") to create an immeasurably large molecular search space. The database, so-called 'EVOspace' will act as a gigantic "pool" of virtual molecules from which to mine novel, synthetically accessible molecular entities for drug research.

    Read the full press release here.

    a new version of LeadIT (2.1.9), our comprehensive SBLD and FBLD suite, is out. Thu, 12 May 2016 09:27:36 +0000 We included minor fixes and an adaptation to a new PDB/RSCB download location. LeadIT includes state-of-the-art tools for docking & scoring, fragment-based design, and visualization de luxe.

    Download from

    new SeeSAR 4.2 for SAR and Lead Optimization is out Fri, 18 Mar 2016 13:21:49 +0000 Continue reading new SeeSAR 4.2 for SAR and Lead Optimization is out]]> Download here.

    The new release sports:

    • The next step in ‪‎covalent‬ binder handling:
      Ligands are no longer static but are now optimized within the HYDE Visual Affinities framework.
    • Process many protein-ligand ‪‎PDB‬ files automatically:
      The ligands are carved out and assessed with HYDE.
    • We augmented platform support with a MS Windows™ 64bit version.
    • Control when HYDE Affinities are computed. Especially helpful if you have many ligands.
    • Plus enhanced filtering, a ‪Windows‬ command line, and more space for loading in SD properties.
    Zealand & BioSolveIT create new therapeutic peptide drug design and development tool Fri, 18 Mar 2016 11:31:59 +0000 Continue reading Zealand & BioSolveIT create new therapeutic peptide drug design and development tool]]> March 14, 2016 - Zealand and BioSolveIT create unique software tool, adding new dimensions to peptide drug design and development.

    • Combining Zealand’s expertise in peptide design and its extensive knowledge database with BiosolveIT’s chemical informatics software capabilities
    • The tool, which is named PepSee, will help Zealand accelerate peptide design with the potential to support innovation and push the boundaries of peptide research
    • The collaboration is in line with Zealand’s strategy to enhance its leading position in the field of peptide-based medicines

    The full press release is here.

    BioSolveIT announces the 3 winners of the Winter Challenge’s phase 1 Mon, 14 Mar 2016 19:00:44 +0000 Continue reading BioSolveIT announces the 3 winners of the Winter Challenge’s phase 1]]>
  • Maria Letizia Barecca: Identification of pharmacological chaperones for cellular prion protein
  • Graeme Rogers: Is there an allosteric site in TCTS?
  • Andrea Astolfi: Structure-Based optimization of a new chemical scaffold acting as p38α MAPK inhibitor
  • In the next 9 months these 3 will battle over the final title and a travel grant of €1,000 to a high impact conference. We will report on the challenge site ( about each of their topics in more details. Watch this space!]]>
    SeeSAR’s 3D comes to Optibrium’s StarDrop Fri, 11 Mar 2016 10:47:30 +0000 Continue reading SeeSAR’s 3D comes to Optibrium’s StarDrop]]> Optibrium announces next version with SeeSAR integration.

    The next step in the outstanding collaboration between Optibrium and BioSolveIT is announced:

    A new, seamless link between 2D and 3D structure-activity relationships guides more efficient
    compound optimisation in StarDrop. The high speed and appealing 3D visualization plus analysis functions from SeeSAR, every chemist's SAR assistant, are now integrated in Optibrium's powerful ADME suite.

    Read the full press release, and stay with us for more outcomes of our joint efforts.

    „Journée de Modélisation pour tous“ in Toulouse, France (in French) Mon, 29 Feb 2016 17:10:58 +0000 Continue reading „Journée de Modélisation pour tous“ in Toulouse, France (in French)]]> BioSolveIT vous invite à une journée "Modélisation pour tous chimistes" à Toulouse en Avril/Mai 

    Ce workshop s'adresse à tous ceux qui cherchent des nouvelles molécules thérapeutiques.

    Avec le logiciel SeeSAR (site web SeeSAR), qui représente une interface graphique dédiée à l’optimisation visuelle de l’interaction ligand-récepteur, on apprendra les notions de base de la modélisation "structure-based": docking et scoring, analyse conformationelle etc.

    SeeSAR, conçu pour être facile à utiliser, permet le calcul de propriétés physico-chimiques, d’affinité, et facilite les modifications de la molécule afin d’utiliser au mieux l’espace disponible au sein du site de liaison. Vous trouverez plus de détails sur le site dont l'adresse est mentionné ci-dessus.

    La rencontre aura lieu sur Toulouse pendant une journée: une matinée d'introduction et présentation, suivie (optionnellement, pour ceux qui souhaitent y participer) par un entrainement pratique, avec la distribution de licences gratuites personnelles de 6 mois - exclusivement pour les adhérents SCT (Société de Chimie Thérapeutique).

    Si vous êtes intéressé(e)s, veuillez marquer vos préférences concernant les dates (et la participation dans l’entrainement) dans le questionnaire Foodle à l’adresse suivante:

    Je participe! (questionnaire Foodle)

    Pour pouvoir joindre le maximum des personnes potentiellement intéressées par l’utilisation de visualisation et modélisation, on vous demande d’avoir la gentillesse de transmettre ce message à vos collègues chimistes médicinaux et modélisateurs.

    BioSolveIT & Optibrium invite you to a free 1-day symposium Fri, 19 Feb 2016 13:32:26 +0000 Continue reading BioSolveIT & Optibrium invite you to a free 1-day symposium]]>

    Streamlining Drug Discovery and Development
    11th April, 2016
    Takeda, Boston, MA, USA

    The symposium targets medicinal chemists and modelers; we have invited high pitch speakers, and the focus will lie on leveraging data effectively, and visual modelling support for compound design. We are grateful to Takeda, Boston for hosting this event.
    More details, including registration, program, and speakers are available here.

    BioSolveIT and Optibrium release first SeeSAR with ADME prediction Integrated Tue, 24 Nov 2015 15:00:03 +0000 Continue reading BioSolveIT and Optibrium release first SeeSAR with ADME prediction Integrated]]> BioSolveIT and Optibrium are proud to announce the first SeeSAR version which comes with integrated 2D and 3D prediction. The rigorously validated ADME predictions from Optibrium are now easily visible in SeeSAR's molecule table. We are happy to deliver value to our customers so quickly after the collaboration agreement has been signed.

    Read the full press release here.

    Get your evaluation copy here.

    BioSolveIT launches prestigious „Scientific Challenge“ award Wed, 21 Oct 2015 20:50:52 +0000 BioSolveIT invites academic teams, non-profit organizations, and individuals to participate in an exciting Scientific Challenge:

    If you are working on a drug discovery problem, exploit the vast breadth of BioSolveIT's software tools to meet your goals quicker and better.

    More background can be found on a dedicated website:

    BioSolveIT and Optibrium™ sign collaboration agreement Tue, 13 Oct 2015 08:05:29 +0000 Breaking News: BioSolveIT and Optibrium signed a collaboration agreement. The partnership will deliver a link between 2D and 3D design on medicinal chemists' desktops.

    The synergies between ADME/Tox experts Optibrium and BioSolveIT will be of huge benefit for researchers in Medicinal Chemistry!

    Read the full joint press release here.

    multinational team publication: SeeSAR results coincide with experiment and MD simulations. Fri, 18 Sep 2015 13:34:10 +0000 Continue reading multinational team publication: SeeSAR results coincide with experiment and MD simulations.]]> Researchers from Sweden, Germany, Spain, the UK, and the USA report on SeeSAR applied in their hunt to understand trans-infections around HIV-I.

    They reveal that SeeSAR results not only relate to their experimental findings but also correlate with much more elaborate MD simulations – indicating the use of SeeSAR being a drastic time saver.

    Read about their findings in the article in the Journal of Biological Chemistry (in the press, free pdf!)

    new BioSolveIT-KNIME packages available! Mon, 14 Sep 2015 19:07:57 +0000 Continue reading new BioSolveIT-KNIME packages available!]]> We just published another update of our KNIME nodes. As usual you may simply use the update-mechanism in KNIME if you have registered our URL, otherwise:
    Help => Install New Software... => Add
    then select this location and follow the instructions.

    Here is what has changed since the last update:

    • Remarkable speedup with Generate 3D Coordinates
    • Speedup with FTrees Similarity (particularly with large files)
    • Includes the latest version of SeeSAR (v3.3 covering covalent binders and Water-improvements)
    • New docking nodes. You may continue to use the old ones (now deprecated) in existing workflows
    • Simplified configure dialog
    • Fix: Empty result table, now has the same format
    • Fixed error table
    • LeadIT: Fixed selection of the correct executable.
    • Fixed Naomi remote call.
    • Fixed extracting binding site in FxxReader.
    • Fixed reading preferences on parallel execution of nodes of the same type.
    Bayer uses FlexX-Pharm as a clever pose filter in cytochrome pockets. Tue, 07 Jul 2015 14:00:30 +0000 Here is a very nice paper from Bayer CropScience utilizing this approach:

    Pesticide Biochemistry and Physiology, Vol. 121, 2015, 31–38

    You can download FlexX-Pharm as integrated into our LeadIT suite here.


    JCIM appoints BioSolveIT co-founder Professor Rarey as new Associate Editor BSI00082 05 May 2014 11:24:00 +0200 End-of-year special and webinar series announcement BSI00081 12 Nov 2013 16:49:00 +0100 LeadIT SBDD: download your updated version (v2.1.5) here BSI00080 28 Oct 2013 16:55:00 +0100 FREE Mona - a handy tool when you work with sets of small molecules BSI00078 09 Sep 2013 14:17:00 +0200 TorsionAnalyzer now also generates high-quality conformation ensembles BSI00077 12 Aug 2013 13:37:00 +0200 BioSolveIT officially launches its new Services division BSI00076 01 Aug 2013 10:00:00 +0200 Novel paper on intuitive substructure definition using SMARTSeditor BSI00075 23 Jul 2013 16:16:00 +0200 TorsionAnalyzer paper made top 10 most read articles. Free download available. BSI00074 06 Jun 2013 10:38:00 +0200 New ReCore Fragment Index from the CSD available for download BSI00073 01 May 2013 17:03:00 +0200 Novel publication: Hyde best untrained scoring function with 0.62 correlation on PDBbind BSI00072 07 Jan 2013 16:25:00 +0100 Another success story usinf FTrees on BI-CLAIM BSI00071a 12 Dec 2012 09:43:00 +0100 Hot off the press: A new whitepaper! Visually Informed Lead Optimization. BSI00071 14 Aug 2012 12:03:00 +0200 With new Pipeline Pilot packages, installation and updates become dead easy. HYDE is included now! BSI00070 14 Jun 2012 18:39:00 +0200 New ReCore Fragment Index from the CSD available for CSD 2012 Customers: BSI00069 5 Apr 2012 23:04:00 +0200 Hyde performs to 96% accuracy in ACS 2011 docking contest: Read the reviewed JCAMD paper. BSI00068 2 Feb 2012 22:44:00 +0100 ACS Emerging Technologies Award Goes to Our Partners in Hamburg for Visualizing SMARTS BSI00067 29 Sep 2011 17:29:00 +0200 Newsletter issue 20: Revolution in binding affinity assessment, KNIME-nodes, 96% redocking success BSI00066 19 May 2011 18:07:00 +0200 KNIME-Node Update: improved installation, now supporting KNIME 2.3 BSI00065 18 May 2011 19:28:00 +0200 LeadOpt Revolutionized: Hyde Affinity Assessment now in LeadIT 2. BSI00064 25 Mar 2011 19:13:00 +0100 BioSolveIT-founder Thomas Lengauer receives AIDS research award BSI00063 24 Feb 2011 12:04:00 +0100 BioSolveIT becomes KNIME(R)-partner. Meet us March 3rd at the KNIME(R)-UGM in Zurich! BSI00062 11 Feb 2011 20:26:00 +0100 RCSB PDB incorporates PoseView! P-L-complexes in 2D available on Structure Summary page. BSI00061 8 Dec 2010 14:08:00 +0100 Greatly improved usability with LeadIT 1.3, Drag&Drop, ReCore&Dock BSI00060 11 Oct 2010 13:03:00 +0200 SMARTSview from our academic partner chosen as cover story of J.Chem.Inf.Model BSI00059 28 Sep 2010 13:06:00 +0200 Draw and understand fuzzy similarities! Download the new FTrees Release 2.3.0! BSI00058 23 Sep 2010 17:23:00 +0200 An update of our Fragment Space Generator CoLibri is out BSI00057 23 Sep 2010 17:13:00 +0200 Get the next release of our fast and highly versatile 3D ligand alignment FlexS. BSI00056 23 Sep 2010 17:03:00 +0200 Article on all PDB Protein-Ligand Complexes Drawn automatically BSI00055 13 Sep 2010 16:03:00 +0200 SMARTS revisited. See how our partner ZBH visualizes them in a revolutionary new way. BSI00054 8 Sep 2010 16:50:00 +0200 FlexX docking helps in finding first low-molecular-weight inhibitors of Matriptase-2 BSI00053 19 Jul 2010 17:42:00 +0200 LeadIT 1.2 released: 2D-plots of Protein-Ligand complexes included! BSI00052 2 Jul 2010 15:11:00 +0200 LeadIT 1.1.1 is out! Screen capture individual 3D views of solutions, write notes and scientists easily share! BSI00051 7 Jun 2010 11:33:00 +0200 The release of LeadIT 1.1 with numerous useful ReCore-features is out BSI00050 3 May 2010 17:12:00 +0200 Software updates: FTrees 2.2.0 and CoLibri 1.3.0 released BSI00049 30 Apr 2010 15:55:00 +0200 Focused library design paper of our academic partner ZBH in JCIM top-10 BSI00048 28 Apr 2010 17:48:00 +0200 KNIME: Updated BioSolveIT nodes available for download BSI00047 19 Apr 2010 21:26:00 +0200 BioSolveIT and CCDC release World Class Fragments for Top Quality Drug Design BSI00046 24 Mar 2010 23:14:00 +0100 Registration open for Pre-Conf Workshop @ FBLD2010 in Philadelphia BSI00045 22 Mar 2010 20:15:00 +0100 A new LeadIT (v1.0.2) waits for you to be downloaded BSI00044 10 Mar 2010 18:54:00 +0100 Major update of free PipelinePilot components available BSI00043 28 Jan 2010 11:15:34 +0100 Major update of free KNIME components available BSI00042 28 Jan 2010 11:15:28 +0100 The world class CSD data now available for download and utilization with LeadIT BSI00041 27 Jan 2010 18:21:03 +0100 Release of LeadIT 1.0 - an integration platform for docking and rescaffolding BSI00040 12 Jan 2010 10:17:42 +0100 Software updates: FTrees 2.1.2 and CoLibri 1.2.0 released BSI00039 1 Dec 2009 20:29:37 +0100 BioSolveIT hosts FREE Scaffold Hopping workshop at 239th ACS Meeting in San Francisco BSI00038 5 Nov 2009 11:56:11 +0100 Free KNIME-components to BioSolveIT solutions BSI00037 17 Sep 2009 03:05:59 +0200 Whitepaper 'Exploiting MedChem in Virtual Screening': 2nd edition issued BSI00036 2 Sep 2009 19:24:43 +0200 Free interactive workshop announced for September 23rd 2009 BSI00035 18 Aug 2009 16:10:05 +0200 Newsletter Issue 17 released (KnowledgeSpace, KNIME modules, FlexNovo, CloudScientific, ...) BSI00034 14 Aug 2009 01:18:22 +0200 New FTrees 2.1 reads SMILES and SD Fragment Spaces! BSI00033 20 Jul 2009 13:53:46 +0200 Easier ligand energetics analysis with 'MATCHING' command in FlexX 3.1.4 BSI00032 2 Jul 2009 18:39:10 +0200 ReCore 1.8.15 - quick, easy installation, get some click and go scaffold replacement BSI00031 30 Jun 2009 12:27:39 +0200 Fragment growing with FlexNovo 1.6.0, grab a copy! BSI00030 5 Jun 2009 17:20:56 +0200 CloudScientific appointed distribution partner in China BSI00029 8 Mar 2009 13:40:28 +0200 "Fragments" Newsletter on Big Pharma prospective successes, ReCore, and more BSI00028 17 Mar 2009 17:53:13 +0100 Free KnowledgeSpace 1.0 with 20 billion compounds released BSI00027 10 Feb 2009 17:58:51 +0100 FlexX 3.1.3 is out. Download here. BSI00026 5 Feb 2009 10:32:26 +0100 Boehringer Paper Lays CLAIM to Fragment Based Screening Success with Publication BSI00025 2 Feb 2009 18:03:46 +0100 FTreesXL minor update completed BSI00024 12 Jan 2009 14:37:03 +0100 A new version of ReCore is ready to download BSI00023 9 Jan 2009 17:05:58 +0100 FlexX Amongst Top 100 Most-Cited Articles in Fifty Years of J.Mol.Biol. Existence! BSI00022 5 Jan 2009 14:23:24 +0100 FlexS: A New minor Release - also available on Windows BSI00021 25 Nov 2008 20:18:20 +0100 Free interactive workshop announced for May 8th 2009 BSI00020 21 Oct 2008 18:13:11 +0200 FlexX 3.1.0 with sophisticated metal and water handling is now available BSI00019 15 Oct 2008 16:50:41 +0200 New Pipeline Pilot modules released (FTrees, FlexX, FlexS, and Fragment Spaces) BSI00018 1 Oct 2008 13:37:42 +0200 Inforsense China appointed distribution partner BSI00017 26 Sep 2008 16:49:03 +0200 BioSolveI PipelinePilot(R) tools featured in SciTegic Newsletter BSI00016 23 Sep 2008 16:51:54 +0200 Large Scale Virtual Screening GUI: FTreesXL 1.1.0 released BSI00015 22 Sep 2008 13:52:16 +0200 Recore 1.8.10 including fragment space released BSI00014 14 Aug 2008 12:28:37 +0200 Newsletter Issue 15 released (FTrees 2.0, ACS 2008, partnering with Dundee, workshops, and more...) BSI00013 7 Aug 2008 17:35:57 +0200 White-paper released: Exploiting Med-Chem in Virtual Screening BSI00012 28 Jul 2008 15:29:58 +0200 Obtain trial licenses instantaneously with new simplified access BSI00011 1 Jul 2008 19:11:38 +0200 Apsara Innovations Ltd. appointed distribution partner in India BSI00010 1 Jun 2008 12:45:23 +0200 Major Release 2.0 of FTrees now available BSI00009 5 May 2008 09:21:03 +0200 FlexX Release 3.0 with integrated GUI is out BSI00008 28 Apr 2008 10:37:53 +0200 Complimentary Workshop on Virtual Screening and De Novo Design on June 5th BSI00007 24 Apr 2008 12:53:46 +0200 Newsletter Issue 14 released (How Pfizer uses BioSolveIT software, FlexX 3.0, free workshop, and more...) BSI00006 22 Apr 2008 16:15:17 +0200 Federal Funding for Fragment-Screening Project of BioSolveIT BSI00005 14 Apr 2008 16:38:26 +0100 Bio-IT Reviews Highlights BioSolveIT's De Novo Tools BSI00004 Mon, 25 Feb 2008 11:14:56 +0100 Bayer-Schering Pharma AG successfully used FlexS for design of peptidomimetics BSI00003 Tue, 19 Feb 2008 15:45:14 +0100 Virtually screen within a few mouse clicks using the new beta FTreesXL GUI BSI00002 Thu, 6 Dec 2007 18:10:49 +0100 Newsletter Issue 13 released - 'Recore', 'FTreesXL', 'Interfaces', 'ACS epilogue', and more.... BSI00001 Mon, 19 Nov 2007 14:35:10 +0100