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Pipeline Pilot® interfaces

Pipeline Pilot® is the famous graphical workflow programming software from BIOVIA. BioSolveIT and BIOVIA entered into a comprehensive partnership agreement with the aim of making the BioSolveIT software-tools accessible to all our users via Pipeline Pilot®. Note that these interfaces are available free of charge. However, you will need a separate Pipeline Pilot® license from BIOVIA as well as a license for the BioSolveIT-software which can be obtained here.


  • Pipeline Pilot® versions 9.2 and later have been tested and confirmed to work with the packages on this page.
  • only the most recent version of the respective software package is guaranteed to work with the Pipeline Pilot® modules

Supported operating systems: Windows and Linux


  • Ah, c'est trop facile, Senior Scientist, Sanofi-Aventis
  • The way you generate components for PP is very clever. We also use something similar in some of our software, and I have not seen it used by any other ISV. Our users love this feature, and I am sure yours will too!, Guillaume Paillard, Senior Consultant, SciTegic/Accelrys
  • Drag&Drop – that's it? – Wow! (speechless), Application Scientist, Servier
  • That is really very, very nice!, Research scientist, Nycomed
  • That's fantastic!, Dr. Chido P. Mpamhanga, University of Dundee, UK


See how it works in practice, watch our webinar recording:

unravel the powers of virtual screening in Pipeline Pilot®

additional downloads: demo material (zip)

BioSolveIT web-installer

For your comfort and convenience, we implemented a fully automatic web-based installer. Simply

download (tar.gz) download (zip)

one of the packages above and drag&drop all xml-files therein into the Pipeline Pilot® Components folder. Double-click on the 'BioSolveIT Web Installer'-component and edit the two red-colored parameters:

  • to provide a directory where the download may temporarily be stored (e.g. your desktop)
  • to provide the name of the BioSolveIT license server or license file

BioSolveIT tools in Pipeline Pilot®

docking (FlexX)

Performing docking calculations is a routine, yet quite delicate task in every structure-based drug discovery process. Rather than framing it as a black-box approach we have made it particularly target-specific. You can now set up your protein-target for docking guided by an interactive wizard in our new LeadIT-GUI. After having satisfied yourself with the performance of the docking you may export all settings including the protein in a so-called Project File (.fxx), which you provide as an input parameter to the module.

similarity searching (FTrees)

Similarity searching is a task that needs to be performed routinely and oftentimes in conjunction with other tools in a workflow. With the release of the Pipeline Pilot® components for FTrees, this is now child's play.

chemical space searching (FTrees-FS)

Feature Trees Fragment Spaces (FTrees-FS) is a unique technology which enables you to perform similarity searches in innumerably large chemical spaces. A public Fragment Space called KnowledgeSpace may be obtained here.

interactive 3D visualization (SeeSAR)

Our flagship tool for 3D structure based design is embedded in the SeeSAR viewer node. Besides superbe visualization it contains an outstanding 3D molecule editor and an efficient and effective way to predict binding affinities. HYDE is a novel ground-breaking technology for this task.

affinity scoring (HYDE)

The crux of virtual screening today is an efficient and effective way to estimate binding affinities. HYDE is a novel ground-breaking technology for this task. Simply provide a PDB and a ligand to define the binding site, then all input molecules are optimized and scored. On the output port you get the optimized molecule conformation and the lower bound of the estimated affinity range, which may then be used for sorting and filtering.

small molecule alignment (FlexS)

3D small molecule alignment is the method of choice when it comes to ligand-based design. This can be done routinely in a virtual screening setup using FlexS. In such a scenario the flexible fit may be used as the critical 3D shape filter or the preparation for SAR analysis.


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