Pipeline Pilot® interfaces

Pipeline Pilot® is the famous graphical workflow programming software from SciTegic/Accelrys. BioSolveIT and SciTegic 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 SciTegic as well as a license for the BioSolveIT-software which can be obtained here.


  • Pipeline Pilot® versions 7.5 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-klick 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

Finally check to see if the server specified under Server Installation List is indeed your Pipeline Pilot® server. Note that you need to have permissions to install software on the server. Now run the installer. It will download stuff to the designated location and install several executables. Finally it will provide an installation report listing the installed software and the results of several basic tests.

If the installation step was successful there is just one more thing to do. From the downloaded package, you need to drag&drop the folder called BioSolveIT/ into your Pipeline Pilot® Components folder. The XML-packages herein are the Pipeline Pilot® interfaces to our software. You may use these now to implement workflows.

Note, is anything goes wrong, please don't hesitate to contact us via our support page, we are happy to help. There is also a user guide with more detailed information in the download packages above.

individual Pipeline Pilot® packages

If you cannot use the web-installer and/or may be interested in individual components only, these are described in the following.


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.

To use the LeadIT-Docking in Pipeline Pilot®, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below.

similarity searching

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. The FTrees package contains multiple XML-files:

  • The Molecule to FTrees component appends a Feature Tree descriptor as a property to each molecule.
  • The FTrees Similarity component compares the molecules in the pipeline to query molecules, and appends the corresponding similarity values to the molecules as new properties.
  • The FTrees Reader and FTrees Writer components can be used to save molecules in the pipeline complete with their Feature Tree descriptor in a special format. By use of these components, a standard workflow can be interrupted at any point and for example previously generated FTrees for a set of molecules may be used for searching time and again.

To use FTrees in Pipeline Pilot, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below.

Fragment Space searching

Feature Trees Fragment Spaces (FTrees-FS) is a unique technology which enables you to perform similarity searches in innumerably large chemistry spaces. To use FTrees-FS in Pipeline Pilot, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below. A public Fragment Space called KnowledgeSpace may be obtained here.

affinity assessment

The crux of virtual screening today is an efficient and effective way to predict binding affinities. HYDE is a novel ground-breaking technology for this task.

To use HYDE in PipelinePilot®, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below.


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 subsequent tasks such as 3D QSAR or CoMFA.

To use FlexS in PipelinePilot®, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below.

super-fast 3D-shape-filter

A novel method combines the efficiency of the FTrees similarity searching with the accurate 3D-alignment of FlexS in a very effective 3D-Shape-Filter. Here the FTrees-Mappings are used as a starting point for the 3D-Optimization.

To use this technology in Pipeline Pilot®, either use the web-installer above or

download (tar.gz) download (zip)

and follow the instructions below.

After the download of the desired packages, unpack them. Then one after the other:

  • drag&drop the installer-components (there may be multiple per package) into Pipeline Pilot®
  • edit the red-colored parameters and run the installer
  • if this was successful you may remove the installer-component, as it contains the executable and is therefore quite memory-consuming

Finally drag&drop the remaining components into the components tab in Pipeline Pilot®. You may use these now to implement workflows. Certainly, please read the documentation within the packages for further details.


stay tuned with all the breaking news.


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