SeeSAR fosters innovation during every step of your drug design process. The app includes all tools vital for handling your compounds and target structures which have been fine-tuned to the needs of any chemist.
Helpful features such as ADME properties assessment, comprehensive color coding, unoccupied binding pocket visualization, and many others, support you in making sound and interactive decisions.
All our tools are based on solid and transparent science cited in over a thousand publications. Follow the button if you want to learn more about the science behind SeeSAR.
— Dr. Stephen Flower, University of Bath, UK
This software was incredibly useful in the running of the coursework exercise in our final year units as SeeSAR was really easy to use for my students.
— Dr. Sharon Shechter, Silicon Therapeutics, USA
SeeSAR is easy to use, and allows scientists from different disciplines to explore new design ideas.
— Dr. Jessica Holien, RMIT Melbourne, Australia
Its super-duper fast! Much much faster than any pharmacophore screening I've ever done before!
— Dr. Agnieszka K. Bronowska, Newcastle University, UK
We are heavy SeeSAR users and our students, undergraduate and postgraduate alike, absolutely love it. Numbers of students interested in computational chemistry increased since we have introduced SeeSAR.
— Dr. Peter Sennhenn, transMedChem, Germany
SeeSAR is by far the best idea generator in Medicinal Chemistry.
— Dr. Sander Nabuurs, LeadPharma, The Netherlands
SeeSAR allowed us to understand a specific halogen substitution pattern crucial for robust activity in our functional assays.
— Robert R. Gotwals, the North Carolina School of Science and Mathematics, Durham, USA
The seamless integration between StarDrop and SeeSAR provides a state-of-the-art drug design and development platform to our very unique high school program.
— Dr. Hans Briem, BAYER
HYDE really gave this improvement!
Set yourself free! Have an interactive dialog with your software. SeeSAR supports you in finding solutions in the most inspiring way by thinking outside the box. You can feel your ideas progressing with swift calculations and stimulating input.
SeeSAR's radical simplicity provides a satisfying experience for drug design veterans and modelling beginners alike. Whether you are a seasoned drug designer, working on a side project, or just have pure curiosity — get started designing your own molecules today.
SeeSAR runs on all established platforms (Windows, Linux, macOS) and is easy to install. No need for expensive, energy-hungry server solutions or long-term maintenance. Just download, and get started!
Navigate your ligand optimization process by evaluating your results at first glance through informative color coding and comprehensive icons. Define the parameters according to your needs, or implement your own KNIME® workflow. Work the way you like.
SeeSAR offers almost instantaneous, precise results, without compromise. Swift calculations and beautiful visualization support you in finding actives with only a few mouse clicks. Each mode contains export functions to easily transfer results for your reports.
SeeSAR helps you to generate new intellectual property or get rid of issues in molecules. Supported by the ReCore tool implemented in our Inspirator mode, SeeSAR searches in pre-processed libraries, so-called “indices”, for fitting replacements in selected molecule areas. Our approach to fragment-based lead discovery (FBLD) delivers suggestions to core replacements, molecule growing, and fragment linking within seconds.
BioSolveIT offers the required index files for free.
The latest version of SeeSAR introduces many improvements for faster and even more elaborate results to support you in your drug discovery process. The search for binding pockets similar to the one of your target with the SeeSAR-implemented SIENA technology has been enhanced: Proposed structures are now displayed with their respective description for you to easily grasp the results at first sight. Additionally, optional coloring of individual structures allows easy site-to-site comparison. The discovered binding site of interest can also be exported and used as input for the HYDE command line tool. Furthermore, improvements deep down in the code let you scroll through ten thousands of ligands in a flash.
For older versions please visit here
60 seconds videos
Align binding sites of multiple proteins
Assess the binding affinity of your ligand
Determine a binding site
Dock your ligand
Do a virtual hit-triage
Find a new scaffold
Improve your ligand
Link two fragment binders
Introduction to SeeSAR 10
Find a “magic methyl”
SeeSAR - Beginner’s Guide (PDF)
HYDE binding assessment approximates and visualizes affinities. The system has NOT been trained to specific targets, instead implicit HYdrogen bond and DEhydration are intrinsically balanced without weighting parameters as seen in all force fields. The user instantly gets interpretative feedback for lead optimization and other design tasks.
HYDE is constantly improved and originated from a collaboration with BAYER, Hamburg University, and BioSolveIT.
Find out more about HYDE here
Replace a given core and generate new intellectual property. You can specify bonds or interactions to be matched by new fragments. The arrangement of the connected residues is taken to a fragment library that has been pre-processed for speed (“indexed”). Results are retrieved using a 4-dimensional vector and the quality of the fit is computed. Indices can be custom designed with in-house compound libraries.
ReCore emerged from a collaboration with Roche Basel and Hamburg University and has been extensively augmented and extended by BioSolveIT thereafter.
Find out more about ReCore here
Based on rigorous statistical analysis of small molecules in crystal structure databases, the “traffic-light” implementation for the torsion angles in molecules reflects the frequency of occurrence of a given dihedral. The underlying assumption is that frequent observations correlate with low energy structures and vice versa.
The Visual Torsions emerged from a collaboration with Roche Basel and Hamburg University.
Publications on visual torsions can be found here and here
Compute proposals for accessible empty pockets, and visualize the results in 3D for further selection. The functionality is based on a heuristic model that employs Gaussian differences on a 3D grid to assess the likelihood of dealing with a pocket shape or not. Global hydrogen bond functionalities and the lipophilic character - plus the solvent accessible surface (SAS) of the putative pocket are taken into account. The computation is further enriched with local measures such as distances between pairs of functional group atoms.
The pocket detection algorithms are part of the DoGSiteScorer that emerged from a collaboration with Merck and Hamburg University.
Publications on our DoGSiteScorer-based pocket detection can be found here and here.
Dock a ligand into a receptor cavity. This state-of-the-art algorithm splits ligands into so-called fragments which are placed into multiple places in the pocket – and scored using a simple, yet very fast pre-scoring scheme. From the n solutions placed, the ligand is further built up, fragment by fragment, and the interim solutions are scored against each other. The best scored survive the process, and those are delivered to the user. The “Single Interaction Scan” (SIS) placement also finds solutions when there are only very few polar groups in a compound.
Find out more about FlexX here
In publications please cite SeeSAR with the respective version number as follows:
SeeSAR version 10.3.0; BioSolveIT GmbH, Sankt Augustin, Germany, 2021, www.biosolveit.de/SeeSAR