SeeSAR SeeSAR
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SeeSAR

The Liberating Drug Design Experience
fast

fast

Dock, design, and analyze your compound in a flash, with swift and informative calculations.
visual

visual

Evaluate ligand-target interactions by intuitive color codes and gorgeous visualization.
easy

easy

We provide a satisfying on-the-fly drug design experience. No learning curve!
What's inside?
protein mode to search and load your protein

Protein Mode

Drag and drop your protein, or search comfortably in an online database. Within seconds, your target is prepared and you can get started.
protein editor mode

Protein Editor Mode

Modify your protein according to your needs. Explore rotamers, introduce mutations, and customize side chains.
binding site mode for target pocket detection

Binding Site Mode

SeeSAR automatically detects the binding site of a ligand for you. In addition, you can precisely expand it by adding individual residues — or with a single click to find empty pockets in your protein.
molecule editor mode for on-the-fly modifications of your compounds

Molecule Editor Mode

Modify molecules to your taste in 2D or 3D on-the-fly. Once you are done, the molecules are directly prepared for your tasks.
analyzer mode for property assessment

Analyzer Mode

Estimate affinities and interpret the results using the visualized HYDE score. Filter your compounds for relevant parameters, calculate ADME properties, and gain full control over ligand-target interactions.
inspirator mode for interesting new structural proposals

Inspirator Mode

Ideate without limits! Discover new scaffolds, explore, and grow into free cavities, or link molecules using fragment libraries for elegant solutions.
docking mode for binding mode predictions

Docking Mode

Dock your compounds with one single click! Screen libraries for actives, and instinctively evaluate your results.

Universal toolkit

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.
Science

What others say

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. Stephen Flower, University of Bath, UK
SeeSAR is easy to use, and allows scientists from different disciplines to explore new design ideas.
—
Dr. Sharon Shechter, Silicon Therapeutics, USA
Its super-duper fast! Much much faster than any pharmacophore screening I've ever done before!
—
Dr. Jessica Holien, RMIT Melbourne, Australia
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. Agnieszka K. Bronowska, Newcastle University, UK
SeeSAR is by far the best idea generator in Medicinal Chemistry.
—
Dr. Peter Sennhenn, transMedChem, Germany
SeeSAR allowed us to understand a specific halogen substitution pattern crucial for robust activity in our functional assays.
—
Dr. Sander Nabuurs, LeadPharma, The Netherlands
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.
—
Robert R. Gotwals, the North Carolina School of Science and Mathematics, Durham, USA
HYDE really gave this improvement!
—
Dr. Hans Briem, BAYER
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Five reasons for SeeSAR

Fragment files

Google-like re-scaffolding

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 CSD SeeSAR index requires a license from CCDC.

Covalent Supplier Libraries

A covalent binding mode may have many advantages — including improved selectivity and prolonged pharmacological duration. With the recent introduction of covalent docking into SeeSAR, you now have everything at hand to explore and discover covalent binders at any suitable residue in your binding site.In a collaborative effort, we have translated several compound supplier libraries into a convenient, ready-to-dock SeeSAR format. Thus, over 30 warheads can be covalently docked at your target of interest and assessed for their binding mode.

Important note: Due to the current limitation of 50,000 entries in SeeSAR tables, we recommend a pre-filtering of the big libraries (e.g. with KNIME®). We offer a "Teaser Set" of 10k randomly selected compounds with warheads targeting CYS residues. Any library can be filtered by target residue, warhead, MW, and much more.
You can use this to test and playfully explore the covalent docking feature of SeeSAR together with the Covalent Docking Guide on your own.

For support in setting up your library or virtual screening please do not hesitate to contact us.

The libraries can be accessed here:
Updates

SeeSAR Version 11.1 — Hephaestus

SeeSAR Hephaestus received a powerful update to support users in their drug discovery efforts. The covalent complex assessment received a visual update where users can easily understand the quality of the binding mode in the well-known Hyde style. With this update covalent virtual screening feels even more sophisticated and ranking of compounds provides a feeling for the differences in scores of the compounds. Another innovation in the latest version is the expansion of the binding site explorer SIENA to arbitrary PDB files. Users can now freely explore and search for topologically similar binding site in in-house structures or external databases (e.g. homology models, AlphaFold) to discover suitable candidates for their projects. This and many other innovations including novel command line support are a must-have for SeeSAR lovers and of those who will become one.

For older versions please visit here

Help
Beginner's Guide First Aid Covalent Docking Guide

60 seconds videos


Tutorial videos

FAQ

Follow these steps to manually enter a license file:
  1. Click on the System settings icon in the top right corner.
  2. Click the key icon (License) to open the license management interface.
  3. Select the license file or drag&drop it in this window.
If the license key is valid, the license period will be updated in the info line.
Alternatively, you can place the license file into the directory of the software executable.
In case you want to add or update a server (floating) license file, please check the corresponding "server license" FAQ entry.
Our software is license key protected. A license can either be bound to a single node or to a dedicated license server.

A server license (als called "floating license") allows a flexible administration and usage as it is hosted by a server and distributed to compute clients on demand. Such a server may manage the license requests for hundreds or thousands of software clients.

How to set up the license server
  1. First, please download the BioSolveIT flexlm package from our download page. Select the suitable package corresponding to your operating system.
  2. Login to the computer, where you want to run the license server. Flexera Software strongly discourages running the license servers with elevated privileges. However, to install the license server as a system service, you might need elevated privileges during installation.
  3. Extract the package on the license server computer.
  4. Follow the installation notes in the chapter License Server Manager “lmadmin” in package file license /doc/fnp_LicAdmin.pdf
  5. Copy the BIOSOLVE vendor daemon from the package directory license/bin to the new lmadmin installation directory. On linux, make sure that BIOSOLVE has executable rights - if in doubt, just execute chmod +x BIOSOLVE.

Making the server license available to local software installations
When you have fed the server with the license file, you have different options to make the license available to local software installations.
No matter which option you choose, if your license needs to be renewed, you only have to feed the license server with the updated file. The local installations don’t need the license again.
  1. Installation directory
    • Just copy the license file into the directory of the software application, right beside the executable.
    • If you are using non-standard ports for the license server communication, you have to enter these ports into the license file.
  2. Environment variable
    • Set the environment variable BIOSOLVE_LICENSE_FILE to point to the server name prepended by "@", e.g. BIOSOLVE_LICENSE_FILE=@my_server
    • If you are using non-standard ports, you have to specify the port number in front of "@", e.g. BIOSOLVE_LICENSE_FILE=12345@my_server
To find out why your license is not working, we need your help:
Please send us the systemlog (open the System settings in the top right, then choose Systemlog). Also, screenshots may be helpful, and errors/warnings in the exact wording.

The most frequent issues are:
  • cannot connect to license server - check:
    • firewall and DNS configuration, any blocked ports?
  • the key cannot be found - check:
    • key expiration (open the System settings in the top right, then choose License)
    • is the “.lic” file extension still there or has the mailer modified the file?
    • old license keys have to be removed
      • go to the software directory and delete outdated or invalid licenses files
      • if you are unsure about the software directory, look into the Systemlog (open the System settings in the top right and choose “Systemlog”, then scroll all the way down)
Our software is license key protected. To generate your license, we need the Host-ID of the machine on which the software shall run.
In case of a server license, we need the Host-ID of the server machine.

There are several options to determine the Host-ID:

License menu
  1. Open the System setting in the top right and select "License"
  2. Click on "Request license"
  3. Choose "individual assistance" in the now open website and submit your machine ID.

Systemlog
  1. Open the System settings in the top right and choose “Systemlog”
  2. You find the Host-IDs when you scroll all the way down, and search for the line "Host-ID" a few lines above.
  3. You can either send us the complete Systemlog (copy and paste it into an email) or reduce the copied content to the HostID(s)

System terminal/Commandline
  1. Open a system terminal/commandline (Windows: cmd, Mac: Terminal)
  2. Change to the directory of the software executable
  3. Call the app with --license-info, e.g. "seesar --license-info" or “infinisee --license-info”
  4. Send us the complete output of this call
Any usage with a graphical user interface requires a local installation and a local graphics card. This can therefore not work from remote.
Commandline and KNIME runs however can be triggered from remote.
Please contact us if you need to work from home during the Corona pandemic.
  1. RAM: 8GB would be good, anything beyond is better.
  2. CPU: Our tools are not very hungry — yet they profit from multiple CPUs, because they have parallelized algorithms implemented. If in doubt rather choose more slower CPUs than one faster one.
  3. Graphics: It is important to know that a local graphics card is mandatory for infiniSee and SeeSAR.

Update to the latest driver, and check — even if Windows tells you that you are up-to-date. Lenovo and other computers with onboard graphics, please navigate to this link to check if there is a newer driver available for you.

Couldn’t find what you are looking for?
Visit our elaborative FAQ section or the first aid section

FAQ First Aid
Science

HYDE - Interactive, desolvation-aware visual ΔG estimates

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

ReCore - 3D scaffold hopping

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

Visual torsions - Statistical assessment of likelihood of dihedrals

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

Pocket detection - Druggable binding sites from 3D structures

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.

FlexX docking - Fast, flexible placement of ligands into cavities

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

Recent success stories

Targeting a prion folding intermediate, Biasini et al. performed a virtual screening campaign with the goal to discover modulators for the predicted folding pathway. Four compounds were discovered and confirmed in vitro as hits thus paving the way for a complete new mechanism of action.
Pharmacological Inactivation of the Prion Protein by Targeting a Folding Intermediate.
Spagnolli, G.; Massignan, T.; Astol, A.; Biggi, S.; Rigoli, M.; Brunelli, P.; Libergoli, M.; Ianeselli, A.; Orioli, S.; Boldrini, A.; Terruzzi, L.; Bonaldo, V.; Maietta, G.; Lorenzo, N. L.; Fernandez, L. C.; Codeseira, Y. B.; Tosatto, L.; Linsenmeier, L.; Vignoli, B.; Petris, G.; Gasparotto, D.; Pennuto, M.; Guella, G.; Canossa, M.; Altmeppen, H. C.; Lolli, G.; Biressi, S.; Pastor, M. M.; Requena, J. R.; Mancini, I.; Barreca, M. L.; Faccioli, P.; Biasini, E.
Nat. Comm. Biol. 2021, 4 (62), 1–16.
Cocklin et al. describe their computational workflow to design novel HIV-1 capsid inhibitors with improved metabolic stability. In only three analog steps they were able to increase the half time 200-fold in comparison to the starting compound.
Rapid Optimization of the Metabolic Stability of a Human Immuno Deficiency Virus Type ‑ 1 Capsid Inhibitor Using a Multistep Computational Workflow.
Meuser, M. E.; Adi, P.; Reddy, N.; Dick, A.; Maurancy, J. M.; Salvino, J. M.; Cocklin, S.
J. Med. Chem. 2021, 64 (7), 3747–376.
In this publication Günther et al. report on the design of novel dual BET-BRD7/9 bromodomain inhibitors containing a 4-acyl pyrrol moiety. Molecular docking studies with SeeSAR were performed to predict the binding mode of the nanomolar compound 11 and elucidate the beneficial effect of an oxygen atom in the terminal group.
4 ‑ Acyl Pyrroles as Dual BET-BRD7 / 9 Bromodomain Inhibitors Address BETi Insensitive Human Cancer Cell Lines.
Hu, M.; Regenass, P.; Warstat, R.; Hau, M.; Schmidtkunz, K.; Lucas, X.; Wohlwend, D.; Einsle, O.; Jung, M.; Breit, B.; Günther, S.
J. Med. Chem. 2020, 63 (24), 15603–15620.

Download SeeSAR 11.1.0 for your operating system:

Windows 64bit Apple macOS Linux x86 64bit

Get your license:

Evaluate Request quote Contact

Covalent libraries:

Asinex™
50k molecules
ChemDiv™
41k molecules
Chemspace™
200k molecules
Enamine™
81k molecules
LifeChemicals™
18k molecules
Reaxense™
12k molecules

How to cite

In publications please cite SeeSAR with the respective version number as follows:
SeeSAR version 11.1.0; BioSolveIT GmbH, Sankt Augustin, Germany, 2021, www.biosolveit.de/SeeSAR