SeeSAR 14 “Atlas”: The Horizon of Chemical Space Exploration

Chemical Space Docking™:
The Horizon of Structure-Based Docking of Ultra-Vast Compound Collections

SeeSAR 14 takes another leap towards uncharted territory with Chemical Space Docking™ (C-S-D)—The next generation of structure-based virtual screening that enables the efficient handling of trillion-sized Chemical Spaces.
With the introduction of SeeSAR's novel Space Docking Mode, we present a sophisticated and visual environment to start the C-S-D workflow conveniently in your beloved drug design dashboard.

Highlights in SeeSAR 'Atlas'

Chemical Space Docking™

C-S-D is the next generation of structure-based virtual screening.
Using a smart twist, it enables you to screen trillion-sized Chemical Spaces for the most promising drug candidates.

Improved Template Molecule Handling

Template molecules can now be directly loaded into the respective modes of SeeSAR with a dedicated place for easy customization.

Native Handling of mmCIF Formats

SeeSAR now fully supports the import and export of the future-oriented mmCIF format of macrostructures.

Highlights in SeeSAR 'Atlas'

Chemical Spaces:
A Field Trip for Drug Hunters

The aim of C-S-D is to enable the screening of incredibly large, combinatorial Chemical Spaces. The billion- and trillion-sized molecule superclusters are the largest on-demand catalogs for drug-like compounds, offering an overwhelming diversity of scaffolds and chemotypes.

WIth the release of SeeSAR 'Atlas', several Partners' Chemical Spaces are available. Search them conveniently for the compounds most relevant to you:
  • AMBrosia by Ambinter
  • CHEMriya by OTAVA
  • eXplore by eMolecules
  • Freedom Space
  • GalaXi by WuXi
  • REAL Space by Enamine
  • And BioSolveIT's ideation generator: Knowledge Space

Screen Smarter, Not Harder

The idea behind C-S-D is to identify the most promising molecules within Chemical Spaces by focusing on the likely best starting points and subsequently grow them into complete compounds. By doing so, C-S-D still covers the entire Chemical Space: A priori, any entry can emerge as a result, yet only a fraction of the associated computational resources are required.
The full concept is explained in our Chemical Space Docking™ Spotlight.

Being the fast, visual, and easy software platform that SeeSAR is, the full workflow of anchoring of the smallest fragments (the so-called 'synthons') up to the extension into drug candidates is integrated into SeeSAR in a sophisticated manner. In each step, you have full control from an instantaneous analysis through the understanding of generated poses up to selection of the best ones to follow up with.

Improved Handling of Template Molecules

Of course, innovation keeps rolling further: In addition to C-S-D, we have added several other improvements to your drug design dashboard. This includes the ability to use a molecule as a template in another mode via a mere right-click.

Now, interesting molecules can be directly loaded into the Docking Mode (local, external, and Space Docking) and the Similarity Scanner.
The active molecule is then displayed in a dedicated 'Template Molecule' table, accessible to customization of visibility and color.

Native Support for mmCIF Formats

Furthermore, SeeSAR 14 now fully supports the mmCIF (Macromolecular Crystallographic Information File) format.
This update ensures seamless handling of large and complex biomolecular structures, both during loading of structures and for their export, addressing the limitations of the traditional *.pdb format. As the scientific community moves towards mmCIF as the future standard for structural data, SeeSAR is fully prepared to meet this demand.

By supporting mmCIF natively, we enable richer metadata integration, improved accuracy, and greater flexibility, ensuring that your workflows remain at the cutting edge of macromolecular research.

SeeSAR 'Atlas' — Supporting you in Lifting the Weight of the Molecular Macrocosm

This concludes our spotlight on the latest enhancements in SeeSAR 14 'Atlas'. With this update, we are bringing trillion-sized Chemical Spaces into an environment designed for efficient processing without compromise. We hope you are as excited as we are to explore ultra-vast Chemical Spaces and experience the next generation of 3D virtual screening with the revolutionary Space Docking Mode.
Dive in and discover a whole new dimension of possibilities!

Get started with the C-S-D Starter Package!

Download SeeSAR 14

Begin by downloading the latest version of SeeSAR 14 Atlas and installing it. Download here!

Download HPSee 2.0

Download and install the latest version of HPSee 2.0. Download here!

Download the C-S-D Starter Package

Download the Starter Package containing guides and a ROCK-1 Test Space. Download here!

Follow the HPSee Deployment Guide

Use the detailed instructions in the HPSee Deployment Guide for proper setup.

Refer to the SeeSAR Beginner Guide

Follow the SeeSAR Beginner Guide to learn the basics and get started with Chemical Space Docking™.

Still stuck?

Watch the SeeSAR 14 Tutorial video here! (YouTube video)

Get started with the C-S-D Starter Package!

Can't get enough?

Read the full changelog More about SeeSAR Good Practice for C-S-D