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SeeSAR

SeeSAR

SeeSAR is a 3D desktop modeling platform. It facilitates interactive, visual, compound prioritization - as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone.
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protein-ligand complex in SeeSAR
infiniSee

infiniSee

infiniSee is a virtual screening platform. Based on similarity, it finds molecules of interest in chemical spaces of (almost) infinite size. Given a template or query molecule, infiniSee returns similar molecules from these chemical spaces — or from screening libraries.
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explore vast chemical spaces with infiniSee to find new scaffolds during drug discovery
Components

Components integrated in SeeSAR

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HYDE

HYDE binding assessment approximates and visualizes affinities based on two major physical driving forces: desolvation and interactions. Also available as a stand-alone command-line version.

Detailed insights can be found here
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FlexX

FlexX is a fast and flexible docking software suited for virtual screening. Apply pharmacophore constraints, and utilize compound series docking, as well as template docking. Also available as a stand-alone command-line version.

Detailed insights can be found here

FlexS

FlexS is a computer program for predicting ligand alignments. For a given pair of ligands, FlexS predicts the conformation and orientation of one of the ligands relative to the other one. Available as a stand-alone command-line version.

Detailed insights can be found here

FastGrow

Fastgrow uses a novel, fast, and accurate shape-based algorithm for structure-based growing into binding pockets. Users can screen tens of thousands of fragments within seconds to receive an optimized suggestion that complements the binding site. Available as a stand-alone command-line version.

Detailed insights can be found here

Components integrated in SeeSAR

Components implemented in infiniSee

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FTrees

Feature Trees (short FTrees) is a highly efficient software tool for fuzzy similarity searching, especially suited for spotting the non-obvious hits in virtual screenings. Also available as a standalone commandline version.

Detailed insights can be found here.

SpaceLight

SpaceLight screens vast Chemical Spaces for close analogs of a query compound based on Tanimoto-type fingerprint similarity. Available as a stand-alone command-line version.

Detailed insights can be found here

Important note: Please use the latest versions of the Chemical Spaces (as of March 8th).

Components implemented in infiniSee

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CoLibri

CoLibri is a toolkit for chemical space exploration that transforms synthetic knowledge into chemical spaces, constituting huge numbers of virtual but synthetically accessible compounds. Available as a stand-alone command-line version.

Detailed insights can be found here

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PoseView

PoseView

PoseView is a 2D visualization software for protein-ligand complexes. It generates publication-quality 2D interaction diagrams of protein-ligand complexes from crystal structures or results from a docking program.
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poseviewer binding pocket
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Mona

Mona is an interactive tool that can be used to prepare and visualize small-molecule datasets.
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SMARTSeditor

SMARTSeditor is an interactive GUI application that lets you draw substructure patterns. SMARTSeditor supports recursions, allowing you to go to any level of complexity without getting lost.
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DoGSiteScorer

DoGSiteScorer is an automated pocket detection and analysis tool, which can be used for protein druggability assessment.

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KNIME® interfaces
Workflows

Workflows

BioSolveIT provides KNIME® workflows tailored to fit the needs of your drug design process. The interfaces are distributed separately of KNIME® and available free of charge.
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FragXplorer

BioSolveIT-FragXplorer is a virtual library builder and docking-workflow designed to explore binding sites MedChem-style.

REALizer

The REALizer-workflow gives you several post-processing options to quickly get an overview of the best compounds after screening chemical spaces.

BioSphere

The BioSphere workflow provides you with all tools to build and search chemical spaces based on user-defined reactions and reagents.

MedChemWizard

The MedChemWizard workflow is designed to assist medicinal chemists with idea generation, ligand design, and lead optimization using a number of common functional group transformations and medicinal chemistry rules-of-thumb.

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