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Related Experiment Video

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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High-Quality Conformer Generation with CONFORGE: Algorithm and Performance Assessment.

Thomas Seidel¹, Christian Permann², Oliver Wieder³

¹Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.

Journal of Chemical Information and Modeling

|August 25, 2023

Summary

This summary is machine-generated.

CONFORGE, a new open-source tool, generates accurate molecular conformations for drug design. It outperforms other open-source options and matches commercial software for small molecules, excelling in accuracy for macrocycles.

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Spatial Separation of Molecular Conformers and Clusters

Spatial Separation of Molecular Conformers and Clusters

Published on: January 9, 2014

Area of Science:

Computational chemistry
Molecular modeling
Drug discovery

Background:

Accurate molecular conformations are crucial for computer-aided drug design (CADD).
Existing open-source conformer generators often lag behind commercial alternatives.
Efficient generation of representative conformer ensembles is needed for predicting molecular binding.

Purpose of the Study:

Introduce CONFORGE, an open-source conformer ensemble generator.
Benchmark CONFORGE against commercial and open-source tools for accuracy and efficiency.
Evaluate performance for both drug-like small molecules and macrocyclic structures.

Main Methods:

Conformer ensemble generation using CONFORGE.
Benchmarking against established commercial and open-source software.
Assessment of accuracy in reproducing experimental 3D structures.
Evaluation of computational efficiency and robustness.

Main Results:

CONFORGE demonstrated superior performance among open-source tools for small molecules.
CONFORGE matched or exceeded the performance of commercial software for small molecules in speed and accuracy.
For macrocycles, CONFORGE achieved the highest average accuracy in the benchmark study.

Conclusions:

CONFORGE offers state-of-the-art performance for generating molecular conformers.
It provides a powerful, accurate, and efficient open-source alternative for drug design.
CONFORGE is particularly effective for generating accurate conformations of macrocyclic compounds.