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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Embracing chemical and structural diversity with UCONGA: A universal conformer generation and analysis program.

Nathaniel R Gunby¹, Sarah L Masters¹, Deborah L Crittenden¹

¹Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch 8041, New Zealand.

Journal of Molecular Graphics & Modelling

|September 16, 2017

Summary

Computational chemists can now generate molecular conformers for any molecule using the Universal CONformer Generation and Analysis (UCONGA) package. This tool avoids the trade-offs between speed and accuracy in conformational analysis.

Keywords:

Computer simulation Drug design Inorganic chemistry Molecular conformation Software Structural chemistry

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Area of Science:

Computational Chemistry
Molecular Modeling
Structural Chemistry

Background:

Molecular properties are dictated by structure, necessitating conformer generation.
Current methods involve trade-offs between accuracy and computational cost.
Existing techniques are limited for non-organic and large molecules.

Purpose of the Study:

Introduce the Universal CONformer Generation and Analysis (UCONGA) program package.
Address the limitations of existing conformer generation methods.
Provide a tool for comprehensive conformational analysis of diverse molecules.

Main Methods:

UCONGA requires only atomic van der Waals radii as input.
Generates sterically allowed conformers for molecules of any composition.
Includes analysis scripts for identifying representative conformers and clustering.

Main Results:

UCONGA enables generation of conformer ensembles without molecule-specific parameters.
Minimizes the need for computationally expensive ab initio calculations.
Facilitates the study of flexible, non-drug-like molecules.

Conclusions:

UCONGA offers a novel solution for comprehensive conformer generation and analysis.
It is particularly valuable for molecules not covered by traditional force fields.
Expected to be a key tool for computational and structural chemists.