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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.

Ajay N Jain1, Ann E Cleves2, Qi Gao3

  • 1Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA. ajain@jainlab.org.

Journal of Computer-Aided Molecular Design
|May 5, 2019
PubMed
Summary
This summary is machine-generated.

ForceGen generates accurate 3D molecular structures from 2D inputs, outperforming other methods for both small molecules and complex macrocycles, even with limited computational resources.

Keywords:
Conformer generationForceGenMacrocycleMulti-coreNMRRDCSurflex

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate 3D structure generation and conformational analysis are crucial for understanding molecular behavior and designing new therapeutics.
  • Existing methods often struggle with complex macrocyclic structures and require significant computational resources or template-based approaches.

Purpose of the Study:

  • To introduce and evaluate ForceGen, a novel template-free, non-stochastic method for 2D to 3D molecular structure generation and conformational elaboration.
  • To assess ForceGen's performance, particularly for macrocycles, comparing it against established methods on diverse benchmarks.

Main Methods:

  • ForceGen employs a template-free, non-stochastic algorithm for generating and refining 3D molecular structures.
  • The method incorporates unique physical movements, including sub-cycle flips and explicit hydrogen bond formation, to explore conformational space.
  • Parallelization across multiple computing cores enables efficient processing, with options for fast and thorough search modes.

Main Results:

  • ForceGen demonstrates superior speed and accuracy for non-macrocycle conformational search compared to existing methods on a large PDB ligand benchmark.
  • For macrocycles, ForceGen significantly outperforms other approaches in terms of overall RMS deviation from experimental coordinates.
  • Computational times are generally rapid, with median times under a minute for typical cases, and manageable increases for highly complex structures.

Conclusions:

  • ForceGen offers a highly effective and efficient solution for 2D to 3D structure generation and conformational analysis of small molecules and macrocycles.
  • The method's ability to accurately model complex macrocyclic structures, including those with internal hydrogen bonding networks, is a significant advancement.
  • ForceGen's performance, speed, and adaptability (e.g., incorporating NMR data) make it a valuable tool for computational chemistry and drug design at interactive timescales.