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Updated: Jun 15, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

An optimized TOPS+ comparison method for enhanced TOPS models.

Mallika Veeramalai1, David Gilbert, Gabriel Valiente

  • 1Joint Center for Molecular Modeling, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA. mallikav@burnham.org

BMC Bioinformatics
|March 19, 2010
PubMed
Summary
This summary is machine-generated.

The advanced TOPS+ method enhances protein structure comparison by incorporating ligand information and optimizing parameters, achieving higher accuracy and biological significance than previous methods.

Related Experiment Videos

Last Updated: Jun 15, 2026

High-Throughput Metabolic Profiling for Model Refinements of Microalgae
11:07

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biochemistry

Background:

  • Traditional protein structure comparison methods like VAST and TOPS are fast but may lack biological significance.
  • The novel TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information) was previously introduced.
  • Parameter optimization significantly improves the results of the TOPS+ method.

Purpose of the Study:

  • To present an optimized version of the TOPS+ method, termed advanced TOPS+ (advTOPS+), for enhanced protein structure comparison.
  • To demonstrate the improved biological significance and accuracy of advTOPS+.
  • To introduce a new TOPS+ string model incorporating loops and ligand information.

Main Methods:

  • Developed a TOPS+ string model representing protein structures, including loops as secondary structure elements (SSEs).
  • Integrated ligand information as first-class objects within the model.
  • Described interactions between SSEs and ligands using annotated arcs indicating direction and type.
  • Performed all-against-all pairwise comparisons on the PDB40 dataset (2,620 non-redundant structures).

Main Results:

  • The TOPS+ string model demonstrated biological significance, validated by SCOP classification at the superfamily level.
  • Benchmarking on the PDB40 dataset confirmed the effectiveness of the TOPS+ comparison method.
  • The advTOPS+ method showed improved performance over the basic TOPS+ and TOPS methods.

Conclusions:

  • The advanced TOPS+ comparison method achieves 90% accuracy for SCOP alpha+beta on the PDB40 dataset, a 6% improvement.
  • advTOPS+ outperforms TOPS, basic TOPS+, and SSAP methods on the Chew-Kedem dataset, reaching 98% accuracy.
  • The optimized TOPS+ method offers a more biologically significant approach to protein structure comparison.