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Protein and Protein Structure02:15

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Updated: Feb 15, 2026

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
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CONFOLD2: improved contact-driven ab initio protein structure modeling.

Badri Adhikari1, Jianlin Cheng2

  • 1Department of Mathematics and Computer Science, University of Missouri-St. Louis, St. Louis, 63121, MO, USA.

BMC Bioinformatics
|January 27, 2018
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Summary
This summary is machine-generated.

CONFOLD2 is a new tool for protein structure prediction using predicted contacts. It quickly generates accurate models, aiding in understanding protein folding and function.

Keywords:
CONFOLDContactsModel selectionProtein folding

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Advances in residue-residue contact prediction are improving contact-guided protein structure prediction.
  • Effective tools are needed to rapidly build high-quality tertiary structural models from predicted contacts.

Purpose of the Study:

  • To develop and evaluate CONFOLD2, an improved contact-driven protein modeling method.
  • To assess CONFOLD2's effectiveness for *ab initio* protein structure prediction using predicted contacts.

Main Methods:

  • CONFOLD2 builds protein models using subsets of predicted contacts.
  • A soft square energy function guides model construction.
  • Model clustering identifies the top five predictions.
  • The method was tested on PSICOV, CASP11, and CASP12 contact datasets.

Main Results:

  • CONFOLD2 achieved an average reconstruction accuracy of 0.57 TM-score on 150 proteins from the PSICOV dataset.
  • On CASP11 and CASP12 datasets, CONFOLD2 attained a mean TM-score of 0.41.
  • The method demonstrated efficient generation of top structural models.

Conclusions:

  • CONFOLD2 rapidly generates top five structural models for a protein sequence given predicted contacts and secondary structures.
  • The source code for CONFOLD2 is publicly available, facilitating further research and application.