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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Related Experiment Video

Updated: Jul 4, 2026

User-friendly, High-throughput, and Fully Automated Data Acquisition Software for Single-particle Cryo-electron Microscopy
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OPUS-Rota: a fast and accurate method for side-chain modeling.

Mingyang Lu1, Athanasios D Dousis, Jianpeng Ma

  • 1Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

Protein Science : a Publication of the Protein Society
|June 17, 2008
PubMed
Summary

OPUS-Rota is a new computational method for modeling protein side chains. It offers accuracy comparable to leading methods but runs significantly faster, making it a valuable tool for structural biology research.

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Published on: October 21, 2018

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Published on: October 21, 2018

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Modeling

Background:

  • Accurate protein side-chain modeling is crucial for understanding protein function and interactions.
  • Existing methods often face trade-offs between speed and accuracy.

Purpose of the Study:

  • To introduce OPUS-Rota, a novel and efficient algorithm for side-chain modeling.
  • To evaluate OPUS-Rota's performance against established methods in terms of speed and accuracy.

Main Methods:

  • Benchmarking OPUS-Rota against SCWRL, NCN, LGA, SPRUCE, Rosetta, and SCAP.
  • Assessing accuracy using chi (1) and chi (1+2) metrics.
  • Evaluating performance on the Wallner and Elofsson homology-modeling benchmark.

Main Results:

  • OPUS-Rota demonstrates significantly faster runtime compared to most benchmarked methods, except for SCWRL which has comparable speed.
  • OPUS-Rota achieves higher accuracy than SCWRL for chi (1) and chi (1+2) predictions.
  • Its accuracy is comparable or superior to the most accurate methods in the literature, with a substantially shorter runtime.
  • Consistent outperformance of SCWRL on homology modeling benchmarks with >40% sequence identity.

Conclusions:

  • OPUS-Rota offers a compelling balance of high accuracy and computational efficiency for protein side-chain modeling.
  • The method is expected to advance high-accuracy protein structure refinement.
  • The OPUS-Rota program is available for academic use.