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Updated: Sep 18, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information.

Yulu Yang¹, Ying Lv², Zhenwei Luo^1,2

¹Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China.

Molecules (Basel, Switzerland)

|June 27, 2025

Summary

This summary is machine-generated.

OPUS-BFactor predicts protein B-factors using sequence and structure data. This tool accurately estimates protein flexibility and dynamics, outperforming existing methods.

Keywords:

protein B-factor protein flexibility protein language model

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Published on: July 25, 2013

Area of Science:

Structural Biology
Computational Biology
Biophysics

Background:

Protein B-factor (Debye-Waller temperature factor) quantifies atomic thermal fluctuations, indicating protein flexibility and dynamics.
Accurate prediction of Cα atom B-factors is essential but remains a significant challenge in structural biology.

Purpose of the Study:

To introduce OPUS-BFactor, a novel computational tool for predicting normalized protein B-factors.
To develop a method that integrates sequence and structural information for enhanced B-factor prediction.

Main Methods:

OPUS-BFactor utilizes a transformer-based module integrating sequence-level and pair-level features.
It incorporates structural attributes from 3D protein structures and evolutionary profiles from the ESM-2 protein language model.
Pair features are integrated as a bias term into the attention matrix derived from sequence-level features.

Main Results:

OPUS-BFactor demonstrated superior performance in predicting normalized protein B-factors across three independent test sets.
The tool significantly outperformed existing B-factor prediction methods, including those evaluated on recent CAMEO and CASP15 targets.
The two-mode operation (sequence-only or structure-based) provides flexibility for diverse prediction scenarios.

Conclusions:

OPUS-BFactor is a highly effective tool for predicting protein B-factors, offering valuable insights into protein flexibility, thermal stability, and regional activity.
The integration of sequence and structural features via a transformer architecture represents a significant advancement in predicting protein dynamics.
This tool has broad applicability in structural biology and related fields requiring accurate B-factor estimations.