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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Fold recognition by concurrent use of solvent accessibility and residue depth
Song Liu1, Chi Zhang, Shide Liang
1Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
Proteins
|May 19, 2007
Summary
Integrating residue depth and solvent accessibility improves protein fold recognition accuracy. The new SP(4) method enhances sequence alignment and model prediction for remote protein homologs.
Area of Science:
- Computational biology
- Structural bioinformatics
- Protein structure prediction
Background:
- Protein structure prediction is crucial for understanding protein function.
- Existing methods like SP(3) utilize sequence and residue depth profiles for fold recognition.
- There's a need to enhance accuracy in recognizing structural similarity, especially for proteins with low sequence identity.
Purpose of the Study:
- To investigate if incorporating solvent accessibility profiles into the SP(3) method can improve protein fold recognition.
- To develop and evaluate a new method, SP(4), for enhanced fold recognition and sequence alignment.
- To assess the performance of SP(4) in terms of accuracy, sensitivity, and model-structure quality.
Main Methods:
- Developed the SP(4) method by combining sequence profiles, secondary-structure profiles, residue-depth dependent profiles, and solvent accessibility profiles.
- Tested SP(4) on the SALIGN benchmark for sequence alignment accuracy.
- Evaluated SP(4) using Lindahl, LiveBench 8, and CASP7 blind prediction datasets for fold recognition sensitivity and model accuracy.
Main Results:
- The SP(4) method demonstrated consistent improvements over SP(3) in remote homology detection.
- SP(4) showed enhanced accuracy in sequence alignment and predicted structural models.
- The sensitivity of fold recognition was significantly improved by the SP(4) method.
Conclusions:
- Concurrent use of residue depth and solvent accessibility profiles effectively improves protein fold recognition accuracy and sensitivity.
- The SP(4) method represents a significant advancement in computational approaches for predicting protein structures.
- The SP(4) server is publicly available for further research and application.
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