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Exploring Caspase Mutations and Post-Translational Modification by Molecular Modeling Approaches

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Template based protein structure modeling by global optimization in CASP11.

Keehyoung Joo^1,2, InSuk Joung^1,3, Sun Young Lee¹

¹Center for in Silico Protein Science, Korea Institute for Advanced Study, Seoul, 130-722, Korea.

|September 3, 2015

Summary

This summary is machine-generated.

New protein modeling protocols improve template-based modeling (TBM) for CASP11 targets. Enhanced methods like CRFalign and conformational space annealing lead to more accurate protein structure predictions.

Keywords:

casp fold recognition global optimization homology modeling protein structure modeling sequence alignment template based modeling

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Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

Template-based modeling (TBM) is crucial for protein structure prediction.
Previous CASP (Critical Assessment of protein Structure Prediction) experiments have driven advancements in modeling protocols.

Purpose of the Study:

To develop and refine protein modeling protocols for the CASP11 competition.
To improve the accuracy of template-based modeling for protein structure prediction.

Main Methods:

Development of three new protocols: nns (server), LEE, and LEER (human).
Application of conformational space annealing for global optimization in alignment, chain building, and side-chain remodeling.
Introduction of CRFalign, a novel alignment method incorporating positional, environmental, and non-linear feature correlations.
Modifications to energy functions and weight parameters for chain building.
Incorporation of residue-type dependence in side-chain remodeling.

Main Results:

The nns server method demonstrated improved performance due to enhanced fold recognition via CRFalign and template integration.
The LEE protocol, using CASP11 server models as templates, showed success, highlighting the value of template screening and clustering.
The developed protocols represent advancements over previous CASP iterations (CASP7-CASP10).

Conclusions:

The new protocols, particularly nns and LEE, show enhanced accuracy in protein structure prediction for CASP11 targets.
CRFalign and conformational space annealing are key components contributing to improved modeling performance.
Effective template screening, clustering, and ranking are vital for advancing protein 3D modeling accuracy.