TITLE

Machine Learning Algorithms for Predicting Protein Folding Rates and Stability of Mutant Proteins: Comparison with Statistical Methods

AUTHOR(S)
Gromiha, M. Michael; Huang, Liang-Tsung
PUB. DATE
September 2011
SOURCE
Current Protein & Peptide Science;Sep2011, Vol. 12 Issue 6, p490
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Machine learning algorithms have wide range of applications in bioinformatics and computational biology such as prediction of protein secondary structures, solvent accessibility, binding site residues in protein complexes, protein folding rates, stability of mutant proteins, and discrimination of proteins based on their structure and function. In this work, we focus on two aspects of predictions: (i) protein folding rates and (ii) stability of proteins upon mutations. We briefly introduce the concepts of protein folding rates and stability along with available databases, features for prediction methods and measures for prediction performance. Subsequently, the development of structure based parameters and their relationship with protein folding rates will be outlined. The structure based parameters are helpful to understand the physical basis for protein folding and stability. Further, basic principles of major machine learning techniques will be mentioned and their applications for predicting protein folding rates and stability of mutant proteins will be illustrated. The machine learning techniques could achieve the highest accuracy of predicting protein folding rates and stability. In essence, statistical methods and machine learning algorithms are complimenting each other for understanding and predicting protein folding rates and the stability of protein mutants. The available online resources on protein folding rates and stability will be listed.
ACCESSION #
66346877

 

Related Articles

  • Structural Modeling of Protein Interactions by Analogy: Application to PSD-95. Korkin, Dmitry; Davis, Fred P.; Alber, Frank; Tinh Luong; Min-Yi Shen; Lucic, Vladan; Kennedy, Mary B.; Sali, Andrej // PLoS Computational Biology;Nov2006, Vol. 2 Issue 11, p1365 

    We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than...

  • Molecular Surface Representation Using 3D Zernike Descriptors for Protein Shape Comparison and Docking. Kihara, Daisuke; Sael, Lee; Chikhi, Rayan; Esquivel-Rodriguez, Juan // Current Protein & Peptide Science;Sep2011, Vol. 12 Issue 6, p520 

    The tertiary structures of proteins have been solved in an increasing pace in recent years. To capitalize the enormous efforts paid for accumulating the structure data, efficient and effective computational methods need to be developed for comparing, searching, and investigating interactions of...

  • A comparative study of structures and structural transitions of secondary transporters with the LeuT fold. Jeschke, Gunnar // European Biophysics Journal;Mar2013, Vol. 42 Issue 2/3, p181 

    Secondary active transporters from several protein families share a core of two five-helix inverted repeats that has become known as the LeuT fold. The known high-resolution protein structures with this fold were analyzed by structural superposition of the core transmembrane domains (TMDs)....

  • Fold and sequence independent protein binding sites prediction algorithm. Janezˇicˇ, Dusˇanka; Konc, Janez; Konc, Joanna Trykowska; Penca, Matej; Janezˇicˇ, Matej // AIP Conference Proceedings;Dec2012, Vol. 1504 Issue 1, p729 

    We have developed fold and sequence independent algorithm for structural similarity search in large databases of protein structures to find conserved binding regions on proteins involved in protein-protein interactions. We have used this algorithm to find conserved regions on protein surfaces...

  • Understanding the Folding-Function Tradeoff in Proteins. Gosavi, Shachi // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    When an amino-acid sequence cannot be optimized for both folding and function, folding can get compromised in favor of function. To understand this tradeoff better, we devise a novel method for extracting the “function-less” folding-motif of a protein fold from a set of structurally...

  • PDBparam: Online Resource for Computing Structural Parameters of Proteins. Nagarajan, R.; Archana, A.; Thangakani, A. Mary; Jemimah, S.; Velmurugan, D.; Gromiha, M. Michael // Bioinformatics & Biology Insights;1/1/2016, Issue 10, p73 

    Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in...

  • Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods. Yao, Bo; Zheng, Dandan; Liang, Shide; Zhang, Chi // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    Accurate prediction of B-cell antigenic epitopes is important for immunologic research and medical applications, but compared with other bioinformatic problems, antigenic epitope prediction is more challenging because of the extreme variability of antigenic epitopes, where the paratope on the...

  • FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Grove, Laurie E.; Hall, David R.; Beglov, Dmitri; Vajda, Sandor; Kozakov, Dima // Bioinformatics;May2013, Vol. 29 Issue 9, p1218 

    Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm,...

  • A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease. Granneman, Sander; Petfalski, Elisabeth; Tollervey, David // EMBO Journal;10/5/2011, Vol. 30 Issue 19, p4006 

    The 5?-exonuclease Rat1 degrades pre-rRNA spacer fragments and processes the 5?-ends of the 5.8S and 25S rRNAs. UV crosslinking revealed multiple Rat1-binding sites across the pre-rRNA, consistent with its known functions. The major 5.8S 5?-end is generated by Rat1 digestion of the internal...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics