Computational Prediction of Important Regions in Protein Sequences [Life Sciences]

This column summarizes the main approaches for predicting protein functional sites from sequence information. Extracting functional regions from linear protein sequences has many similarities with prototypical problems in signal processing, and some of the methodologies used are taken from this discipline.

[1]  Alfonso Valencia,et al.  JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures , 2012, Bioinform..

[2]  M. Bolognesi,et al.  Function and Structure of Inherently Disordered Proteins This Review Comes from a Themed Issue on Proteins Edited Prediction of Non-folding Proteins and Regions Frequency of Disordered Regions Protein Evolution Partitioning Unstructured Proteins and Regions into Groups Involvement of Inherently Diso , 2022 .

[3]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[4]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[5]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[6]  W. S. Valdar,et al.  Scoring residue conservation , 2002, Proteins.

[7]  R. Russell,et al.  Analysis and prediction of functional sub-types from protein sequence alignments. , 2000, Journal of molecular biology.

[8]  Burkhard Rost,et al.  ISIS: interaction sites identified from sequence , 2007, Bioinform..

[9]  A. Bairoch.  PROSITE: a dictionary of sites and patterns in proteins. , 1991, Nucleic acids research.

[10]  A. Valencia,et al.  Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.

[11]  A. Lesk,et al.  The relation between the divergence of sequence and structure in proteins. , 1986, The EMBO journal.

[12]  Alfonso Valencia,et al.  Phylogeny-independent detection of functional residues , 2006, Bioinform..

[13]  Alfonso Valencia,et al.  Protein interactions and ligand binding: From protein subfamilies to functional specificity , 2010, Proceedings of the National Academy of Sciences.

[14]  C. Sander,et al.  A method to predict functional residues in proteins , 1995, Nature Structural Biology.

[15]  N. Ben-Tal,et al.  ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.