Literature DB >> 27160393

Computational approaches for predicting mutant protein stability.

Shweta Kulshreshtha1,2, Vigi Chaudhary3, Girish K Goswami4, Nidhi Mathur3.   

Abstract

Mutations in the protein affect not only the structure of protein, but also its function and stability. Prediction of mutant protein stability with accuracy is desired for uncovering the molecular aspects of diseases and design of novel proteins. Many advanced computational approaches have been developed over the years, to predict the stability and function of a mutated protein. These approaches based on structure, sequence features and combined features (both structure and sequence features) provide reasonably accurate estimation of the impact of amino acid substitution on stability and function of protein. Recently, consensus tools have been developed by incorporating many tools together, which provide single window results for comparison purpose. In this review, a useful guide for the selection of tools that can be employed in predicting mutated proteins' stability and disease causing capability is provided.

Keywords:  Computational tools; Databases; Mutated protein; Protein function; Protein stability

Mesh:

Substances:

Year:  2016        PMID: 27160393     DOI: 10.1007/s10822-016-9914-3

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  74 in total

1.  Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations.

Authors:  Sarah E Flanagan; Ann-Marie Patch; Sian Ellard
Journal:  Genet Test Mol Biomarkers       Date:  2010-08

2.  Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility.

Authors:  Vijaya Parthiban; M Michael Gromiha; Christian Hoppe; Dietmar Schomburg
Journal:  Proteins       Date:  2007-01-01

3.  Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model.

Authors:  Liang-Tsung Huang; M Michael Gromiha; Shinn-Ying Ho
Journal:  J Mol Model       Date:  2007-03-30       Impact factor: 1.810

4.  SNPMeta: SNP annotation and SNP metadata collection without a reference genome.

Authors:  Thomas J Y Kono; Kiran Seth; Jesse A Poland; Peter L Morrell
Journal:  Mol Ecol Resour       Date:  2013-11-16       Impact factor: 7.090

5.  Evolutionary diagnosis method for variants in personal exomes.

Authors:  Sudhir Kumar; Maxwell Sanderford; Vanessa E Gray; Jieping Ye; Li Liu
Journal:  Nat Methods       Date:  2012-09       Impact factor: 28.547

6.  dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.

Authors:  Xiaoming Liu; Xueqiu Jian; Eric Boerwinkle
Journal:  Hum Mutat       Date:  2013-07-10       Impact factor: 4.878

7.  ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions.

Authors:  M D Shaji Kumar; K Abdulla Bava; M Michael Gromiha; Ponraj Prabakaran; Koji Kitajima; Hatsuho Uedaira; Akinori Sarai
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

8.  CUPSAT: prediction of protein stability upon point mutations.

Authors:  Vijaya Parthiban; M Michael Gromiha; Dietmar Schomburg
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

9.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

Authors:  Simon A Forbes; David Beare; Prasad Gunasekaran; Kenric Leung; Nidhi Bindal; Harry Boutselakis; Minjie Ding; Sally Bamford; Charlotte Cole; Sari Ward; Chai Yin Kok; Mingming Jia; Tisham De; Jon W Teague; Michael R Stratton; Ultan McDermott; Peter J Campbell
Journal:  Nucleic Acids Res       Date:  2014-10-29       Impact factor: 16.971

10.  SNAP: predict effect of non-synonymous polymorphisms on function.

Authors:  Yana Bromberg; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2007-05-25       Impact factor: 16.971

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  18 in total

1.  Consensus sequence design as a general strategy to create hyperstable, biologically active proteins.

Authors:  Matt Sternke; Katherine W Tripp; Doug Barrick
Journal:  Proc Natl Acad Sci U S A       Date:  2019-05-20       Impact factor: 11.205

Review 2.  Tailoring Proteins to Re-Evolve Nature: A Short Review.

Authors:  Angelica Jimenez-Rosales; Miriam V Flores-Merino
Journal:  Mol Biotechnol       Date:  2018-12       Impact factor: 2.695

3.  Prediction of impacts of mutations on protein structure and interactions: SDM, a statistical approach, and mCSM, using machine learning.

Authors:  Arun Prasad Pandurangan; Tom L Blundell
Journal:  Protein Sci       Date:  2019-11-25       Impact factor: 6.725

4.  Improving antibody thermostability based on statistical analysis of sequence and structural consensus data.

Authors:  Lei Jia; Mani Jain; Yaxiong Sun
Journal:  Antib Ther       Date:  2022-07-22

5.  Identification of missense SNP-mediated mutations in the regulatory sites of aldose reductase (ALR2) responsible for treatment failure in diabetic complications.

Authors:  Bhawna Vyas; Shalki Choudhary; Himanshu Verma; Manoj Kumar; Ashok Kumar Malik
Journal:  J Mol Model       Date:  2022-08-19       Impact factor: 2.172

6.  SDM: a server for predicting effects of mutations on protein stability.

Authors:  Arun Prasad Pandurangan; Bernardo Ochoa-Montaño; David B Ascher; Tom L Blundell
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

7.  Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study.

Authors:  Leidy D Ardila-Leal; Pedro A Monterey-Gutiérrez; Raúl A Poutou-Piñales; Balkys E Quevedo-Hidalgo; Johan F Galindo; Aura M Pedroza-Rodríguez
Journal:  BMC Biotechnol       Date:  2021-06-04       Impact factor: 2.563

8.  Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.

Authors:  Fang Ge; Ying Zhang; Jian Xu; Arif Muhammad; Jiangning Song; Dong-Jun Yu
Journal:  Brief Bioinform       Date:  2022-01-17       Impact factor: 11.622

9.  Phenotype inference in an Escherichia coli strain panel.

Authors:  Marco Galardini; Alexandra Koumoutsi; Lucia Herrera-Dominguez; Juan Antonio Cordero Varela; Anja Telzerow; Omar Wagih; Morgane Wartel; Olivier Clermont; Erick Denamur; Athanasios Typas; Pedro Beltrao
Journal:  Elife       Date:  2017-12-27       Impact factor: 8.140

10.  KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability.

Authors:  Carter J Wilson; Megan Chang; Mikko Karttunen; Wing-Yiu Choy
Journal:  Int J Mol Sci       Date:  2021-05-20       Impact factor: 5.923

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