Literature DB >> 29092002

pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration.

Soundhararajan Gopi1, Devanshu Devanshu1, Praveen Krishna1, Athi N Naganathan1.   

Abstract

Summary: We present a web-server for rapid prediction of changes in protein stabilities over a range of temperatures and experimental conditions upon single- or multiple-point substitutions of charged residues. Potential mutants are identified by a charge-shuffling procedure while the stability changes (i.e. an unfolding curve) are predicted employing an ensemble-based statistical-mechanical model. We expect this server to be a simple yet detailed tool for engineering stabilities, identifying electrostatically frustrated residues, generating local stability maps and in constructing fitness landscapes. Availability and implementation: The web-server is freely available at http://pbl.biotech.iitm.ac.in/pStab and supports recent versions of all major browsers. Contact: athi@iitm.ac.in. Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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Year:  2018        PMID: 29092002      PMCID: PMC6049017          DOI: 10.1093/bioinformatics/btx697

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  8 in total

Review 1.  To charge or not to charge?

Authors:  J M Sanchez-Ruiz; G I Makhatadze
Journal:  Trends Biotechnol       Date:  2001-04       Impact factor: 19.536

2.  A simple model for calculating the kinetics of protein folding from three-dimensional structures.

Authors:  V Muñoz; W A Eaton
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

3.  Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.

Authors:  Raphael Guerois; Jens Erik Nielsen; Luis Serrano
Journal:  J Mol Biol       Date:  2002-07-05       Impact factor: 5.469

4.  Predictions from an Ising-like Statistical Mechanical Model on the Dynamic and Thermodynamic Effects of Protein Surface Electrostatics.

Authors:  Athi N Naganathan
Journal:  J Chem Theory Comput       Date:  2012-10-22       Impact factor: 6.006

5.  Protein stability and surface electrostatics: a charged relationship.

Authors:  Samantha S Strickler; Alexey V Gribenko; Alexander V Gribenko; Timothy R Keiffer; Jessica Tomlinson; Tracey Reihle; Vakhtang V Loladze; George I Makhatadze
Journal:  Biochemistry       Date:  2006-03-07       Impact factor: 3.162

6.  iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations.

Authors:  Liang-Tsung Huang; M Michael Gromiha; Shinn-Ying Ho
Journal:  Bioinformatics       Date:  2007-03-22       Impact factor: 6.937

7.  A rapid, ensemble and free energy based method for engineering protein stabilities.

Authors:  Athi N Naganathan
Journal:  J Phys Chem B       Date:  2013-04-11       Impact factor: 2.991

8.  SDM--a server for predicting effects of mutations on protein stability and malfunction.

Authors:  Catherine L Worth; Robert Preissner; Tom L Blundell
Journal:  Nucleic Acids Res       Date:  2011-05-18       Impact factor: 16.971

  8 in total
  3 in total

1.  The Role of Electrostatics and Folding Kinetics on the Thermostability of Homologous Cold Shock Proteins.

Authors:  Paulo Henrique Borges Ferreira; Frederico Campos Freitas; Michelle E McCully; Gabriel Gouvêa Slade; Ronaldo Junio de Oliveira
Journal:  J Chem Inf Model       Date:  2020-01-17       Impact factor: 4.956

Review 2.  The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2.

Authors:  Jim Warwicker
Journal:  Front Mol Biosci       Date:  2022-02-18

Review 3.  The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics.

Authors:  Koji Ooka; Runjing Liu; Munehito Arai
Journal:  Molecules       Date:  2022-07-12       Impact factor: 4.927

  3 in total

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