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Literature DB >> 15923205

COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.

Jason Vertrees¹, Phillip Barritt, Steve Whitten, Vincent J Hilser.

Abstract

SUMMARY: Utilizing the user-supplied coordinates of a protein structure, the COREX/BEST Server generates a structural thermodynamic ensemble. This conformational ensemble can then be used to calculate the regional variations in stability of a protein structure, and the stabilities are presented in units of energy (kcal/mol). The regional stabilities, which are calculated at the resolution of individual residues, can be mapped onto the protein structure for visual representation and downloaded from the site in the form of tab delimited text. The site provides an easy to follow summary of the theoretical and algorithmic approaches and provides links to references for more detailed descriptions. AVAILABILITY: The COREX/BEST Server may be accessed through a typical web browser by visiting http://best.utmb.edu/BEST/.

Mesh：

Substances：
Proteins

Year: 2005 PMID： 15923205 DOI： 10.1093/bioinformatics/bti520

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

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Cited

27 in total

1. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

Authors: Jason B Brokaw; Jhih-Wei Chu
Journal: Biophys J Date: 2010-11-17 Impact factor: 4.033

2. Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin.

Authors: Loren Stagg; Shao-Qing Zhang; Margaret S Cheung; Pernilla Wittung-Stafshede
Journal: Proc Natl Acad Sci U S A Date: 2007-11-16 Impact factor: 11.205

3. An energetic representation of protein architecture that is independent of primary and secondary structure.

Authors: Jason Vertrees; James O Wrabl; Vincent J Hilser
Journal: Biophys J Date: 2009-09-02 Impact factor: 4.033

4. Comprehensive analysis of contributions from protein conformational stability and major histocompatibility complex class II-peptide binding affinity to CD4+ epitope immunogenicity in HIV-1 envelope glycoprotein.

Authors: Tingfeng Li; N Kalaya Steede; Hong-Nam P Nguyen; Lucy C Freytag; James B McLachlan; Ramgopal R Mettu; James E Robinson; Samuel J Landry
Journal: J Virol Date: 2014-06-11 Impact factor: 5.103

COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures.

1. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

2. Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin.

3. An energetic representation of protein architecture that is independent of primary and secondary structure.

4. Comprehensive analysis of contributions from protein conformational stability and major histocompatibility complex class II-peptide binding affinity to CD4+ epitope immunogenicity in HIV-1 envelope glycoprotein.

Review 5. The role of protein conformational fluctuations in allostery, function, and evolution.

6. CD4+ T-cell epitope prediction using antigen processing constraints.

7. Molecular dynamics reveal the essential role of linker motions in the function of cullin-RING E3 ligases.

8. Investigating homology between proteins using energetic profiles.

9. Energetic profiling of protein folds.

10. Analysing the origin of long-range interactions in proteins using lattice models.