Literature DB >> 24413526

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites.

Alejandro Panjkovich1, Xavier Daura.   

Abstract

The regulation of protein activity is a key aspect of life at the molecular level. Unveiling its details is thus crucial to understanding signalling and metabolic pathways. The most common and powerful mechanism of protein-function regulation is allostery, which has been increasingly calling the attention of medicinal chemists due to its potential for the discovery of novel therapeutics. In this context, PARS is a simple and fast method that queries protein dynamics and structural conservation to identify pockets on a protein structure that may exert a regulatory effect on the binding of a small-molecule ligand.

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Year:  2014        PMID: 24413526     DOI: 10.1093/bioinformatics/btu002

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


  27 in total

Review 1.  Computational Advances for the Development of Allosteric Modulators and Bitopic Ligands in G Protein-Coupled Receptors.

Authors:  Zhiwei Feng; Guanxing Hu; Shifan Ma; Xiang-Qun Xie
Journal:  AAPS J       Date:  2015-05-05       Impact factor: 4.009

2.  PASSer2.0: Accurate Prediction of Protein Allosteric Sites Through Automated Machine Learning.

Authors:  Sian Xiao; Hao Tian; Peng Tao
Journal:  Front Mol Biosci       Date:  2022-07-11

3.  Mixed-solvent molecular dynamics simulation-based discovery of a putative allosteric site on regulator of G protein signaling 4.

Authors:  Wallace K B Chan; Debarati DasGupta; Heather A Carlson; John R Traynor
Journal:  J Comput Chem       Date:  2021-09-07       Impact factor: 3.672

Review 4.  Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction.

Authors:  Dirk Walther
Journal:  Methods Mol Biol       Date:  2023

5.  Allosteric Hotspots in the Main Protease of SARS-CoV-2.

Authors:  Léonie Strömich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki
Journal:  J Mol Biol       Date:  2022-07-16       Impact factor: 6.151

6.  Construction of feasible and accurate kinetic models of metabolism: A Bayesian approach.

Authors:  Pedro A Saa; Lars K Nielsen
Journal:  Sci Rep       Date:  2016-07-15       Impact factor: 4.379

7.  Nonlinear backbone torsional pair correlations in proteins.

Authors:  Shiyang Long; Pu Tian
Journal:  Sci Rep       Date:  2016-10-06       Impact factor: 4.379

8.  Some Dietary Phenolic Compounds Can Activate Thyroid Peroxidase and Inhibit Lipoxygenase-Preliminary Study in the Model Systems.

Authors:  Ewa Habza-Kowalska; Agnieszka A Kaczor; Damian Bartuzi; Jacek Piłat; Urszula Gawlik-Dziki
Journal:  Int J Mol Sci       Date:  2021-05-12       Impact factor: 5.923

9.  Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy.

Authors:  Duan Ni; Jiacheng Wei; Xinheng He; Ashfaq Ur Rehman; Xinyi Li; Yuran Qiu; Jun Pu; Shaoyong Lu; Jian Zhang
Journal:  Chem Sci       Date:  2020-11-02       Impact factor: 9.825

10.  AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.

Authors:  Joe G Greener; Michael J E Sternberg
Journal:  BMC Bioinformatics       Date:  2015-10-23       Impact factor: 3.169

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