Literature DB >> 25810427

ASBench: benchmarking sets for allosteric discovery.

Wenkang Huang1, Guanqiao Wang1, Qiancheng Shen1, Xinyi Liu1, Shaoyong Lu1, Lv Geng1, Zhimin Huang1, Jian Zhang1.   

Abstract

Allostery allows for the fine-tuning of protein function. Targeting allosteric sites is gaining increasing recognition as a novel strategy in drug design. The key challenge in the discovery of allosteric sites has strongly motivated the development of computational methods and thus high-quality, publicly accessible standard data have become indispensable. Here, we report benchmarking data for experimentally determined allosteric sites through a complex process, including a 'Core set' with 235 unique allosteric sites and a 'Core-Diversity set' with 147 structurally diverse allosteric sites. These benchmarking sets can be exploited to develop efficient computational methods to predict unknown allosteric sites in proteins and reveal unique allosteric ligand-protein interactions to guide allosteric drug design.
© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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Year:  2015        PMID: 25810427     DOI: 10.1093/bioinformatics/btv169

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


  18 in total

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

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Journal:  Front Mol Biosci       Date:  2022-07-11

4.  AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations.

Authors:  Zhen Wah Tan; Enrico Guarnera; Wei-Ven Tee; Igor N Berezovsky
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

5.  AlloMAPS: allosteric mutation analysis and polymorphism of signaling database.

Authors:  Zhen Wah Tan; Wei-Ven Tee; Enrico Guarnera; Lauren Booth; Igor N Berezovsky
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

6.  Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch.

Authors:  Wei Wang; Cheng Jiang; Jinmai Zhang; Wei Ye; Ray Luo; Hai-Feng Chen
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7.  The Structural Basis of Oncogenic Mutations G12, G13 and Q61 in Small GTPase K-Ras4B.

Authors:  Shaoyong Lu; Hyunbum Jang; Ruth Nussinov; Jian Zhang
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8.  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

9.  ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks.

Authors:  Qiancheng Shen; Guanqiao Wang; Shuai Li; Xinyi Liu; Shaoyong Lu; Zhongjie Chen; Kun Song; Junhao Yan; Lv Geng; Zhimin Huang; Wenkang Huang; Guoqiang Chen; Jian Zhang
Journal:  Nucleic Acids Res       Date:  2015-09-13       Impact factor: 16.971

10.  AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses.

Authors:  Min Huang; Kun Song; Xinyi Liu; Shaoyong Lu; Qiancheng Shen; Renxiao Wang; Jingze Gao; Yuanyuan Hong; Qian Li; Duan Ni; Jianrong Xu; Guoqiang Chen; Jian Zhang
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

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