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Allosite: a method for predicting allosteric sites

Wenkang Huang, Shaoyong Lu, Zhimin Huang, Xinyi Liu, Linkai Mou, Yu Luo, Yanlong Zhao, Yaqin Liu, Zhongjie Chen, Tingjun Hou, Jian Zhang
2013 Computer applications in the biosciences : CABIOS  
Allosite is a newly developed automatic tool for the prediction of allosteric sites in proteins of interest and is now available through a web server.  ...  Therefore, the computational prediction of allosteric sites in proteins is receiving increased attention in the field of drug discovery.  ...  For Permissions, please email: journals.permissions@oup.com at Suzhou University on December 23, 2013 http://bioinformatics.oxfordjournals.org/ Downloaded from Allosite: a method for predicting  ... 
doi:10.1093/bioinformatics/btt399 pmid:23842804 fatcat:mw6wu7gn6zfjppo4ds4xwpef3u

A novel allosteric site in casein kinase 2α discovered using combining bioinformatics and biochemistry methods

Hai-ming Jiang, Jiang-kai Dong, Kun Song, Tong-dan Wang, Wen-kang Huang, Jing-miao Zhang, Xiu-yan Yang, Ying Shen, Jian Zhang
2017 Acta Pharmacologica Sinica  
Using Allosite based on protein dynamics and structural alignment, we predicted a new allosteric site that was partly located in the αC helix of CK2α.  ...  In conclusion, we identified a new allosteric site in CK2α that can be altered to modulate the activity of the kinase.  ...  Acknowledgments We sincerely thank Prof Ai-wu ZHOU at the Shanghai Jiao Tong University for help with the protein expression and  ... 
doi:10.1038/aps.2017.55 pmid:28748912 fatcat:lfchlyeqonbrtkg7lsum5ld7ra

Unraveling allosteric landscapes of allosterome with ASD

2019 Nucleic Acids Research  
Allosteric regulation is one of the most direct and efficient ways to fine-tune protein function; it is induced by the binding of a ligand at an allosteric site that is topographically distinct from an  ...  Over the past ten years, the ASD has become a central resource for studying allosteric regulation and will play more important roles in both target identification and allosteric drug discovery in the future  ...  (i) The high-quality allosteric site benchmarking dataset (ASBench) derived from the ASD can be used to develop computational allosteric site prediction methods such as Allosite and AllositePro.  ... 
doi:10.1093/nar/gkz958 pmid:31665428 pmcid:PMC7145546 fatcat:5fmt4tq7rfbinolrvvccvn2vqi

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

Joe G Greener, Michael JE Sternberg
2015 BMC Bioinformatics  
Results: AlloPred, a novel method to predict allosteric pockets on proteins, was developed.  ...  Computational methods to predict allosteric sites on proteins are needed to aid the discovery of allosteric drugs, as well as to advance our fundamental understanding of allostery.  ...  Acknowledgements We would like to thank Dr Suhail Islam for his invaluable help with deploying the web server and Dr Ioannis Filippis for useful discussions.  ... 
doi:10.1186/s12859-015-0771-1 pmid:26493317 pmcid:PMC4619270 fatcat:6uetgviebbggxfh3y2fcy5o44y

Recent computational advances in the identification of allosteric sites in proteins

Shaoyong Lu, Wenkang Huang, Jian Zhang
2014 Drug Discovery Today  
We also discuss the challenges in developing reliable methods for predicting allosteric sites and tactics to resolve demanding tasks. Reviews POST SCREEN  ...  Allosteric modulators have the potential to fine-tune protein functional activity. Therefore, the targeting of allosteric sites, as a strategy in drug design, is gaining increasing attention.  ...  of Higher Learning and the Program for New Century Excellent Talents in University (NCET-12-0355).  ... 
doi:10.1016/j.drudis.2014.07.012 pmid:25107670 fatcat:246n7yf3jbcbbmaglng24veu5a

Ligand-Binding Sites On The Mycobacterium Tuberculosis Urease

Lisnyak, Yu. V.,, A. V. Martynov
2017 Zenodo  
To predict allosteric pockets on MTU, AlloPred and AlloSite servers were applied.  ...  A useful tool for the search of novel inhibitors is a computational drug design. The inhibitor design is significantly easier if binding sites on the enzyme are identified in advance.  ...  Mapping of M. tuberculosis urease surface by AlloPred and AlloSite. AlloPred is a novel method to predict allosteric pockets on proteins [46] which uses the normal mode analysis (NMA) [47] .  ... 
doi:10.5281/zenodo.1000136 fatcat:3ahxcdjbezbt5hzgetmueii77m

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

Sian Xiao, Hao Tian, Peng Tao
2022 Frontiers in Molecular Biosciences  
Here, we define a baseline model for allosteric site prediction and present a computational model using automated machine learning.  ...  Several computational methods have been developed previously to predict allosteric sites using static pocket features and protein dynamics.  ...  CONCLUSION Several machine learning-based methods have been developed for allosteric site prediction over the past few years.  ... 
doi:10.3389/fmolb.2022.879251 pmid:35898310 pmcid:PMC9309527 fatcat:o6bgn6qcwbhozkirvycpxm37ku

Alloscore: a method for predicting allosteric ligand–protein interactions

Shuai Li, Qiancheng Shen, Minyi Su, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Renxiao Wang, Jian Zhang
2016 Bioinformatics  
Herein, we introduce Alloscore, a web server that predicts the binding affinities of allosteric ligand-protein interactions.  ...  This method exhibits prominent performance in describing allosteric binding and could be useful in allosteric virtual screening and the structural optimization of allosteric agonists/antagonists.  ...  Thus, there is a pressing need for the development of a novel method to assess the binding affinities of unique allosteric ligand-protein interactions.  ... 
doi:10.1093/bioinformatics/btw036 pmid:26803160 fatcat:pjonoiqxubdiri7e7huqbknhdy

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

Alejandro Panjkovich, Xavier Daura
2014 Computer applications in the biosciences : CABIOS  
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  ...  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  ...  et al., 2013) , which study the allosteric communication across residues in a protein structure, and Allosite (Huang et al., 2013) , which predicts allosteric sites on protein structures using a machine-learning  ... 
doi:10.1093/bioinformatics/btu002 pmid:24413526 fatcat:uswf4otuu5bnjofb2pf3fy4i5q

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

Zhiwei Feng, Guanxing Hu, Shifan Ma, Xiang-Qun Xie
2015 AAPS Journal  
Discovering allosteric modulators or bitopic ligands for GPCRs has become an emerging research area, in which the design of allosteric modulators is a key step in the detection of bitopic ligands.  ...  This review summarizes the state-of-the-art computational methods for the discovery of modulators and bitopic ligands. The challenges and opportunities for future drug discovery are also discussed.  ...  ACKNOWLEDGMENTS The authors would like to acknowledge the funding support for the Xie laboratory at the University of Pittsburgh from the NIDA P30DA035778A1 and NIH R01DA025612.  ... 
doi:10.1208/s12248-015-9776-y pmid:25940084 pmcid:PMC4540734 fatcat:itsxo47p3rd33jxjx34qnqvhzy

Structure-based prediction of protein allostery

Joe G Greener, Michael JE Sternberg
2018 Current Opinion in Structural Biology  
In order for the benefits of allostery to be taken advantage of, both for basic understanding of proteins and to develop new classes of drugs, the structure-based prediction of allosteric binding sites  ...  Here we review the recently emerging field of allosteric prediction, focusing mainly on computational methods.  ...  This work also includes a quantitative comparison of available allosteric site prediction methods.  ... 
doi:10.1016/j.sbi.2017.10.002 pmid:29080471 fatcat:lxfjcncgyza4lbwofbteux5gna

AlloDriver: a method for the identification and analysis of cancer driver targets

2019 Nucleic Acids Research  
receptor type K (PTPRK) through a L1143F driver mutation located at the allosteric site of PTPRK, which was experimentally validated by cell proliferation assay.  ...  Identifying the variants that alter protein function is a promising strategy for deciphering the biological consequences of somatic mutations during tumorigenesis, which could provide novel targets for  ...  Jinke Cheng at the Shanghai Jiaotong University School of Medicine for fruitful discussions on the allosteric driver mutations.  ... 
doi:10.1093/nar/gkz350 pmid:31069394 pmcid:PMC6602569 fatcat:jvf234kzyfdddodcx22oq2xyyy

Coupling Dynamics and Evolutionary Information with Structure to Identify Protein Regulatory and Functional Binding Sites

Sambit Kumar Mishra, Gaurav Kandoi, Robert L. Jernigan
2019 Proteins: Structure, Function, and Bioinformatics  
Our models for active site prediction yield a median area under the curve (AUC) of 91% and Matthews correlation coefficient (MCC) of 0.68, whereas the less well-defined allosteric sites are predicted at  ...  When tested on an independent set of proteins, our models for active site prediction show comparable performance to two existing methods and gains compared to two others, while the allosteric site models  ...  Our goal is to develop prediction models for active and allosteric site residues using a common subset of features. We are calling our method AR-Pred.  ... 
doi:10.1002/prot.25749 pmid:31141211 pmcid:PMC6718341 fatcat:oc453tatajeclbytuuxil6djqi

Computational Study of SARS-CoV-2 RNA Dependent RNA Polymerase Allosteric Site Inhibition

Shah Faisal, Syed Lal Badshah, Bibi Kubra, Mohamed Sharaf, Abdul-Hamid Emwas, Mariusz Jaremko, Mohnad Abdalla
2021 Molecules  
Despite the availability of vaccines for this disease, new strains are causing rapid ailment and are a continuous threat to vaccine efficacy.  ...  These results provide new information for the design of novel allosteric inhibitors against SARS-CoV-2 RdRp.  ...  After the prediction of the allosteric site by Allosite Pro (2016), the protein PDB file with the predicted site was downloaded and its allosteric site viewed via Pymol Molecular Graphic Visualizer software  ... 
doi:10.3390/molecules27010223 pmid:35011458 pmcid:PMC8746673 fatcat:ljydq4rmefftdfjt5nxqsytcvi

Repurposing ciclopirox as a pharmacological chaperone in a model of congenital erythropoietic porphyria

Pedro Urquiza, Ana Laín, Arantza Sanz-Parra, Jorge Moreno, Ganeko Bernardo-Seisdedos, Pierre Dubus, Esperanza González, Virginia Gutiérrez-de-Juan, Sandra García, Hasier Eraña, Itxaso San Juan, Iratxe Macías (+15 others)
2018 Zenodo  
Ciclopirox targeted the enzyme at an allosteric site distant from the active center and did not affect the enzyme's catalytic role.  ...  Congenital erythropoietic porphyria is a rare autosomal recessive disease produced by deficient activity of uroporphyrinogen III synthase, the fourth enzyme in the heme biosynthetic pathway.  ...  NMR spectroscopy and computational methods were used throughout the screening to identify the protein-binding site (the C-allosite) and to provide mechanistic information.  ... 
doi:10.5281/zenodo.3606661 fatcat:4tieqxpdkvbsfnaltexguy673m
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