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

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Greener, Joe G ^a   Sternberg, Michael JE ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Allostery; Machine learning; Normal modes; Pocket prediction; Web server

Indexed keywords

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL METHODS; FORECASTING; LEARNING SYSTEMS; WEB SERVICES; WORLD WIDE WEB;

ALLOSTERIC PROTEINS; ALLOSTERY; BIOLOGICAL PROCESS; MACHINE LEARNING APPROACHES; NORMAL MODE PERTURBATIONS; NORMAL MODES; UNIVERSAL MECHANISMS; WEB SERVERS;

PROTEINS;

LIGAND; PROTEIN;

ALGORITHM; BINDING SITE; METABOLISM; PROTEIN CONFORMATION;

ALGORITHMS; ALLOSTERIC SITE; LIGANDS; PROTEIN CONFORMATION; PROTEINS;

EID: 84944735748     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0771-1     Document Type: Article

References (34)

1. Nussinov R, Tsai CJ. Allostery in disease and in drug discovery. Cell. 2013; 153:293-305.
2. Gunasekaran K, Ma B, Nussinov R. Is allostery an intrinsic property of all dynamic proteins?Proteins. 2004; 57:433-43.
3. Motlagh HN, Wrabl JO, Li J, Hilser VJ. The ensemble nature of allostery. Nature. 2014; 508:331-9.
4. Nussinov R, Tsai CJ. Unraveling structural mechanisms of allosteric drug action. Trends Pharmacol Sci. 2014; 35(5):256-64.
5. Wenthur CJ, Gentry PR, Mathews TP, Lindsley CW. Drugs for allosteric sites on receptors. Annu Rev Pharmacol. 2014; 54:165-84.
6. Csermely P, Nussinov R, Szilágyi A. From allosteric drugs to allo-network drugs: State of the art and trends of design, synthesis and computational methods. Curr Top Med Chem. 2013; 13(1):2-4.
7. Pei J, Yin N, Ma X, Lai L. Systems biology brings new dimensions for structure-based drug design. J Am Chem Soc. 2014; 136:11556-65.
8. Panjkovich A, Daura X. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery. BMC Struct Biol. 2010; 10(9):1-14.
9. Mitternacht S, Berezovsky IN. Binding leverage as a molecular basis for allosteric regulation. PLoS Comput Biol. 2011; 7(9):1002148.
10. Panjkovich A, Daura X. Exploiting protein flexibility to predict the location of allosteric sites. BMC Bioinf. 2012; 13(273):1-12.
11. Huang W, Lu S, Huang Z, Liu X, Mou L, Luo Y, et al. Allosite: a method for predicting allosteric sites. Bioinformatics. 2013; 29(18):2357-9.
12. Qi Y, Wang Q, Tang B, Luhua L. Identifying allosteric binding sites in proteins with a two-state Gomodel for novel allosteric effector discovery. J Chem Theory Comput. 2012; 8:2962-971.
13. Laine E, Goncalves C, Karst JC, Lesnard A, Rault S, Tang WJ, et al. Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor. P Natl Acad Sci USA. 2010; 107(25):11277-82.
14. Lockless SW, Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 1999; 286:295-9.
15. Demerdash ONA, Daily MD, Mitchell JC. Structure-based predictive models for allosteric hot spots. PLoS Comput Biol. 2009; 5(10):1000531.
16. Balabin IA, Yang W, Beratan DN. Coarse-grained modeling of allosteric regulation in protein receptors. P Natl Acad Sci USA. 2009; 106(34):14253-8.
17. Kidd BA, Baker D, Thomas WE. Computation of conformational coupling in allosteric proteins. PLoS Comput Biol. 2009; 5(8):1000484.
18. Panjkovich A, Daura X. PARS: a web server for the prediction of protein allosteric and regulatory sites. Bioinformatics. 2014; 30(9):1314-5.
19. Kaya C, Armutlulu A, Ekesan S, Haliloglu T. MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues. Nucleic Acids Res. 2013; 41(Web Server issue):249-55.
20. Goncearenco A, Mitternacht S, Yong T, Eisenhaber B, Eisenhaber F, Berezovsky IN. SPACER: server for predicting allosteric communication and effects of regulation. Nucleic Acids Res. 2013; 41(Web Server issue):266-72.
21. Rodgers TL, Townsend PD, Burnell D, Jones ML, Richards SA, McLeish TCB, et al. Modulation of global low-frequency motions underlies allosteric regulation: Demonstration in CRP/FNR family transcription factors. PLoS Biol. 2013; 11(9):1001651.
22. Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophysical J. 2007; 93(7):2289-99.
23. Hayward S, de Groot BL. Normal modes and essential dynamics. Methods Mol Biol. 2008; 443:89-106.
24. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struc Biol. 2005; 15:586-92.
25. Collier G, Ortiz V. Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys. 2013; 538:6-15.
26. Le Guilloux V, Schmidtke P, Tuffery P. Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics. 2009; 10(168):1-11.
27. Huang W, Wang G, Shen Q, Liu X, Lu S, Geng L, et al. ASBench: benchmarking sets for allosteric discovery. Bioinformatics. in press.
28. The UniProt Consortium. Uniprot: a hub for protein information. Nucleic Acids Res. 2015; 43(Database issue):204-12.
29. Furnham N, Holliday GL, de Beer TAP, Jacobsen JOB, Pearson WR, Thornton JM. The catalytic site atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014; 42(Database issue):485-9.
30. Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett. 1996; 77(9):1905-8.
31. Bakan A, Meireles LM, Bahar I. ProDy: Protein dynamics inferred from theory and experiments. Bioinformatics. 2011; 27(11):1575-7.
32. Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using Weka. Bioinformatics. 2004; 20(15):2479-81.
33. Joachims T. Making large-scale svm learning practical. Advances in Kernel Methods - Support Vector Learning. Cambridge, USA: MIT Press; 1998.
34. Wang Q, Zheng M, Huang Z, Liu X, Zhou H, Chen Y, et al. Toward understanding the molecular basis for chemical allosteric modulator design. J Mol Graph Model. 2012; 38:324-33.