Multistructural hot spot characterization with FTProd

Bioinformatics

Volumn 29, Issue 3, 2013, Pages 393-394

  Votapka, Lane ^a   Amaro, Rommie E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; COMPUTER PROGRAM; METABOLISM; MOLECULAR DYNAMICS;

BINDING SITES; MOLECULAR DYNAMICS SIMULATION; PROTEINS; SOFTWARE;

MLCS; MLOWN;

EID: 84873295761     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts689     Document Type: Article

References (14)

1. Allen, K.N. et al. (1996) An experimental approach to mapping the binding surfaces of crystalline proteins. J. Phys. Chem., 100, 2605-2611. (Pubitemid 126793213)
2. Amaro, R.E. et al. (2011) Mechanism of 150-cavity formation in influenza neuraminidase. Nat. Commun., 2, 388.
3. Brenke, R. et al. (2009) Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics, 25, 621-627.
4. Hajduk, P.J. et al. (2005) Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem., 48, 2518-2525. (Pubitemid 40516441)
5. Humphrey, W. et al. (1996) VMD: visual molecular dynamics. J. Mol. Graph. Model, 14, 33-38. (Pubitemid 26152973)
6. Landon, M.R. et al. (2008) Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem. Biol. Drug Des., 71, 106-116. (Pubitemid 351160979)
7. Li, Q. et al. (2010) The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nat. Struct. Mol. Biol., 17, 1266-1268.
8. Mattos, C. and Ringe, D. (1996) Locating and characterizing binding sites on proteins. Nat. Biotechnol., 14, 595-599. (Pubitemid 26135122)
9. Morrow, J.K. and Zhang, S.X. (2012) Computational prediction of protein hot spot residues. Curr. Pharma. Des., 18, 1255-1265.
10. Russell, R.J. et al. (2006) The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature, 443, 45-49. (Pubitemid 44344043)
11. Sperandio, O. et al. (2008) Screening outside the catalytic site: inhibition of macromolecular inter-actions through structure-based virtual ligand screening experiments. Open Biochem. J., 2, 29-37.
12. Vajda, S. and Guarnieri, F. (2006) Characterization of protein-ligand interaction sites using experimental and computational methods. Curr. Opin. Drug Discov. Dev., 9, 354-362. (Pubitemid 43774164)
13. Varghese, J.N. et al. (1997) Structural evidence for a second sialic acid binding site in avian influenza virus neuraminidases. Proc. Natl Acad. Sci. USA, 94, 11808-11812. (Pubitemid 27467799)
14. Votapka, L. et al. (2012) Variable ligand-and receptor-binding hot spots in key strains of influenza neuraminidase. J. Mol. Genet. Med., 6, 293-300.