Network view: 3D display and analysis of protein ·rNA interaction networks

Bioinformatics

Volumn 28, Issue 22, 2012, Pages 3000-3001

  Eargle, John ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; RNA BINDING PROTEIN;

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

MOLECULAR DYNAMICS SIMULATION; RNA; RNA-BINDING PROTEINS; SOFTWARE;

EID: 84869418186     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts546     Document Type: Article

References (14)

1. Alexander, R.W. et al. (2010) Experimental and computational determination of tRNA dynamics. FEBS Lett., 584, 376-386.
2. Bhattacharyya, M. and Vishveshwara, S. (2011) Probing the allosteric mechanism in pyrrolysyl-tRNA synthetase using energy-weighted network formalism. Biochemistry, 50, 6225-6236.
3. Black Pyrkosz, A. et al. (2010) Exit strategies for charged tRNA from GluRS. J. Mol. Biol., 397, 1350-1371.
4. Csermely, P. et al. (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem. Sci., 35, 539-546.
5. Daily et al. (2008) Contact rearrangements form coupled networks from local motions in allosteric proteins. Prot. Struct. Func. Bioinf., 71, 455-466. (Pubitemid 351358624)
6. Doncheva, N. et al. (2011) Analyzing and visualizing residue networks of protein structures. Trends Biochem. Sci., 36, 179-182.
7. Girvan, M. and Newman, M. (2002) Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA, 99, 7821-7826. (Pubitemid 34650963)
8. Glykos, N.M. (2006) Software news and updates. CARMA: a molecular dynamics analysis program. J. Comp. Chem., 27, 1765-1768. (Pubitemid 44476671)
9. Humphrey, W. et al. (1996) VMD-visual molecular dynamics. J. Mol. Graphics, 14, 33-38.
10. Rahat, O. et al. (2009) Understanding hydrogen-bond patterns in proteins using network motifs. Bioinformatics, 25, 2921-2928.
11. Roberts, E. et al. (2006) MultiSeq: unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics, 7, 382.
12. Sethi, A. et al. (2009) Dynamical networks in tRNA: protein complexes. Proc. Natl. Acad. Sci. USA, 106, 6620-6625.
13. Süel, G. et al. (2002) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Mol. Biol., 10, 59-69. (Pubitemid 36034178)
14. Trabuco, L.G. et al. (2010) The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J. Mol. Biol., 402, 741-760.