Analyzing and visualizing residue networks of protein structures

Trends in Biochemical Sciences

Volumn 36, Issue 4, 2011, Pages 179-182

  Doncheva, Nadezhda T ^a   Klein, Karsten ^b   Domingues, Francisco S ^a,c   Albrecht, Mario ^a  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b TU DORTMUND UNIVERSITY   (Germany)

^c INSTITUTE FOR RENEWABLE ENERGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

COMPUTER PROGRAM; GENETIC CONSERVATION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SHORT SURVEY;

HUMANS; MODELS, MOLECULAR; PROTEINS; SOFTWARE DESIGN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 79954415213     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2011.01.002     Document Type: Short Survey

References (25)

1. O'Donoghue S.I., et al. Visualization of macromolecular structures. Nat. Methods 2010, 7:42-55.
2. Morris J.H., et al. Computational tools for the interactive exploration of proteomic and structural data. Mol. Cell. Proteomics 2010, 9:1703-1715.
3. Csermely P. Creative elements: network-based predictions of active centres in proteins and cellular and social networks. Trends Biochem. Sci. 2008, 33:569-576.
4. Vishveshwara S., et al. Intra and inter-molecular communications through protein structure network. Curr. Protein Pept. Sci. 2009, 10:146-160.
5. Vendruscolo M., et al. Three key residues form a critical contact network in a protein folding transition state. Nature 2001, 409:641-645.
6. Krishnan A., et al. Proteins as networks: usefulness of graph theory in protein science. Curr. Protein Pept. Sci. 2008, 9:28-38.
7. Swint-Kruse L. Using networks to identify fine structural differences between functionally distinct protein states. Biochemistry 2004, 43:10886-10895.
8. Swint-Kruse L., et al. Resmap: automated representation of macromolecular interfaces as two-dimensional networks. Bioinformatics 2005, 21:3327-3328.
9. Amitai G., et al. Network analysis of protein structures identifies functional residues. J. Mol. Biol. 2004, 344:1135-1146.
10. Süel G.M., et al. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 2003, 10:59-69.
11. del Sol A., et al. Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol. Syst. Biol. 2006, 2:0019.
12. Reichmann D., et al. The molecular architecture of protein-protein binding sites. Curr. Opin. Struct. Biol. 2007, 17:67-76.
13. Sathyapriya R., et al. Insights into protein-DNA interactions through structure network analysis. PLoS Comput. Biol. 2008, 4:e1000170.
14. Cheng T.M., et al. Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PLoS Comput. Biol. 2008, 4:e1000135.
15. Welsch C., et al. Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus. Genome Biol. 2008, 9:R16.
16. Susser P., et al. Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients. Hepatology 2009, 50:1709-1718.
17. Prongay A.J., et al. Discovery of the HCV NS3/4A protease inhibitor (1R,5S)-N-[3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl]-3-[2(S)-[[[(1,1-dimethylethyl)amino]carbonyl]amino]-3,3-dimethyl-1-oxobutyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-2(S)-carboxamide (Sch 503034) II. Key steps in structure-based optimization. J. Med. Chem. 2007, 50:2310-2318.
18. Zhou P., et al. 2D molecular graphics: a flattened world of chemistry and biology. Brief. Bioinform. 2009, 10:247-258.
19. Shannon P., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
20. Morris J.H., et al. structureViz: linking Cytoscape and UCSF Chimera. Bioinformatics 2007, 23:2345-2347.
21. Pettersen E.F., et al. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
22. Zhou Y., et al. Phenotypic characterization of resistant Val36 variants of hepatitis C virus NS3-4A serine protease. Antimicrob. Agents Chemother. 2008, 52:110-120.
23. Yoon S.I., et al. Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain. Structure 2005, 13:551-564.
24. Jones B.C., et al. Crystal structure of human cytomegalovirus IL-10 bound to soluble human IL-10R1. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:9404-9409.
25. Word J.M., et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J. Mol. Biol. 1999, 285:1711-1733.