Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2009 Oct 1:353–410. doi: 10.1007/978-3-211-75123-7_17

Protein-protein interactions: analysis and prediction

D Frishman 3,4,✉, M Albrecht 5, H Blankenburg 5, P Bork 6,7, E D Harrington 6, H Hermjakob 8, L Juhl Jensen 6,9, D A Juan 10, T Lengauer 5, P Pagel 4, V Schachter 11, A Valencia 10
Editors: Dmitrij Frishman1, Alfonso Valencia2
PMCID: PMC7120725

Abstract

Proteins represent the tools and appliances of the cell — they assemble into larger structural elements, catalyze the biochemical reactions of metabolism, transmit signals, move cargo across membrane boundaries and carry out many other tasks. For most of these functions proteins cannot act in isolation but require close cooperation with other proteins to accomplish their task. Often, this collaborative action implies physical interaction of the proteins involved. Accordingly, experimental detection, in silico prediction and computational analysis of protein-protein interactions (PPI) have attracted great attention in the quest for discovering functional links among proteins and deciphering the complex networks of the cell.

Keywords: Protein Interaction, Protein Interaction Network, Binary Interaction, Domain Pair, Protein Interaction Data

Contributor Information

D. Frishman, Email: d.frishman@wzw.tum.de

M. Albrecht, Email: mario.albrecht@mpi-sb.mpg.de

H. Blankenburg, Email: hagen@mpi-inf.mpg.de

E. D. Harrington, Email: eogham.harrington@embl.de

H. Hermjakob, Email: hhe@ebi.ac.uk

D. A. Juan, Email: dadejuan@cnio.es

T. Lengauer, Email: lengauer@mpi-sb.mpg.de

P. Pagel, Email: p.pagel@wzw.tum.de

V. Schachter, Email: vs@genoscope.cns.fr

A. Valencia, Email: valencia@cnio.es

References

  1. Abagyan R., Totrov M., Kuznetsov D. ICM-a method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comput Chem. 1994;15:488–506. doi: 10.1002/jcc.540150503. [DOI] [Google Scholar]
  2. Aerts S., Lambrechts D., Maity S., Van Loo P., Coessens B., De Smet F., Tranchevent L.C., De Moor B., Marynen P., Hassan B., Carmeliet P., Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006;24:537–544. doi: 10.1038/nbt1203. [DOI] [PubMed] [Google Scholar]
  3. Albert R. Scale-free networks in cell biology. J Cell Sci. 2005;118:4947–4957. doi: 10.1242/jcs.02714. [DOI] [PubMed] [Google Scholar]
  4. Aloy P., Ceulemans H., Stark A., Russell R.B. The relationship between sequence and interaction divergence in proteins. J Mol Biol. 2003;332:989–998. doi: 10.1016/j.jmb.2003.07.006. [DOI] [PubMed] [Google Scholar]
  5. Aloy P., Russell R.B. Ten thousand interactions for the molecular biologist. Nat Biotechnol. 2004;22:1317–1321. doi: 10.1038/nbt1018. [DOI] [PubMed] [Google Scholar]
  6. Aloy P., Russell R.B. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol. 2006;7:188–197. doi: 10.1038/nrm1859. [DOI] [PubMed] [Google Scholar]
  7. Andreeva A., Howorth D., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004;32:D226–D229. doi: 10.1093/nar/gkh039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 2001;310:311–325. doi: 10.1006/jmbi.2001.4776. [DOI] [PubMed] [Google Scholar]
  9. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–29. doi: 10.1038/75556. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Assenov Y., Ramirez F., Schelhorn S.E., Lengauer T., Albrecht M. Computing topological parameters of biological networks. Bioinformatics. 2008;24:282–284. doi: 10.1093/bioinformatics/btm554. [DOI] [PubMed] [Google Scholar]
  11. Bader G.D., Betel D., Hogue C.W. BIND: the Biomolecular interaction network database. Nucleic Acids Res. 2003;31:248–250. doi: 10.1093/nar/gkg056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–113. doi: 10.1038/nrg1272. [DOI] [PubMed] [Google Scholar]
  13. Barker D., Meade A., Pagel M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics. 2007;23:14–20. doi: 10.1093/bioinformatics/btl558. [DOI] [PubMed] [Google Scholar]
  14. Barker D., Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol. 2005;1:e3. doi: 10.1371/journal.pcbi.0010003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Barrios-Rodiles M., Brown K.R., Ozdamar B., Bose R., Liu Z., Donovan R.S., Shinjo F., Liu Y., Dembowy J., Taylor I.W., Luga V., Przulj N., Robinson M., Suzuki H., Hayashizaki Y., Jurisica I., Wrana J.L. High-throughput mapping of a dynamic signaling network in mammalian cells. Science. 2005;307:1621–1625. doi: 10.1126/science.1105776. [DOI] [PubMed] [Google Scholar]
  16. Berman H., Henrick K., Nakamura H., Markley J.L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007;35:D301–D303. doi: 10.1093/nar/gkl971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Bock J.R., Gough D.A. Predicting protein-protein interactions from primary structure. Bioinformatics. 2001;17:455–460. doi: 10.1093/bioinformatics/17.5.455. [DOI] [PubMed] [Google Scholar]
  18. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32:D267–D270. doi: 10.1093/nar/gkh061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Bouwmeester T., Bauch A., Ruffner H., Angrand P.O., Bergamini G., Croughton K., Cruciat C., Eberhard D., Gagneur J., Ghidelli S., Hopf C., Huhse B., Mangano R., Michon A.M., Schirle M., Schlegl J., Schwab M., Stein M.A., Bauer A., Casari G., Drewes G., Gavin A.C., Jackson D.B., Joberty G., Neubauer G., Rick J., Kuster B., Superti-Furga G. A physical and functional map of the human TNF-alpha/ NF-kappa B signal transduction pathway. Nat Cell Biol. 2004;6:97–105. doi: 10.1038/ncb1086. [DOI] [PubMed] [Google Scholar]
  20. Bowers P.M., Cokus S.J., Eisenberg D., Yeates T.O. Use of logic relationships to decipher protein network organization. Science. 2004;306:2246–2249. doi: 10.1126/science.1103330. [DOI] [PubMed] [Google Scholar]
  21. Breitkreutz B.J., Stark C., Tyers M. The GRID: the General Repository for Interaction Datasets. Genome Biol. 2003;4:R23. doi: 10.1186/gb-2003-4-3-r23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Butland G., Peregrin-Alvarez J.M., Li J., Yang W., Yang X., Canadien V., Starostine A., Richards D., Beattie B., Krogan N., Davey M., Parkinson J., Greenblatt J., Emili A. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature. 2005;433:531–537. doi: 10.1038/nature03239. [DOI] [PubMed] [Google Scholar]
  23. Calderwood M.A., Venkatesan K., Xing L., Chase M.R., Vazquez A., Holthaus A.M., Ewence A.E., Li N., Hirozane-Kishikawa T., Hill D.E., Vidal M., Kieff E., Johannsen E. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci USA. 2007;104:7606–7611. doi: 10.1073/pnas.0702332104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Calvano S.E., Xiao W., Richards D.R., Felciano R.M., Baker H.V., Cho R.J., Chen R.O., Brownstein B.H., Cobb J.P., Tschoeke S.K., Miller-Graziano C., Moldawer L.L., Mindrinos M.N., Davis R.W., Tompkins R.G., Lowry S.F. A network-based analysis of systemic inflammation in humans. Nature. 2005;437:1032–1037. doi: 10.1038/nature03985. [DOI] [PubMed] [Google Scholar]
  25. Camargo L.M., Collura V., Rain J.C., Mizuguchi K., Hermjakob H., Kerrien S., Bonnert T.P., Whiting P.J., Brandon N.J. Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia. Mol Psychiatry. 2006;12:74–86. doi: 10.1038/sj.mp.4001880. [DOI] [PubMed] [Google Scholar]
  26. Carlson H.A. Protein flexibility is an important component of structure-based drug discovery. Curr Pharm Des. 2002;8:1571–1578. doi: 10.2174/1381612023394232. [DOI] [PubMed] [Google Scholar]
  27. Chatr-aryamontri A., Ceol A., Palazzi L.M., Nardelli G., Schneider M.V., Castagnoli L., Cesareni G. MINT: the Molecular INTeraction database. Nucleic Acids Res. 2007;35:D572–D574. doi: 10.1093/nar/gkl950. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Chen H., Lyne P.D., Giordanetto F., Lovell T., Li J. On evaluating molecular-docking methods for pose prediction and enrichment factors. J Chem Inf Model. 2006;46:401–415. doi: 10.1021/ci0503255. [DOI] [PubMed] [Google Scholar]
  29. Chen X.W., Liu M. Prediction of protein-protein interactions using random decision forest framework. Bioinformatics. 2005;21:4394–4400. doi: 10.1093/bioinformatics/bti721. [DOI] [PubMed] [Google Scholar]
  30. Chen Y., Dokholyan N.V. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends Genet. 2006;22:416–419. doi: 10.1016/j.tig.2006.06.008. [DOI] [PubMed] [Google Scholar]
  31. Chuang H.Y., Lee E., Liu Y.T., Lee D., Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol. 2007;3:140. doi: 10.1038/msb4100180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Claußen H., Buning C., Rarey M., Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol. 2001;308:377–395. doi: 10.1006/jmbi.2001.4551. [DOI] [PubMed] [Google Scholar]
  33. Cline M.S., Smoot M., Cerami E., Kuchinsky A., Landys N., Workman C., Christmas R., Avila-Campilo I., Creech M., Gross B., Hanspers K., Isserlin R., Kelley R., Killcoyne S., Lotia S., Maere S., Morris J., Ono K., Pavlovic V., Pico A.R., Vailaya A., Wang P.L., Adler A., Conklin B.R., Hood L., Kuiper M., Sander C., Schmulevich I., Schwikowski B., Warner G.J., Ideker T., Bader G.D. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007;2:2366–2382. doi: 10.1038/nprot.2007.324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Colland F., Daviet L. Integrating a functional proteomic approach into the target discovery process. Biochimie. 2004;86:625–632. doi: 10.1016/j.biochi.2004.09.014. [DOI] [PubMed] [Google Scholar]
  35. Colland F., Rain J.C., Gounon P., Labigne A., Legrain P., De Reuse H. Identification of the Helicobacter pylori anti-sigma28 factor. Mol Microbiol. 2001;41:477–487. doi: 10.1046/j.1365-2958.2001.02537.x. [DOI] [PubMed] [Google Scholar]
  36. Cui Q., Ma Y., Jaramillo M., Bari H., Awan A., Yang S., Zhang S., Liu L., Lu M., O’Connor-McCourt M., Purisima E.O., Wang E. A map of human cancer signaling. Mol Syst Biol. 2007;3:152. doi: 10.1038/msb4100200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Cusick M.E., Klitgord N., Vidal M., Hill D.E. Interactome: gateway into systems biology. Hum Mol Genet. 2005;14:R171–R181. doi: 10.1093/hmg/ddi335. [DOI] [PubMed] [Google Scholar]
  38. Dandekar T., Snel B., Huynen M., Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci. 1998;23:324–328. doi: 10.1016/S0968-0004(98)01274-2. [DOI] [PubMed] [Google Scholar]
  39. Date S.V., Marcotte E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol. 2003;21:1055–1062. doi: 10.1038/nbt861. [DOI] [PubMed] [Google Scholar]
  40. Deng M., Mehta S., Sun F., Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Res. 2002;12:1540–1548. doi: 10.1101/gr.153002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Dunker A.K., Cortese M.S., Romero P., Iakoucheva L.M., Uversky V.N. Flexible nets. The roles of intrinsic disorder in protein interaction networks. Febs J. 2005;272:5129–5148. doi: 10.1111/j.1742-4658.2005.04948.x. [DOI] [PubMed] [Google Scholar]
  42. Eddy S.R. Profile hidden Markov models. Bioinformatics. 1998;14:755–763. doi: 10.1093/bioinformatics/14.9.755. [DOI] [PubMed] [Google Scholar]
  43. Englebienne P., Fiaux H., Kuntz D.A., Corbeil C.R., Gerber-Lemaire S., Rose D.R., Moitessier N. Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography. Proteins. 2007;69:160–176. doi: 10.1002/prot.21479. [DOI] [PubMed] [Google Scholar]
  44. Enright A.J., Iliopoulos I., Kyrpides N.C., Ouzounis C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature. 1999;402:86–90. doi: 10.1038/47056. [DOI] [PubMed] [Google Scholar]
  45. Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature. 1989;340:245–246. doi: 10.1038/340245a0. [DOI] [PubMed] [Google Scholar]
  46. Finn R.D., Marshall M., Bateman A. iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics. 2005;21:410–412. doi: 10.1093/bioinformatics/bti011. [DOI] [PubMed] [Google Scholar]
  47. Finn R.D., Mistry J., Schuster-Bockler B., Griffiths-Jones S., Hollich V., Lassmann T., Moxon S., Marshall M., Khanna A., Durbin R., Eddy S.R., Sonnhammer E.L., Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res. 2006;34:D247–D251. doi: 10.1093/nar/gkj149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Fishman M.C., Porter J.A. Pharmaceuticals: a new grammar for drug discovery. Nature. 2005;437:491–493. doi: 10.1038/437491a. [DOI] [PubMed] [Google Scholar]
  49. Flajolet M., Rotondo G., Daviet L., Bergametti F., Inchauspe G., Tiollais P., Transy C., Legrain P. A genomic approach of the hepatitis C virus generates a protein interaction map. Gene. 2000;242:369–379. doi: 10.1016/S0378-1119(99)00511-9. [DOI] [PubMed] [Google Scholar]
  50. Franke L., Bakel H., Fokkens L., de Jong E.D., Egmont-Petersen M., Wijmenga C. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet. 2006;78:1011–1025. doi: 10.1086/504300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., Shenkin P.S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47:1739–1749. doi: 10.1021/jm0306430. [DOI] [PubMed] [Google Scholar]
  52. Fryxell K.J. The coevolution of gene family trees. Trends Genet. 1996;12:364–369. doi: 10.1016/S0168-9525(96)80020-5. [DOI] [PubMed] [Google Scholar]
  53. Gaasterland T., Ragan M.A. Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. Microb Comp Genomics. 1998;3:199–217. doi: 10.1089/omi.1.1998.3.199. [DOI] [PubMed] [Google Scholar]
  54. Gandhi T.K., Zhong J., Mathivanan S., Karthick L., Chandrika K.N., Mohan S.S., Sharma S., Pinkert S., Nagaraju S., Periaswamy B., Mishra G., Nandakumar K., Shen B., Deshpande N., Nayak R., Sarker M., Boeke J.D., Parmigiani G., Schultz J., Bader J.S., Pandey A. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006;38:285–293. doi: 10.1038/ng1747. [DOI] [PubMed] [Google Scholar]
  55. Gavin A.C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., Edelmann A., Heurtier M.A., Hoffman V., Hoefert C., Klein K., Hudak M., Michon A.M., Schelder M., Schirle M., Remor M., Rudi T., Hooper S., Bauer A., Bouwmeester T., Casari G., Drewes G., Neubauer G., Rick J.M., Kuster B., Bork P., Russell R.B., Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature. 2006;440:631–636. doi: 10.1038/nature04532. [DOI] [PubMed] [Google Scholar]
  56. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M., Remor M., Hofert C., Schelder M., Brajenovic M., Ruffner H., Merino A., Klein K., Hudak M., Dickson D., Rudi T., Gnau V., Bauch A., Bastuck S., Huhse B., Leutwein C., Heurtier M.A., Copley R.R., Edelmann A., Querfurth E., Rybin V., Drewes G., Raida M., Bouwmeester T., Bork P., Seraphin B., Kuster B., Neubauer G., Superti-Furga G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 2002;415:141–147. doi: 10.1038/415141a. [DOI] [PubMed] [Google Scholar]
  57. Gerdes S.Y., Scholle M.D., Campbell J.W., Balazsi G., Ravasz E., Daugherty M.D., Somera A.L., Kyrpides N.C., Anderson I., Gelfand M.S., Bhattacharya A., Kapatral V., D’Souza M., Baev M.V., Grechkin Y., Mseeh F., Fonstein M.Y., Overbeek R., Barabasi A.L., Oltvai Z.N., Osterman A.L. Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol. 2003;185:5673–5684. doi: 10.1128/JB.185.19.5673-5684.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Giaever G., Chu A.M., Ni L., Connelly C., Riles L., Veronneau S., Dow S., Lucau-Danila A., Anderson K., Andre B., Arkin A.P., Astromoff A., El-Bakkoury M., Bangham R., Benito R., Brachat S., Campanaro S., Curtiss M., Davis K., Deutschbauer A., Entian K.D., Flaherty P., Foury F., Garfinkel D.J., Gerstein M., Gotte D., Guldener U., Hegemann J.H., Hempel S., Herman Z., Jaramillo D.F., Kelly D.E., Kelly S.L., Kotter P., LaBonte D., Lamb D.C., Lan N., Liang H., Liao H., Liu L., Luo C., Lussier M., Mao R., Menard P., Ooi S.L., Revuelta J.L., Roberts C.J., Rose M., Ross-Macdonald P., Scherens B., Schimmack G., Shafer B., Shoemaker D.D., Sookhai-Mahadeo S., Storms R.K., Strathern J.N., Valle G., Voet M., Volckaert G., Wang C.Y., Ward T.R., Wilhelmy J., Winzeler E.A., Yang Y., Yen G., Youngman E., Yu K., Bussey H., Boeke J.D., Snyder M., Philippsen P., Davis R.W., Johnston M. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002;418:387–391. doi: 10.1038/nature00935. [DOI] [PubMed] [Google Scholar]
  59. Giallourakis C., Henson C., Reich M., Xie X., Mootha V.K. Disease gene discovery through integrative genomics. Annu Rev Genomics Hum Genet. 2005;6:381–406. doi: 10.1146/annurev.genom.6.080604.162234. [DOI] [PubMed] [Google Scholar]
  60. Gillet V.J., Willett P., Bradshaw J. Similarity searching using reduced graphs. J Chem Inf Comput Sci. 2003;43:338–345. doi: 10.1021/ci025592e. [DOI] [PubMed] [Google Scholar]
  61. Giot L. A protein interaction map of Drosophila melanogaster. Science. 2003;302:1727–1736. doi: 10.1126/science.1090289. [DOI] [PubMed] [Google Scholar]
  62. Goehler H., Lalowski M., Stelzl U., Waelter S., Stroedicke M., Worm U., Droege A., Lindenberg K.S., Knoblich M., Haenig C., Herbst M., Suopanki J., Scherzinger E., Abraham C., Bauer B., Hasenbank R., Fritzsche A., Ludewig A.H., Bussow K., Coleman S.H., Gutekunst C.A., Landwehrmeyer B.G., Lehrach H., Wanker E.E. A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington’s disease. Mol Cell. 2004;15:853–865. doi: 10.1016/j.molcel.2004.09.016. [DOI] [PubMed] [Google Scholar]
  63. Goh C.S., Bogan A.A., Joachimiak M., Walther D., Cohen F.E. Co-evolution of proteins with their interaction partners. J Mol Biol. 2000;299:283–293. doi: 10.1006/jmbi.2000.3732. [DOI] [PubMed] [Google Scholar]
  64. Goll J., Uetz P. Analyzing Protein Interaction Networks. In: Lengauer T., editor. Bioinformatics — from genomes to therapies. Weinheim: Wiley-VCH; 2007. pp. 1121–1179. [Google Scholar]
  65. Goh K.I., Cusick M.E., Valle D., Childs B., Vidal M., Barabasi A.L. The human disease network. Proc Natl Acad Sci USA. 2007;104:8685–8690. doi: 10.1073/pnas.0701361104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Graham D.L., Lowe P.N., Grime G.W., Marsh M., Rittinger K., Smerdon S.J., Gamblin S.J., Eccleston J.F. MgF(3)(-) as a transition state analog of phosphoryl transfer. Chem Biol. 2002;9:375–381. doi: 10.1016/S1074-5521(02)00112-6. [DOI] [PubMed] [Google Scholar]
  67. Greene L.H., Lewis T.E., Addou S., Cuff A., Dallman T., Dibley M., Redfern O., Pearl F., Nambudiry R., Reid A., Sillitoe I., Yeats C., Thornton J.M., Orengo C.A. The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 2007;35:D291–D297. doi: 10.1093/nar/gkl959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Guidener U., Munsterkotter M., Oesterheld M., Pagel P., Ruepp A., Mewes H.W., Stumpflen V. MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res. 2006;34:D436–D441. doi: 10.1093/nar/gkj003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Hamosh A., Scott A.F., Amberger J.S., Bocchini C.A., McKusick V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33:D514–D517. doi: 10.1093/nar/gki033. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Han D.S., Kim H.S., Jang W.H., Lee S.D., Suh J.K. PreSPI: a domain combination based prediction system for protein-protein interaction. Nucleic Acids Res. 2004;32:6312–6320. doi: 10.1093/nar/gkh972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C., Richter J., Rubin G.M., Blake J.A., Bult C., Dolan M., Drabkin H., Eppig J.T., Hill D.P., Ni L., Ringwald M., Balakrishnan R., Cherry J.M., Christie K.R., Costanzo M.C., Dwight S.S., Engel S., Fisk D.G., Hirschman J.E., Hong E.L., Nash R.S., Sethuraman A., Theesfeld C.L., Botstein D., Dolinski K., Feierbach B., Berardini T., Mundodi S., Rhee S.Y., Apweiler R., Barrell D., Camon E., Dimmer E., Lee V., Chisholm R., Gaudet P., Kibbe W., Kishore R., Schwarz E.M., Sternberg P., Gwinn M., Hannick L., Wortman J., Berriman M., Wood V., de la Cruz N., Tonellato P., Jaiswal P., Seigfried T., White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004;32:D258–D261. doi: 10.1093/nar/gkh066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  72. Hartwell L.H., Hopfield J.J., Leibler S., Murray A.W. From molecular to modular cell biology. Nature. 1999;402:C47–C52. doi: 10.1038/35011540. [DOI] [PubMed] [Google Scholar]
  73. He X., Zhang J. Why do hubs tend to be essential in protein networks? PLoS Genet. 2006;2:e88. doi: 10.1371/journal.pgen.0020088. [DOI] [PMC free article] [PubMed] [Google Scholar]
  74. Hermjakob H., Montecchi-Palazzi L., Bader G., Wojcik J., Salwinski L., Ceol A., Moore S., Orchard S., Sarkans U., von Mering C., Roechert B., Poux S., Jung E., Mersch H., Kersey P., Lappe M., Li Y., Zeng R., Rana D., Nikolski M., Husi H., Brun C., Shanker K., Grant S.G., Sander C., Bork P., Zhu W., Pandey A., Brazma A., Jacq B., Vidal M., Sherman D., Legrain P., Cesareni G., Xenarios I., Eisenberg D., Steipe B., Hogue C., Apweiler R. The HUPO PSI’s molecular interaction format — a community standard for the representation of protein interaction data. Nat Biotechnol. 2004;22:177–183. doi: 10.1038/nbt926. [DOI] [PubMed] [Google Scholar]
  75. Hildebrandt A., Kohlbacher O., Lenhof H.-P. Modeling protein-protein and protein-DNA docking. In: Lengauer T., editor. Bioinformatics — from genomes to therapies. Weinheim: Wiley-VCH; 2007. pp. 601–650. [Google Scholar]
  76. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K., Yang L., Wolting C., Donaldson I., Schandorff S., Shewnarane J., Vo M., Taggart J., Goudreault M., Muskat B., Alfarano C., Dewar D., Lin Z., Michalickova K., Willems A.R., Sassi H., Nielsen P.A., Rasmussen K.J., Andersen J.R., Johansen L.E., Hansen L.H., Jespersen H., Podtelejnikov A., Nielsen E., Crawford J., Poulsen V., Sorensen B.D., Matthiesen J., Hendrickson R.C., Gleeson F., Pawson T., Moran M.F., Durocher D., Mann M., Hogue C.W., Figeys D., Tyers M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 2002;415:180–183. doi: 10.1038/415180a. [DOI] [PubMed] [Google Scholar]
  77. Hu Z., Mellor J., Wu J., Kanehisa M., Stuart J.M., DeLisi C. Towards zoomable multidimensional maps of the cell. Nat Biotechnol. 2007;25:547–554. doi: 10.1038/nbt1304. [DOI] [PubMed] [Google Scholar]
  78. Hu Z., Mellor J., Wu J., Yamada T., Holloway D., Delisi C. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 2005;33:W352–W357. doi: 10.1093/nar/gki431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. Huang S.Y., Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem. 2006;27:1876–1882. doi: 10.1002/jcc.20505. [DOI] [PubMed] [Google Scholar]
  80. Huynen M.A., Bork P. Measuring genome evolution. Proc Natl Acad Sci USA. 1998;95:5849–5856. doi: 10.1073/pnas.95.11.5849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Itzhaki Z., Akiva E., Altuvia Y., Margalit H. Evolutionary conservation of domain-domain interactions. Genome Biol. 2006;7:R125. doi: 10.1186/gb-2006-7-12-r125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  82. Jansen R., Yu H., Greenbaum D., Kluger Y., Krogan N.J., Chung S., Emili A., Snyder M., Greenblatt J.F., Gerstein M. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003;302:449–453. doi: 10.1126/science.1087361. [DOI] [PubMed] [Google Scholar]
  83. Jeong H., Mason S.P., Barabasi A.L., Oltvai Z.N. Lethality and centrality in protein networks. Nature. 2001;411:41–42. doi: 10.1038/35075138. [DOI] [PubMed] [Google Scholar]
  84. Jones G., Willett P., Glen R.C., Leach A.R., Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997;267:727–748. doi: 10.1006/jmbi.1996.0897. [DOI] [PubMed] [Google Scholar]
  85. Jones R.B., Gordus A., Krall J.A., MacBeath G. A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature. 2006;439:168–174. doi: 10.1038/nature04177. [DOI] [PubMed] [Google Scholar]
  86. Jonsson P.F., Bates P.A. Global topological features of cancer proteins in the human interactome. Bioinformatics. 2006;22:2291–2297. doi: 10.1093/bioinformatics/btl390. [DOI] [PMC free article] [PubMed] [Google Scholar]
  87. Jothi R., Cherukuri P.F., Tasneem A., Przytycka T.M. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol. 2006;362:861–875. doi: 10.1016/j.jmb.2006.07.072. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Juan D., Pazos F., Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proc Natl Acad Sci USA. 2008;105:934–939. doi: 10.1073/pnas.0709671105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Kaltenbach L.S., Romero E., Becklin R.R., Chettier R., Bell R., Phansalkar A., Strand A., Torcassi C., Savage J., Hurlburt A., Cha G.H., Ukani L., Chepanoske C.L., Zhen Y., Sahasrabudhe S., Olson J., Kurschner C., Ellerby L.M., Peltier J.M., Botas J., Hughes R.E. Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS Genet. 2007;3:e82. doi: 10.1371/journal.pgen.0030082. [DOI] [PMC free article] [PubMed] [Google Scholar]
  90. Kämper A., Rognan D., Lengauer T. Lead Identification by virtual screaning. In: Lengauer T., editor. Bioinformatics — from genomes to therapies. Weinheim: Wiley-VCH; 2007. pp. 651–704. [Google Scholar]
  91. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480–D484. doi: 10.1093/nar/gkm882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  92. Kann M.G. Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform. 2007;8:333–346. doi: 10.1093/bib/bbm031. [DOI] [PubMed] [Google Scholar]
  93. Kann M.G., Jothi R., Cherukuri P.F., Przytycka T.M. Predicting protein domain interactions from coevolution of conserved regions. Proteins. 2007;67:811–820. doi: 10.1002/prot.21347. [DOI] [PubMed] [Google Scholar]
  94. Keiser M.J., Roth B.L., Armbruster B.N., Ernsberger P., Irwin J.J., Shoichet B.K. Relating protein pharmacology by ligand chemistry. Nat Biotechnol. 2007;25:197–206. doi: 10.1038/nbt1284. [DOI] [PubMed] [Google Scholar]
  95. Kellenberger E., Rodrigo J., Muller P., Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins. 2004;57:225–242. doi: 10.1002/prot.20149. [DOI] [PubMed] [Google Scholar]
  96. Kerrien S., Alam-Faruque Y., Aranda B., Bancarz I., Bridge A., Derow C., Dimmer E., Feuermann M., Friedrichsen A., Huntley R., Kohler C., Khadake J., Leroy C., Liban A., Lieftink C., Montecchi-Palazzi L., Orchard S., Risse J., Robbe K., Roechert B., Thorneycroft D., Zhang Y., Apweiler R., Hermjakob H. IntAct-open source resource for molecular interaction data. Nucleic Acids Res. 2007;35:D561–D565. doi: 10.1093/nar/gkl958. [DOI] [PMC free article] [PubMed] [Google Scholar]
  97. Kerrien S., Orchard S., Montecchi-Palazzi L., Aranda B., Quinn A.F., Vinod N., Bader G.D., Xenarios I., Wojcik J., Sherman D., Tyers M., Salama J.J., Moore S., Ceol A., Chatr-Aryamontri A., Oesterheld M., Stumpflen V., Salwinski L., Nerothin J., Cerami E., Cusick M.E., Vidal M., Gilson M., Armstrong J., Woollard P., Hogue C., Eisenberg D., Cesareni G., Apweiler R., Hermjakob H. Broadening the Horizon — Level 2.5 of the HUPO-PSI Format for Molecular Interactions. BMC Biol. 2007;5:44. doi: 10.1186/1741-7007-5-44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  98. Kitano H. A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov. 2007;6:202–210. doi: 10.1038/nrd2195. [DOI] [PubMed] [Google Scholar]
  99. Korbel J.O., Doerks T., Jensen L.J., Perez-Iratxeta C., Kaczanowski S., Hooper S.D., Andrade M.A., Bork P. Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol. 2005;3:e134. doi: 10.1371/journal.pbio.0030134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  100. Korbel J.O., Jensen L.J., von Mering C., Bork P. Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol. 2004;22:911–917. doi: 10.1038/nbt988. [DOI] [PubMed] [Google Scholar]
  101. Krämer A., Horn H.W., Rice J.E. Fast 3D molecular superposition and similarity search in databases of flexible molecules. J Comput Aided Mol Des. 2003;17:13–18. doi: 10.1023/A:1024503712135. [DOI] [PubMed] [Google Scholar]
  102. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., Punna T., Peregrin-Alvarez J.M., Shales M., Zhang X., Davey M., Robinson M.D., Paccanaro A., Bray J.E., Sheung A., Beattie B., Richards D.P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M.M., Vlasblom J., Wu S., Orsi C., Collins S.R., Chandran S., Haw R., Rilstone J.J., Gandi K., Thompson N.J., Musso G., St Onge P., Ghanny S., Lam M.H., Butland G., Altaf-Ul A.M., Kanaya S., Shilatifard A., O’Shea E., Weissman J.S., Ingles C.J., Hughes T.R., Parkinson J., Gerstein M., Wodak S.J., Emili A., Greenblatt J.F. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006;440:637–643. doi: 10.1038/nature04670. [DOI] [PubMed] [Google Scholar]
  103. Kuhn M., von Mering C., Campillos M., Jensen L.J., Bork P. STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res. 2008;36:D684–D688. doi: 10.1093/nar/gkm795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  104. LaCount D.J., Vignali M., Chettier R., Phansalkar A., Bell R., Hesselberth J.R., Schoenfeld L.W., Ota I., Sahasrabudhe S., Kurschner C., Fields S., Hughes R.E. A protein interaction network of the malaria parasite Plasmodium falciparum. Nature. 2005;438:103–107. doi: 10.1038/nature04104. [DOI] [PubMed] [Google Scholar]
  105. Lage K., Karlberg E.O., Sterling Z.M., Olason P.I., Pedersen A.G., Rigina O., Hinsby A.M., Tumer Z., Pociot F., Tommerup N., Moreau Y., Brunak S. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol. 2007;25:309–316. doi: 10.1038/nbt1295. [DOI] [PubMed] [Google Scholar]
  106. Legrain P., Selig L. Genome-wide protein interaction maps using two-hybrid systems. FEBS Lett. 2000;480:32–36. doi: 10.1016/S0014-5793(00)01774-9. [DOI] [PubMed] [Google Scholar]
  107. Lemmen C., Lengauer T., Klebe G. FLEXS: a method for fast flexible ligand superposition. J Med Chem. 1998;41:4502–4520. doi: 10.1021/jm981037l. [DOI] [PubMed] [Google Scholar]
  108. Lengauer T., Lemmen C., Rarey M., Zimmermann M. Novel technologies for virtual screening. Drug Discov Today. 2004;9:27–34. doi: 10.1016/S1359-6446(04)02939-3. [DOI] [PubMed] [Google Scholar]
  109. Letunic I., Copley R.R., Pils B., Pinkert S., Schultz J., Bork P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 2006;34:D257–D260. doi: 10.1093/nar/gkj079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  110. Lim J., Hao T., Shaw C., Patel A.J., Szabo G., Rual J.F., Fisk C.J., Li N., Smolyar A., Hill D.E., Barabasi A.L., Vidal M., Zoghbi H.Y. A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell. 2006;125:801–814. doi: 10.1016/j.cell.2006.03.032. [DOI] [PubMed] [Google Scholar]
  111. Lin J., Gan C.M., Zhang X., Jones S., Sjoblom T., Wood L.D., Parsons D.W., Papadopoulos N., Kinzler K.W., Vogelstein B., Parmigiani G., Velculescu V.E. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007;17:1304–1318. doi: 10.1101/gr.6431107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Liu M., Liberzon A., Kong S.W., Lai W.R., Park P.J., Kohane I.S., Kasif S. Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet. 2007;3:e96. doi: 10.1371/journal.pgen.0030096. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. Loscalzo J., Kohane I., Barabasi A.L. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol. 2007;3:124. doi: 10.1038/msb4100163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  114. Lu X., Jain V.V., Finn P.W., Perkins D.L. Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol. 2007;3:98. doi: 10.1038/msb4100138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Marchler-Bauer A., Anderson J.B., Derbyshire M.K., De Weese-Scott C., Gonzales N.R., Gwadz M., Hao L., He S., Hurwitz D.I., Jackson J.D., Ke Z., Krylov D., Lanczycki C.J., Liebert C.A., Liu C., Lu F., Lu S., Marchler G.H., Mullokandov M., Song J.S., Thanki N., Yamashita R.A., Yin J.J., Zhang D., Bryant S.H. CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res. 2007;35:D237–D240. doi: 10.1093/nar/gkl951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  116. Marcotte E.M., Pellegrini M., Ng H.L., Rice D.W., Yeates T.O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 1999;285:751–753. doi: 10.1126/science.285.5428.751. [DOI] [PubMed] [Google Scholar]
  117. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature. 1999;402:83–86. doi: 10.1038/47048. [DOI] [PubMed] [Google Scholar]
  118. Marcotte E.M., Pellegrini M., Thompson M.J., Yeates T.O., Eisenberg D. A combined algorithm for genome-wide prediction of protein function [see comments] Nature. 1999;402:83–86. doi: 10.1038/47048. [DOI] [PubMed] [Google Scholar]
  119. McGann M.R., Almond H.R., Nicholls A., Grant J.A., Brown F.K. Gaussian docking functions. Biopolymers. 2003;68:76–90. doi: 10.1002/bip.10207. [DOI] [PubMed] [Google Scholar]
  120. McGregor M.J., Muskal S.M. Pharmacophore fingerprinting. 1. Application to QSAR and focused library design. J Chem Inf Comput Sci. 1999;39:569–574. doi: 10.1021/ci980159j. [DOI] [PubMed] [Google Scholar]
  121. Mintseris J., Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci USA. 2005;102:10930–10935. doi: 10.1073/pnas.0502667102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  122. Mishra G.R., Suresh M., Kumaran K., Kannabiran N., Suresh S., Bala P., Shivakumar K., Anuradha N., Reddy R., Raghavan T.M., Menon S., Hanumanthu G., Gupta M., Upendran S., Gupta S., Mahesh M., Jacob B., Mathew P., Chatterjee P., Arun K.S., Sharma S., Chandrika K.N., Deshpande N., Palvankar K., Raghavnath R., Krishnakanth R., Karathia H., Rekha B., Nayak R., Vishnupriya G., Kumar H.G., Nagini M., Kumar G.S., Jose R., Deepthi P., Mohan S.S., Gandhi T.K., Harsha H.C., Deshpande K.S., Sarker M., Prasad T.S., Pandey A. Human protein reference database—2006 update. Nucleic Acids Res. 2006;34:D411–D414. doi: 10.1093/nar/gkj141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Morett E., Korbel J.O., Rajan E., Saab-Rincon G., Olvera L., Olvera M., Schmidt S., Snel B., Bork P. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol. 2003;21:790–795. doi: 10.1038/nbt834. [DOI] [PubMed] [Google Scholar]
  124. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Compu Chem. 1998;19:1639–1662. doi: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B. [DOI] [Google Scholar]
  125. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McAnulla C., McDowall J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Sigrist C.J., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C. New developments in the InterPro database. Nucleic Acids Res. 2007;35:D224–D228. doi: 10.1093/nar/gkl841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  126. Neduva V., Linding R., Su-Angrand I., Stark A., de Masi F., Gibson T.J., Lewis J., Serrano L., Russell R.B. Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol. 2005;3:e405. doi: 10.1371/journal.pbio.0030405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  127. Ng S.K., Zhang Z., Tan S.H. Integrative approach for computationally inferring protein domain interactions. Bioinformatics. 2003;19:923–929. doi: 10.1093/bioinformatics/btg118. [DOI] [PubMed] [Google Scholar]
  128. Ng S.K., Zhang Z., Tan S.H., Lin K. InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 2003;31:251–254. doi: 10.1093/nar/gkg079. [DOI] [PMC free article] [PubMed] [Google Scholar]
  129. Nicastro G., Menon R.P., Masino L., Knowles P.P., McDonald N.Q., Pastore A. The solution structure of the Josephin domain of ataxin-3: structural determinants for molecular recognition. Proc Natl Acad Sci USA. 2005;102:10493–10498. doi: 10.1073/pnas.0501732102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  130. Noirot P., Noirot-Gros M.F. Protein interaction networks in bacteria. Curr Opin Microbiol. 2004;7:505–512. doi: 10.1016/j.mib.2004.08.005. [DOI] [PubMed] [Google Scholar]
  131. Nooren I.M., Thornton J.M. Diversity of protein-protein interactions. EMBO J. 2003;22:3486–3492. doi: 10.1093/emboj/cdg359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  132. Oda K., Kitano H. A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol. 2006;2:2006 0015. doi: 10.1038/msb4100057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  133. Oda K., Matsuoka Y., Funahashi A., Kitano H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol. 2005;1:2005 0010. doi: 10.1038/msb4100014. [DOI] [PMC free article] [PubMed] [Google Scholar]
  134. Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H (2007a) Submit Your Interaction Data the IMEx Way: a Step by Step Guide to Trouble-free Deposition. Proteomics: 28–34 [DOI] [PubMed]
  135. Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stumpflen V., Ceol A., Chatraryamontri A., Armstrong J., Woollard P., Salama J.J., Moore S., Wojcik J., Bader G.D., Vidal M., Cusick M.E., Gerstein M., Gavin A.C., Superti-Furga G., Greenblatt J., Bader J., Uetz P., Tyers M., Legrain P., Fields S., Mulder N., Gilson M., Niepmann M., Burgoon L., De Las Rivas J., Prieto C., Perreau V.M., Hogue C., Mewes H.W., Apweiler R., Xenarios I., Eisenberg D., Cesareni G., Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx) Nat Biotechnol. 2007;25:894–898. doi: 10.1038/nbt1324. [DOI] [PubMed] [Google Scholar]
  136. Orengo C.A., Thornton J.M. Protein families and their evolution-a structural perspective. Annu Rev Biochem. 2005;74:867–900. doi: 10.1146/annurev.biochem.74.082803.133029. [DOI] [PubMed] [Google Scholar]
  137. Oti M., Brunner H.G. The modular nature of genetic diseases. Clin Genet. 2007;71:1–11. doi: 10.1111/j.1399-0004.2006.00708.x. [DOI] [PubMed] [Google Scholar]
  138. Overbeek R., Fonstein M., D’Souza M., Pusch G.D., Maltsev N. Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1999;1:93–108. [PubMed] [Google Scholar]
  139. Pacifico S., Liu G., Guest S., Parrish J.R., Fotouhi F., Finley R.L., Jr A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila. BMC Bioinformatics. 2006;7:195. doi: 10.1186/1471-2105-7-195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  140. Pagel P., Kovac S., Oesterheld M., Brauner B., Dunger-Kaltenbach I., Frishman G., Montrone C., Mark P., Stumpflen V., Mewes H.W., Ruepp A., Frishman D. The MIPS mammalian protein-protein interaction database. Bioinformatics. 2005;21:832–834. doi: 10.1093/bioinformatics/bti115. [DOI] [PubMed] [Google Scholar]
  141. Pagel P., Oesterheld M., Tovstukhina O., Strack N., Stumpflen V., Frishman D. DIMA 2.0 predicted and known domain interactions. Nucleic Acids Res. 2007;36:D651–D655. doi: 10.1093/nar/gkm996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  142. Pagel P., Wong P., Frishman D. A domain interaction map based on phylogenetic profiling. J Mol Biol. 2004;344:1331–1346. doi: 10.1016/j.jmb.2004.10.019. [DOI] [PubMed] [Google Scholar]
  143. Pages S., Belaich A., Belaich J.P., Morag E., Lamed R., Shoham Y., Bayer E.A. Species-specificity of the cohesin-dockerin interaction between Clostridium thermocellum and Clostridium cellulolyticum: prediction of specificity determinants of the dockerin domain. Proteins. 1997;29:517–527. doi: 10.1002/(SICI)1097-0134(199712)29:4<517::AID-PROT11>3.0.CO;2-P. [DOI] [PubMed] [Google Scholar]
  144. Paolini G.V., Shapland R.H., van Hoorn W.P., Mason J.S., Hopkins A.L. Global mapping of pharmacological space. Nat Biotechnol. 2006;24:805–815. doi: 10.1038/nbt1228. [DOI] [PubMed] [Google Scholar]
  145. Park J., Lappe M., Teichmann S.A. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. 2001;307:929–938. doi: 10.1006/jmbi.2001.4526. [DOI] [PubMed] [Google Scholar]
  146. Parrish J.R., Yu J., Liu G., Hines J.A., Chan J.E., Mangiola B.A., Zhang H., Pacifico S., Fotouhi F., Dirita V.J., Ideker T., Andrews P., Finley R.L., Jr A proteome-wide protein interaction map for Campylobacter jejuni. Genome Biol. 2007;8:R130. doi: 10.1186/gb-2007-8-7-r130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  147. Pasek S., Bergeron A., Risler J.L., Louis A., Ollivier E., Raffinot M. Identification of genomic features using microsyntenies of domains: domain teams. Genome Res. 2005;15:867–874. doi: 10.1101/gr.3638405. [DOI] [PMC free article] [PubMed] [Google Scholar]
  148. Pawson T., Nash P. Assembly of cell regulatory systems through protein interaction domains. Science. 2003;300:445–452. doi: 10.1126/science.1083653. [DOI] [PubMed] [Google Scholar]
  149. Pazos F., Ranea J.A., Juan D., Sternberg M.J. Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol. 2005;352:1002–1015. doi: 10.1016/j.jmb.2005.07.005. [DOI] [PubMed] [Google Scholar]
  150. Pazos F., Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 2001;14:609–614. doi: 10.1093/protein/14.9.609. [DOI] [PubMed] [Google Scholar]
  151. Pearlman R.S. Rapid generation of high quality approximate 2-dimension molecular structures. Chem Des Auto News. 1987;2:1–6. [Google Scholar]
  152. Pellegrini M., Marcotte E.M., Thompson M.J., Eisenberg D., Yeates T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 1999;96:4285–4288. doi: 10.1073/pnas.96.8.4285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  153. Pujana M.A., Han J.D., Starita L.M., Stevens K.N., Tewari M., Ahn J.S., Rennert G., Moreno V., Kirchhoff T., Gold B., Assmann V., Elshamy W.M., Rual J.F., Levine D., Rozek L.S., Gelman R.S., Gunsalus K.C., Greenberg R.A., Sobhian B., Bertin N., Venkatesan K., Ayivi-Guedehoussou N., Sole X., Hernandez P., Lazaro C., Nathanson K.L., Weber B.L., Cusick M.E., Hill D.E., Offit K., Livingston D.M., Gruber S.B., Parvin J.D., Vidal M. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007;39:1338–1349. doi: 10.1038/ng.2007.2. [DOI] [PubMed] [Google Scholar]
  154. Puntervoll P., Linding R., Gemund C., Chabanis-Davidson S., Mattingsdal M., Cameron S., Martin D.M., Ausiello G., Brannetti B., Costantini A., Ferre F., Maselli V., Via A., Cesareni G., Diella F., Superti-Furga G., Wyrwicz L., Ramu C., McGuigan C., Gudavalli R., Letunic I., Bork P., Rychlewski L., Kuster B., Helmer-Citterich M., Hunter W.N., Aasland R., Gibson T.J. ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. 2003;31:3625–3630. doi: 10.1093/nar/gkg545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  155. Raghavachari B., Tasneem A., Przytycka T.M., Jothi R. DOMINE: a database of protein domain interactions. Nucleic Acids Res. 2008;36:D656–D661. doi: 10.1093/nar/gkm761. [DOI] [PMC free article] [PubMed] [Google Scholar]
  156. Ralser M., Albrecht M., Nonhoff U., Lengauer T., Lehrach H., Krobitsch S. An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol. 2005;346:203–214. doi: 10.1016/j.jmb.2004.11.024. [DOI] [PubMed] [Google Scholar]
  157. Ramírez F., Schlicker A., Assenov Y., Lengauer T., Albrecht M. Computational analysis of human protein interaction networks. Proteomics. 2007;7:2541–2552. doi: 10.1002/pmic.200600924. [DOI] [PubMed] [Google Scholar]
  158. Rarey M., Degen J., Reulecke I. Docking and scoring for structure-based drug design. In: Lengauer T., editor. Bioinformatics — from genomes to therapies. Weinheim: Wiley-VCH; 2007. pp. 541–600. [Google Scholar]
  159. Rarey M., Dixon J.S. Feature trees: a new molecular similarity measure based on tree matching. J Comput Aided Mol Des. 1998;12:471–490. doi: 10.1023/A:1008068904628. [DOI] [PubMed] [Google Scholar]
  160. Rarey M., Kramer B., Lengauer T., Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol. 1996;261:470–489. doi: 10.1006/jmbi.1996.0477. [DOI] [PubMed] [Google Scholar]
  161. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Seraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999;17:1030–1032. doi: 10.1038/13732. [DOI] [PubMed] [Google Scholar]
  162. Riley R., Lee C., Sabatti C., Eisenberg D. Inferring protein domain interactions from databases of interacting proteins. Genome Biol. 2005;6:R89. doi: 10.1186/gb-2005-6-10-r89. [DOI] [PMC free article] [PubMed] [Google Scholar]
  163. Ruepp A., Brauner B., Dunger-Kaltenbach I., Frishman G., Montrone C., Stransky M., Waegele B., Schmidt T., Doudieu O.N., Stumpflen V., Mewes H.W. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2008;36:D646–D650. doi: 10.1093/nar/gkm936. [DOI] [PMC free article] [PubMed] [Google Scholar]
  164. Ruffner H., Bauer A., Bouwmeester T. Human protein-protein interaction networks and the value for drug discovery. Drug Discov Today. 2007;12:709–716. doi: 10.1016/j.drudis.2007.07.011. [DOI] [PubMed] [Google Scholar]
  165. Sadowski J., Gasteiger J., Klebe G. Comparison of automatic three-dimensional models builders using 639 X-ray structures. J Chem Inf Comput Sci. 1994;34:1000–1008. [Google Scholar]
  166. Saito R., Suzuki H., Hayashizaki Y. Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Res. 2002;30:1163–1168. doi: 10.1093/nar/30.5.1163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  167. Salwinski L., Miller C.S., Smith A.J., Pettit F.K., Bowie J.U., Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004;32:D449–D451. doi: 10.1093/nar/gkh086. [DOI] [PMC free article] [PubMed] [Google Scholar]
  168. Santonico E., Castagnoli L., Cesareni G. Methods to reveal domain networks. Drug Discov Today. 2005;10:1111–1117. doi: 10.1016/S1359-6446(05)03513-0. [DOI] [PubMed] [Google Scholar]
  169. Sato T., Yamanishi Y., Horimoto K., Kanehisa M., Toh H. Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics. 2006;22:2488–2492. doi: 10.1093/bioinformatics/btl419. [DOI] [PubMed] [Google Scholar]
  170. Sato T., Yamanishi Y., Kanehisa M., Toh H. The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics. 2005;21:3482–3489. doi: 10.1093/bioinformatics/bti564. [DOI] [PubMed] [Google Scholar]
  171. Schlicker A., Huthmacher C., Ramirez F., Lengauer T., Albrecht M. Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics. 2007;23:859–865. doi: 10.1093/bioinformatics/btm012. [DOI] [PubMed] [Google Scholar]
  172. Schuster-Bockler B., Bateman A. Reuse of structural domain-domain interactions in protein networks. BMC Bioinformatics. 2007;8:259. doi: 10.1186/1471-2105-8-259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  173. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–2504. doi: 10.1101/gr.1239303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  174. Sharan R., Suthram S., Kelley R.M., Kuhn T., McCuine S., Uetz P., Sittler T., Karp R.M., Ideker T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA. 2005;102:1974–1979. doi: 10.1073/pnas.0409522102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  175. Sharan R., Ulitsky I., Shamir R. Network-based prediction of protein function. Mol Syst Biol. 2007;3:88. doi: 10.1038/msb4100129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  176. Sherman W., Day T., Jacobson M.P., Friesner R.A., Farid R. Novel procedure for modeling ligand/ receptor induced fit effects. J Med Chem. 2006;49:534–553. doi: 10.1021/jm050540c. [DOI] [PubMed] [Google Scholar]
  177. Snel B., Huynen M.A. Quantifying modularity in the evolution of biomolecular systems. Genome Res. 2004;14:391–397. doi: 10.1101/gr.1969504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  178. Sousa S.F., Fernandes P.A., Ramos M.J. Protein-ligand docking: Current status and future challenges. Proteins. 2006;65:15–26. doi: 10.1002/prot.21082. [DOI] [PubMed] [Google Scholar]
  179. Spirin V., Mirny L.A. Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA. 2003;100:12123–12128. doi: 10.1073/pnas.2032324100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  180. Sprinzak E., Margalit H. Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol. 2001;311:681–692. doi: 10.1006/jmbi.2001.4920. [DOI] [PubMed] [Google Scholar]
  181. Stark C., Breitkreutz B.J., Reguly T., Boucher L., Breitkreutz A., Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006;34:D535–D539. doi: 10.1093/nar/gkj109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  182. Stein A., Russell R.B., Aloy P. 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res. 2005;33:D413–D417. doi: 10.1093/nar/gki037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  183. Stelzl U., Wanker E.E. The value of high quality protein-protein interaction networks for systems biology. Curr Opin Chem Biol. 2006;10:551–558. doi: 10.1016/j.cbpa.2006.10.005. [DOI] [PubMed] [Google Scholar]
  184. Suderman M., Hallett M. Tools for visually exploring biological networks. Bioinformatics. 2007;23:2651–2659. doi: 10.1093/bioinformatics/btm401. [DOI] [PubMed] [Google Scholar]
  185. Tewari M., Hu P.J., Ahn J.S., Ayivi-Guedehoussou N., Vidalain P.O., Li S., Milstein S., Armstrong C.M., Boxem M., Butler M.D., Busiguina S., Rual J.F., Ibarrola N., Chaklos S.T., Bertin N., Vaglio P., Edgley M.L., King K.V., Albert P.S., Vandenhaute J., Pandey A., Riddle D.L., Ruvkun G., Vidal M. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-β signaling network. Mol Cell. 2004;13:469–482. doi: 10.1016/S1097-2765(04)00033-4. [DOI] [PubMed] [Google Scholar]
  186. Uetz P. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 2000;403:623–627. doi: 10.1038/35001009. [DOI] [PubMed] [Google Scholar]
  187. Uetz P., Dong Y.A., Zeretzke C., Atzler C., Baiker A., Berger B., Rajagopala S.V., Roupelieva M., Rose D., Fossum E., Haas J. Herpesviral protein networks and their interaction with the human proteome. Science. 2006;311:239–242. doi: 10.1126/science.1116804. [DOI] [PubMed] [Google Scholar]
  188. Uetz P., Rajagopala S.V., Dong Y.A., Haas J. From ORFeomes to protein interaction maps in viruses. Genome Res. 2004;14:2029–2033. doi: 10.1101/gr.2583304. [DOI] [PubMed] [Google Scholar]
  189. Vastrik I., D’Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., Matthews L., Wu G., Birney E., Stein L. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007;8:R39. doi: 10.1186/gb-2007-8-3-r39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  190. Vogel C., Bashton M., Kerrison N.D., Chothia C., Teichmann S.A. Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol. 2004;14:208–216. doi: 10.1016/j.sbi.2004.03.011. [DOI] [PubMed] [Google Scholar]
  191. von Brunn A., Teepe C., Simpson J.C., Pepperkok R., Friedel C.C., Zimmer R., Roberts R., Baric R., Haas J. Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS ONE. 2007;2:e459. doi: 10.1371/journal.pone.0000459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  192. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Kruger B., Snel B., Bork P. STRING 7 — recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007;35:D358–D362. doi: 10.1093/nar/gkl825. [DOI] [PMC free article] [PubMed] [Google Scholar]
  193. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002;417:399–403. doi: 10.1038/nature750. [DOI] [PubMed] [Google Scholar]
  194. Wang H., Segal E., Ben-Hur A., Li Q.R., Vidal M., Koller D. InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol. 2007;8:R192. doi: 10.1186/gb-2007-8-9-r192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  195. Wang R., Lu Y., Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J Med Chem. 2003;46:2287–2303. doi: 10.1021/jm0203783. [DOI] [PubMed] [Google Scholar]
  196. Wang R.S., Wang Y., Wu L.Y., Zhang X.S., Chen L. Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformatics. 2007;8:391. doi: 10.1186/1471-2105-8-391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  197. Weininger D. SMILES, a chemical language and information system. 1. Introduction and encoding rules. J Chem Inf Comput Sci. 1988;28:31–36. [Google Scholar]
  198. Wells J.A., McClendon C.L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature. 2007;450:1001–1009. doi: 10.1038/nature06526. [DOI] [PubMed] [Google Scholar]
  199. Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., Church D.M., DiCuccio M., Edgar R., Federhen S., Geer L.Y., Kapustin Y., Khovayko O., Landsman D., Lipman D.J., Madden T.L., Maglott D.R., Ostell J., Miller V., Pruitt K.D., Schuler G.D., Sequeira E., Sherry S.T., Sirotkin K., Souvorov A., Starchenko G., Tatusov R.L., Tatusova T.A., Wagner L., Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2007;35:D5–D12. doi: 10.1093/nar/gkl1031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  200. Winzeler E.A., Shoemaker D.D., Astromoff A., Liang H., Anderson K., Andre B., Bangham R., Benito R., Boeke J.D., Bussey H., Chu A.M., Connelly C., Davis K., Dietrich F., Dow S.W., El Bakkoury M., Foury F., Friend S.H., Gentalen E., Giaever G., Hegemann J.H., Jones T., Laub M., Liao H., Liebundguth N., Lockhart D.J., Lucau-Danila A., Lussier M., M’Rabet N., Menard P., Mittmann M., Pai C., Rebischung C., Revuelta J.L., Riles L., Roberts C.J., Ross-MacDonald P., Scherens B., Snyder M., Sookhai-Mahadeo S., Storms R.K., Veronneau S., Voet M., Volckaert G., Ward T.R., Wysocki R., Yen G.S., Yu K., Zimmermann K., Philippsen P., Johnston M., Davis R.W. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999;285:901–906. doi: 10.1126/science.285.5429.901. [DOI] [PubMed] [Google Scholar]
  201. Wojcik J., Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics. 2001;17(Suppl 1):S296–S305. doi: 10.1093/bioinformatics/17.suppl_1.s296. [DOI] [PubMed] [Google Scholar]
  202. Xia Y., Yu H., Jansen R., Seringhaus M., Baxter S., Greenbaum D., Zhao H., Gerstein M. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem. 2004;73:1051–1087. doi: 10.1146/annurev.biochem.73.011303.073950. [DOI] [PubMed] [Google Scholar]
  203. Xu J., Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics. 2006;22:2800–2805. doi: 10.1093/bioinformatics/btl467. [DOI] [PubMed] [Google Scholar]
  204. Xue H., Xian B., Dong D., Xia K., Zhu S., Zhang Z., Hou L., Zhang Q., Zhang Y., Han J.D. A modular network model of aging. Mol Syst Biol. 2007;3:147. doi: 10.1038/msb4100189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  205. Xue L., Godden J.W., Bajorath J. Evaluation of descriptors and mini-fingerprints for the identification of molecules with similar activity. J Chem Inf Comput Sci. 2000;40:1227–1234. doi: 10.1021/ci000327j. [DOI] [PubMed] [Google Scholar]
  206. Yaffe M.B. “Bits” and pieces. Sci STKE. 2006;2006:pe28. doi: 10.1126/stke.3402006pe28. [DOI] [PubMed] [Google Scholar]
  207. Yildirim M.A., Goh K.I., Cusick M.E., Barabasi A.L., Vidal M. Drug-target network. Nat Biotechnol. 2007;25:1119–1126. doi: 10.1038/nbt1338. [DOI] [PubMed] [Google Scholar]
  208. Yook S.H., Oltvai Z.N., Barabasi A.L. Functional and topological characterization of protein interaction networks. Proteomics. 2004;4:928–942. doi: 10.1002/pmic.200300636. [DOI] [PubMed] [Google Scholar]
  209. Yu H., Kim P.M., Sprecher E., Trifonov V., Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol. 2007;3:e59. doi: 10.1371/journal.pcbi.0030059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  210. Zarrinpar A., Bhattacharyya R.P., Lim W.A. The structure and function of proline recognition domains. Sci STKE. 2003;2003:RE8. doi: 10.1126/stke.2003.179.re8. [DOI] [PubMed] [Google Scholar]

Articles from Modern Genome Annotation are provided here courtesy of Nature Publishing Group

RESOURCES