The Jena Protein-Protein Interaction Website (PPI) : Selected Publications

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Selected Publications

2002

Aloy, P.; Russell, R.B.; Proc. Natl. Acad. Sci. USA 2002, 99(9), 5896-5901. Interrogating protein interaction networks through structural biology. [PDF I PubMed]
Aloy, P.; Russell, R.B.; FEBS Lett. 2002, 530(1-3), 253. Potential artefacts in protein-interaction networks. [PDF I PubMed]
Anantharaman, V.; Aravind, L.; Genome Biol. 2002, 3(5), research0023. The GOLD domain, a novel protein module involved in Golgi function and secretion. [PDF I PubMed]
Arai, R.; Nakagawa, H.; Kitayama, A.; Ueda, H.; Nagamune, T.; J. Biosci. Bioeng. 2002, 94(4), 362-364. Detection of protein-protein interaction by bioluminescence resonance energy transfer from firefly luciferase to red fluorescent protein. [PubMed]
Aravind, L.; Iyer, L.M.; Genome Res. 2002, 12(8), 1156-1158. Intraproteomic networks: new forays into predicting interaction partners. [PDF I PubMed]
Aronson, M.N.; Complainville, A.; Clerot, D.; Alcalde, H.; Katul, L.; Vetten, H.J.; Gronenborn, B.; Timchenko, T.; Plant J. 2002, 31(6), 767-775. In planta protein-protein interactions assessed using a nanovirus-based replication and expression system. [PDF I PubMed]
Auerbach, D.; Galeuchet-Schenk, B.; Hottiger, M.O.; Stagljar, I.; J. Recept. Signal Transduct. Res. 2002, 22(1-4), 471-481. Genetic approaches to the identification of interactions between membrane proteins in yeast. [PDF I PubMed]
Auerbach, D.; Thaminy, S.; Hottiger, M.O.; Stagljar, I.; Proteomics 2002, 2(6), 611-623. The post-genomic era of interactive proteomics: facts and perspectives. [PDF I PubMed]

Bader, G.D.; Hogue, C.W.; Nat. Biotechnol. 2002, 20(10), 991-997. Analyzing yeast protein-protein interaction data obtained from different sources. [PDF I PubMed]
Behre, G.; Reddy, V.A.; Tenen, D.G.; Hiddemann, W.; Zada, A.A.; Singh, S.M.; Expert Opin. Ther. Targets 2002, 6(4), 491-495. Proteomic analysis of transcription factor interactions in myeloid stem cell development and leukaemia. [PDF I PubMed]
Bilu, Y.; Linial, M.; J. Comput. Biol. 2002, 9(2), 193-210. The advantage of functional prediction based on clustering of yeast genes and its correlation with non-sequence based classifications. [PDF I PubMed]
Biran, I.; Walt, D.R.; Anal. Chem. 2002, 74(13), 3046-3054. Optical imaging fiber-based single live cell arrays: a high-density cell assay platform. [PDF I PubMed]
Blaschke, C.; Hirschman, L.; Valencia, A.; Brief Bioinform. 2002, 3(2), 154-165. Information extraction in molecular biology. [PDF I PubMed]
Bock, J.R.; Gough, D.A.; Mol. Cell Proteomics 2002, 1(11), 904-910. A new method to estimate ligand-receptor energetics. [PDF I PubMed]
Bogdanove, A.J.; Plant Mol. Biol. 2002, 50(6), 981-989. Protein-protein interactions in pathogen recognition by plants. [PDF I PubMed]
Bork, P.; Bioinformatics 2002, 18(Suppl. 2), S64. Comparative analysis of protein interaction networks. [PDF I PubMed]
Boulton, S.J.; Gartner, A.; Reboul, J.; Vaglio, P.; Dyson, N.; Hill, D.E.; Vidal, M.; Science 2002, 295(5552), 127-131. Combined functional genomic maps of the C. elegans DNA damage response. [PDF I PubMed]
Boute, N.; Jockers, R.; Issad, T.; Trends Pharmacol. Sci. 2002, 23(8), 351. The use of resonance energy transfer in high-throughput screening: BRET versus FRET. [PDF I PubMed]
Breitkreutz, B.J.; Stark, C.; Tyers, M.; Genome Biol. 2002, 3(12), preprint0013.1-0013.5. The GRID: the general repository for interaction datasets. [PDF I PubMed]
Brock, A.; Huang, S.; Trends Biotechnol. 2002, 20(4), 145. A novel trap for dynamic protein interactions in cytokine signaling. [PDF I PubMed]
Brooijmans, N.; Sharp, K.A.; Kuntz, I.D.; Proteins 2002, 48(4), 645-653. Stability of macromolecular complexes. [PDF I PubMed]
Brosh, R.M.; Bohr, V.A.; Exp. Gerontol. 2002, 37(4), 491-506. Roles of the Werner syndrome protein in pathways required for maintenance of genome stability. [PDF I PubMed]
Burbaum, J.; Tobal, G.M.; Curr. Opin. Chem. Biol. 2002, 6(4), 427-433. Proteomics in drug discovery. [PDF I PubMed]
Burbelo, P.D.; Kisailus, A.E.; Peck, J.W.; BioTechniques 2002, 33(5), 1044-1048, 1050. Detecting protein-protein interactions using Renilla luciferase fusion proteins. [PubMed]

Camacho, C.J.; Vadja, S.; Curr. Opin. Struct. Biol. 2002, 12(1), 36-40. Protein-protein association kinetics and protein docking. [PDF I PubMed]
Causier, B.; Davies, B.; Plant Mol. Biol. 2002, 50(6), 855-870. Analysing protein-protein interactions with the yeast two-hybrid system. [PDF I PubMed]
Cesareni, G.; Panni, S.; Nardelli, G.; Castagnoli, L.; FEBS Lett. 2002, 513(1), 38-44. Can we infer peptide recognition specificity mediated by SH3 domains? [PDF I PubMed]
Chakrabarti, P.; Janin, J.; Proteins 2002, 47(3), 334-343. Dissecting protein-protein recognition sites. [PDF I PubMed]
Chakravarti, D.N.; BioTechniques 2002, 32, S2-S3. From the decline and fall of protein chemistry to proteomics. [PDF I PubMed]
Chen, R.; Weng, Z.; Proteins 2002, 47(3), 281-294. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. [PDF I PubMed]
Cole, C.; Warwicker, J.; Protein Sci. 2002, 11(12), 2860-2870. Side-chain conformational entropy at protein-protein interfaces. [PDF I PubMed]
Contreras-Moreira, B.; Fitzjohn, P.W.; Bates, P.A.; Appl. Bioinformatics 2002, 1(4), 177-190. Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era. [PubMed]
Copley, R.R.; Doerks, T.; Letunic, I.; Bork, P.; FEBS Lett. 2002, 513(1), 129-134. Protein domain analysis in the era of complete genomes. [PDF I PubMed]
Costenaro, L.; Ebel, C.; Acta Crystallogr. D Biol. Crystallogr. 2002, 58(Pt. 10, Pt. 1), 1554-1559. Thermodynamic relationships between protein-solvent and protein-protein interactions. [PDF I PubMed]
Costenaro, L.; Zaccai, G.; Ebel, C.; Biochemistry 2002, 41(44), 13245-13252. Link between protein-solvent and weak protein-protein interactions gives insight into halophilic adaptation. [PDF I PubMed]
Curtis, R.A.; Steinbrecher, C.; Heinemann, M.; Blanch, H.W.; Prausnitz, J.M.; Biophys. Chem. 2002, 98(3), 249-265. Hydrophobic forces between protein molecules in aqueous solutions of concentrated electrolyte. [PDF I PubMed]
Curtis, R.A.; Ulrich, J.; Montaser, A.; Prausnitz, J.M.; Blanch, H.W.; Biotechnol. Bioeng. 2002, 79(4), 367-380. Protein-protein interactions in concentrated electrolyte solutions. [PDF I PubMed]

Deane, C.M.; Salwinski, L.; Xenarios, I.; Eisenberg, D.; Mol. Cell Proteomics 2002, 1(5), 349-356. Protein interactions: two methods for assessment of the reliability of high throughput observations. [PDF I PubMed]
De Francesco, L.; The Scientist 2002, 16(8), 28. Probing protein interactions. [HTML]
De Genst, E.; Areskoug, D.; Decanniere, K.; Muyldermans, S.; Andersson, K.; J. Biol. Chem. 2002, 277(33), 29897-29907. Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design. [PDF I PubMed]
DeLano, W.L.; Curr. Opin. Struct. Biol. 2002, 12(1), 14-20. Unraveling hot spots in binding interfaces: progress and challenges. [PDF I PubMed]
Del Carpio-Munoz, C.A.; Ichiishi, E.; Yoshimori, A.; Yoshikawa, T.; Proteins 2002, 48(4), 696-732. MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases. [PDF I PubMed]
Deng, M.; Mehta, S.; Sun, F.; Chen, T.; Genome Res. 2002, 12(10), 1540-1548. Inferring domain-domain interactions from protein-protein interactions. [PDF I PubMed]
Deng, M.; Zhang, K.; Mehta, S.; Chen, T.; Sun, F.; Proc. IEEE Comput. Soc. Bioinform. Conf. 2002, 1, 197-206. Prediction of protein function using protein-protein interaction data. [PDF I PubMed]
Deshaies, R.J.; Seol, J.H.; McDonald, W.H.; Cope, G.; Lyapina, S.; Shevchenko, A.; Shevchenko, A.; Verma, R.; Yates, J.R.; Mol. Cell Proteomics 2002, 1(1), 3-10. Charting the protein complexome in yeast by mass spectrometry. [PDF I PubMed]
Dietmann, S.; Frömmel, C.; Bioinformatics 2002, 18(1), 167-174. Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks. [PDF I PubMed]
Doerks, T.; Copley, R.R.; Schultz, J.; Ponting, C.P.; Bork, P.; Genome Res. 2002, 12(1), 47-56. Systematic identification of novel protein domain families associated with nuclear functions. [PDF I PubMed]
Doi, N.; Takashima, H.; Kinjo, M.; Sakata, K.; Kawahashi, Y.; Oishi, Y.; Oyama, R.; Miyamoto-Sato, E.; Sawasaki, T.; Endo, Y.; Yanagawa, H.; Genome Res. 2002, 12(3), 487-492. Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. [PDF I PubMed]
Duan, X.J.; Xenarios, I.; Eisenberg, D.; Mol. Cell Proteomics 2002, 1(2), 104-116. Describing biological protein interactions in terms of protein states and state transitions : the LiveDIP database. [PDF I PubMed]
Duffy, H.S.; Delmar, M.; Spray, D.C.; J. Physiol. Paris 2002, 96(3-4), 243-249. Formation of the gap junction nexus: binding partners for connexins. [PDF I PubMed]

Edwards, A.; Kus, B.; Jansen, R.; Greenbaum, D.; Greenblatt, J.; Gerstein, M.; Trends Genet. 2002, 18(10), 529. Bridging structural biology and genomics: assessing protein interaction data with known complexes. [PDF I PubMed]
Elangovan, M.; Day, R.N.; Periasamy, A.; J. Microsc. 2002, 205(Pt. 1), 3-14. Nanosecond fluorescence resonance energy transfer-fluorescence lifetime imaging microscopy to localize the protein interactions in a single living cell. [PDF I PubMed]
Ellis, C.; Turner, J.G.; Devoto, A.; Plant Mol. Biol. 2002, 50(6), 971-980. Protein complexes mediate signalling in plant responses to hormones, light, sucrose and pathogens. [PDF I PubMed]
Ely, K.R.; Li, C.; J. Mol. Recognit. 2002, 15(5), 286-290. Structurally adaptive hot spots at a protein interaction interface on TRAF3. [PDF I PubMed]
Endoh, H.; Vincent, S.; Jacob, Y.; Real, E.; Walhout, A.J.; Vidal, M.; Methods Enzymol. 2002, 350, 525-545. Integrated version of reverse two-hybrid system for the postproteomic era. [PubMed]
Espejo, A.; Cote, J.; Bednarek, A.; Richard, S.; Bedford, M.T.; Biochem. J. 2002, 367(Pt. 3), 697-702. A protein-domain microarray identifies novel protein-protein interactions. [PDF I PubMed]
Eyckerman, S.; Lemmens, I.; Lievens, S.; Van der Heyden, J.; Verhee, A.; Vandekerckhove, J.; Tavernier, J.; Sci. STKE 2002, 2002(162), PL18. Design and use of a mammalian protein-protein interaction trap (MAPPIT). [PDF I PubMed]
Eyckerman, S.; Tavernier, J.; Eur. Cytokine Netw. 2002, 13(3), 276-284. Methods to map protein interactions in mammalian cells: different tools to address different questions. [PubMed]

Fahmy, A.; Wagner, G.; J. Am. Chem. Soc. 2002, 124(7), 1241-1250. TreeDock: a tool for protein docking based on minimizing van der Waals energies. [PDF I PubMed]
Fang, Y. Macool, D.J. Xue, Z. Heppard, E.P. Hainey, C.F. Tingey, S.V. Miao. G.H. Mol. Genet. Genomics 2002, 267(2), 142-153. Development of a high-throughput yeast two-hybrid screening system to study protein-protein interactions in plants. [PDF I PubMed]
Fariselli, P.; Pazos, F.; Valencia, A.; Casadio, R.; Eur. J. Biochem. 2002, 269(5), 1356-1361. Prediction of protein-protein interaction sites in heterocomplexes with neural networks. [PDF I PubMed]
Fernandez-Recio, J.; Totrov, M.; Abagyan, R.; Pac. Symp. Biocomput. 2002, 552-563. Screened charge electrostatic model in protein-protein docking simulations. [PDF I PubMed]
Fernandez-Recio, J.; Totrov, M.; Abagyan, R.; Protein Sci. 2002, 11(2), 280-291. Soft protein-protein docking in internal coordinates. [PDF I PubMed]
Figeys, D.; Curr. Opin. Mol. Ther. 2002, 4(3), 210-215. Functional proteomics: mapping protein-protein interactions and pathways. [PubMed]
Flöck, D.; Helms, V.; Proteins 2002, 47(1), 75-85. Protein-protein docking of electron transfer complexes: cytochrome c oxidase and cytochrome c. [PDF I PubMed]
Forster, M.J.; Micron 2002, 33(4), 365-384. Molecular modelling in structural biology. [PDF I PubMed]
Fraser, H.B.; Hirsh, A.E.; Steinmetz, L.M.; Scharfe, C.; Feldman, M.W.; Science 2002, 296(5568), 750-752. Evolutionary rate in the protein interaction network. [PDF I PubMed]
Fromont-Racine, M.; Rain, J.C.; Legrain, P.; Methods Enzymol. 2002, 350, 513-524. Building protein-protein networks by two-hybrid mating strategy. [PubMed]
Fujiwara, K.; Poikonen, K.; Aleman, L.; Valtavaara, M.; Saksela, K.; Mayer, B.J.; Biochemistry 2002, 41(42), 12729-12738. A single-chain antibody/epitope system for functional analysis of protein-protein interactions. [PDF I PubMed]

Gabdoulline, R.R.; Wade, R.C.; Curr. Opin. Struct. Biol. 2002, 12(2), 204-213. Biomolecular diffusional association. [PDF I PubMed]
Galarneau, A.; Primeau, M.; Trudeau, L.E.; Michnick, S.W.; Nat. Biotechnol. 2002, 20(6), 619-622. beta-Lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein-protein interactions. [PDF I PubMed]
Gavin, A.C.; Bösche, M.; Krause, R.; Grandi, P.; Marzioch, M.; Bauer, A.; Schultz, J.; Rick, J.M.; Michon, A.-M.; Cruciat, C.-M.; Remor, M.; Höfert, 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.; Nature 2002, 415, 141-147. Functional organization of the yeast proteome by systematic analysis of protein complexes. [PDF I PubMed]
Gera, J.F.; Hazbun, T.R.; Fields, S.; Methods Enzymol. 2002, 350, 499-512. Array-based methods for identifying protein-protein and protein-nucleic acid interactions. [PubMed]
Gerber, D.; Shai, Y.; J. Mol. Biol. 2002, 322(3), 491-495. Chirality-independent protein-protein recognition between transmembrane domains in vivo. [PDF I PubMed]
Gerstein, M.; Lan, N.; Jansen, R.; Science 2002, 295(5553), 284-287. Proteomics. Integrating interactomes. [PDF I PubMed]
Goh, C.S.; Cohen, F.E.; J. Mol. Biol. 2002, 324(1), 177-192. Co-evolutionary analysis reveals insights into protein-protein interactions. [PDF I PubMed]
Goh, K.I.; Oh, E.; Jeong, H.; Kahng, B.; Kim, D.; Proc. Natl. Acad. Sci. USA 2002, 99(20), 12583-12588. Classification of scale-free networks. [PDF I PubMed]
Golemis, E.A.; Tew, K.D.; Dadke, D.; Biotechniques 2002, 32(3), 636-638, 640, 642. Protein interaction-targeted drug discovery: evaluating critical issues. [PubMed]
Gomez, S.M.; Rzhetsky, A.; Pac. Symp. Biocomp. 2002, 7, 413-424. Towards the prediction of complete protein-protein interaction networks. [PDF I PubMed]

Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R.; Proteins 2002, 47(4), 409-443. Principles of docking: an overview of search algorithms and a guide to scoring functions. [PDF I PubMed]
Hartig, J.S.; Najafi-Shoushtari, S.H.; Grune, I.; Yan, A.; Ellington, A.D.; Famulok, M.; Nat. Biotechnol. 2002, 20(7), 717-722. Protein-dependent ribozymes report molecular interactions in real time. [PDF I PubMed]
Hatzivassiloglou, V.; Weng, W.; Int. J. Med. Inf. 2002, 67(1-3), 19-32. Learning anchor verbs for biological interaction patterns from published text articles. [PDF I PubMed]
Heifetz, A.; Katchalski-Katzir, E.; Eisenstein, M.; Protein Sci. 2002, 11(3), 571-587. Electrostatics in protein-protein docking. [PDF I PubMed]
Henthorn, D.C.; Jaxa-Chamiec, A.A.; Meldrum, E.; Biochem. Pharmacol. 2002, 63(9), 1619-1628. A GAL4-based yeast three-hybrid system for the identification of small molecule-target protein interactions. [PDF I PubMed]
Hertveldt, K.; Robben, J.; Volckaert, G.; Yeast 2002, 19(6), 499-508. In vivo selectively infective phage as a tool to detect protein interactions: evaluation of a novel vector system with yeast Ste7p-Fus3p interacting proteins. [PDF I PubMed]
Hetenyi, C.; Van Der Spoel, D.; Protein Sci. 2002, 11(7), 1729-1737. Efficient docking of peptides to proteins without prior knowledge of the binding site. [PDF I PubMed]
Hink, M.A.; Bisselin, T.; Visser, A.J.; Plant Mol. Biol. 2002, 50(6), 871-883. Imaging protein-protein interactions in living cells. [PDF I PubMed]
Hirschman, L.; Park, J.C.; Tsujii, J.; Wong, L.; Wu, C.H.; Bioinformatics 2002, 18(12), 1553-1561. Accomplishments and challenges in literature data mining for biology. [PDF I PubMed]
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.; Sörensen, B.D.; Matthiesen, J.; Hendrickson, R.C.; Gleeson, F.; Pawson, T.; Moran, M.F.; Durocher, D.; Mann, M.; Hogue, C.W.V.; Figeys, D.; Tyers, M.; Nature 2002, 415, 180-183. Systematic identifcation of protein complexes in Saccharomyces cerevisiae by mass spectrometry. [PDF I PubMed]
Houser-Scott, F.; Xiao, S.; Millikin, C.E.; Zengel, J.M.; Lindahl, L.; Engelke, D.R.; Proc. Natl. Acad. Sci. USA 2002, 99(5), 2684-2689. Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P. [PDF I PubMed]
Huang, L.; Baldwin, M.A.; Maltby, D.A.; Medzihradszky, K.F.; Baker, P.R.; Allen, N.; Rexach, M.; Edmondson, R.D.; Campbell, J.; Juhasz, P.; Martin, S.A.; Vestal, M.L.; Burlingame, A.L.; Mol. Cell Proteomics 2002, 1(6), 434-450. The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry. [PDF I PubMed]
Hughes, T.R.; Funct. Integr. Genomics 2002, 2(4-5), 199-211. Yeast and drug discovery. [PDF I PubMed]
Hurley, J.H.; Anderson, D.E.; Beach, B.; Canagarajah, B.; Ho, Y.S.; Jones, E.; Miller, G.; Misra, S.; Pearson, M.; Saidi, L.; Suer, S.; Trievel, R.; Tsujishita, Y.; Trends Biochem. Sci. 2002, 27(1), 48-53. Structural genomics and signaling domains. [PDF I PubMed]

Ideker, T.; Ozier, O.; Schwikowski, B.; Siegel, A.F.; Bioinformatics 2002, 18(Suppl. 1), S233-S240. Discovering regulatory and signalling circuits in molecular interaction networks. [PDF I PubMed]
Immink, R.G.; Angenent, G.C.; Trends Plant Sci. 2002, 7(12), 531-534. Transcription factors do it together: the hows and whys of studying protein-protein interactions. [PDF I PubMed]
Immink, R.G.; Gadella, T.W.; Ferrario, S.; Busscher, M.; Angenent, G.C.; Proc. Natl. Acad. Sci. USA 2002, 99(4), 2416-2421. Analysis of MADS box protein-protein interactions in living plant cells. [PDF I PubMed]
Issaq, H.J.; Veenstra, T.D.; Conrads, T.P.; Felschow, D.; Biochem. Biophys. Res. Commun. 2002, 292(3), 587-592. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. [PDF I PubMed]
Ito, T.; Ota, K.; Kubota, H.; Yamaguchi, Y.; Chiba, T.; Sakuraba, K.; Yoshida, M.; Mol. Cell. Proteomics 2002, 1(8), 561-566. Roles for the two-hybrid system in exploration of the yeast protein interactome. [PDF I PubMed]

Janetopoulos, C.; Devreotes, P.; Methods 2002, 27(4), 366-373. Monitoring receptor-mediated activation of heterotrimeric G-proteins by fluorescence resonance energy transfer. [PDF I PubMed]
Janin, J.; Proteins 2002, 47, 257. Welcome to CAPRI: a critical assessment of predicted interactions. [PDF]
Janin, J.; Wodak, S.J.; Adv. Protein Chem. 2002, 61, 1-8. Protein modules and protein-protein interaction. Introduction. [PubMed]
Jansen, R.; Greenbaum, D.; Gerstein, M.; Genome Res. 2002, 12(1), 37-46. Relating whole-genome expression data with protein-protein interactions. [PDF I PubMed]
Jansen, R.; Lan, N.; Qian, J.; Gerstein, M.; CABM Symposium, J. Struct. Funct. Gen. 2002, 2, 71-81. Integration of genomic datasets to predict protein complexes in yeast. [PDF]
Jiang, L.; Gao, Y.; Mao, F.; Liu, Z.; Lai, L.; Proteins 2002, 46(2), 190-196. Potential of mean force for protein-protein interaction studies. [PDF I PubMed]
Jiang, L.; Lai, L.; J. Biol. Chem. 2002, 277(40), 37732-37740. CH...O hydrogen bonds at protein-protein interfaces. [PDF I PubMed]
Jiang, F.; Lin, W.; Rao, Z.; Protein Eng. 2002, 15(4), 257-263. SOFTDOCK: understanding of molecular recognition through a systematic docking study. [PDF I PubMed]

Kanehisa, M.; Novartis Found. Symp. 2002, 247, 91-103, 119-128, 244-252. The KEGG database. [PubMed]
Kanehisa, M.; Goto, S.; Kawashima, S.; Nakaya, A.; Nucleic Acids Res. 2002, 30(1), 42-46. The KEGG databases at GenomeNet. [PDF I PubMed]
Kariakin, A.; Davydov, D.; Peterson, J.A.; Jung, C.; Biochemistry 2002, 41(46), 13514-13525. A new approach to the study of protein-protein interaction by FTIR: complex formation between cytochrome P450BM-3 heme domain and FMN reductase domain. [PDF I PubMed]
Karimova, G.; Ladant, D.; Ullmann, A.; Int. J. Med. Microbiol. 2002, 292(1), 17-25. Two-hybrid systems and their usage in infection biology. [PubMed]
Kato, N.; Pontier, D.; Lam, E.; Plant Physiol. 2002, 129(3), 931-942. Spectral profiling for the simultaneous observation of four distinct fluorescent proteins and detection of protein-protein interaction via fluorescence resonance energy transfer in tobacco leaf nuclei. [PDF I PubMed]
Kawarasaki, Y.; Sasaki, Y.; Ikeuchi, A.; Yamamoto, S.; Yamane, T.; Anal. Biochem. 2002, 303(1), 34-41. A method for functional mapping of protein-protein binding domain by preferential amplification of the shortest amplicon using PCR. [PDF I PubMed]
Kemmeren, P.; van Berkum, N.L.; Vilo, J.; Bijma, T.; Donders, R.; Holstege, F.C.P.; Mol. Cell 2002, 9(5), 1133-1143. Protein interaction verification and functional annotation by integrated analysis of genome-scale data. [PDF I PubMed I Suppl. Website]
Kersten, B.; Bürkle, L.; Kuhn, E.J.; Giavalisco, P.; Konthur, Z.; Lueking, A.; Walter, G.; Eickhoff, H.; Schneider, U.; Plant Mol. Biol. 2002, 48, 133-141. Large-scale plant proteomics. [PDF I PubMed]
Kessels, H.W.; Ward, A.C.; Schumacher, T.N.; Proc. Natl. Acad. Sci. USA 2002, 99(13), 8524-8529. Specificity and affinity motifs for Grb2 SH2-ligand interactions. [PDF I PubMed]
Kim, J.; Krapivsky, P.L.; Kahng, B.; Redner, S.; Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2002, 66(5, Pt. 2), 055101. Infinite-order percolation and giant fluctuations in a protein interaction network. [PDF I PubMed]
Kim, W.K.; Park, J.; Suh, J.K.; Genome Informatics 2002, 13, 42-50. Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair. [PDF]
Kitano, H.; Curr. Genet. 2002, 41(1), 1-10. Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology. [PDF I PubMed]
Klaholz, B.; Moras, D.; Structure (Camb.) 2002, 10(9), 1197-1204. C-H...O hydrogen bonds in the nuclear receptor RARgamma - a potential tool for drug selectivity. [PDF I PubMed]
Kortemme, T.; Baker, D.; Proc. Natl. Acad. Sci. USA 2002, 99(22), 14116-14121. A simple physical model for binding energy hot spots in protein-protein complexes. [PDF I PubMed]
Krauthammer, M.; Kra, P.; Iossifov, I.; Gomez, S.M.; Hripcsak, G.; Hatzivassiloglou, V.; Friedman, C.; Rzhetsky, A.; Bioinformatics 2002, 18(Suppl. 1), S249-S257. Of truth and pathways: chasing bits of information through myriads of articles. [PDF I PubMed]
Kukar, T.; Eckenrode, S.; Gu, Y.; Lian, W.; Megginson, M.; She, J.X.; Wu, D.; Anal. Biochem. 2002, 306(1), 50-54. Protein microarrays to detect protein-protein interactions using red and green fluorescent proteins. [PDF I PubMed]
Kumar, A.; Snyder, M.; Nature, 2002, 415, 123-124. Protein complexes take the bait. [PDF I PubMed]

Legrain, P.; Nat. Biotechnol. 2002, 20(2), 128-129. Protein domain networking. [PDF I PubMed]
Legrain, P.; Trends Biotechnol. 2002, 20(8), 358-359. Protein interactions contribute to protein function. [PDF I PubMed]
Legrain, P.; Strosberg, D.; Curr. Pharm. Des. 2002, 8(13), 1189-1198. Protein interaction domain mapping for the selection of validated targets and lead compounds in the anti-infectious area. [PubMed]
Lehming, N.; Brief Funct. Genomic. Proteomic. 2002, 1(3), 230-238. Analysis of protein-protein proximities using the split-ubiquitin system. [PubMed]
Leung, H.C.; Leung, S.M.; Karavanov, A.; Curr. Protoc. Protein Sci. 2002, Chapter 3, Unit 3.9. Solid-phase profiling of proteins. [PubMed]
Lichtarge, O.; Sowa, M.E.; Curr. Opin. Struct. Biol. 2002, 12(1), 21-27. Evolutionary predictions of binding surfaces and interactions. [PDF I PubMed]
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