Ahrends, R.; Kosinski, J.; Kirsch, D.; Manelyte, L.; Giron-Monzon, L.; Hummerich, L.; Schulz, O.; Spengler, B.; Friedhoff, P.; Nucleic Acids Res.2006, 34(10), 3169-3180.
Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. [PDF I PubMed]
Aivaliotis, M.; Karas, M.; Tsiotis, G.; Photosynth. Res. 2006, 88(2), 143-157. High throughput two-dimensional blue-native electrophoresis: a tool for functional proteomics of cytoplasmatic protein complexes from Chlorobium tepidum. [PubMed]
Akashi, S.; Med. Res. Rev.2006, 26(3), 339-368. Investigation of molecular interaction within biological macromolecular complexes by mass spectrometry. [PubMed]
Almlof, M.; Aqvist, J.; Smalas, A.O.; Brandsdal, B.O.; Biophys. J. 2006, 90(2), 433-442. Probing the effect of point mutations at protein-protein interfaces with free energy calculations. [PDF I PubMed]
Altaf-Ul-Amin, M.; Shinbo, Y.; Mihara, K.; Kurokawa, K.; Kanaya, S.; BMC Bioinformatics2006, 7(1), 207. Development and implementation of an algorithm for detection of protein complexes in large interaction networks. [PDF I PubMed]
Antonsson, A.; Payne, E.; Hengst, K.; McMillan, D.N.; J. Interferon Cytokine Res. 2006, 26(7), 455-461. The human papillomavirus type 16 E7 protein binds human interferon regulatory factor-9 via a novel PEST domain required for transformation [PDF I PubMed]
Aragues, R.; Jaeggi, D.; Oliva, B.; Bioinformatics2006, 22(8), 1015-1017. PIANA: protein interactions and network analysis. [PDF I PubMed]
Arifuzzaman, M.; Maeda, M.; Itoh, A.; Nishikata, K.; Takita, C.; Saito, R.; Ara, T.; Nakahigashi, K.; Huang, H.C.; Hirai, A.; Tsuzuki, K.; Nakamura, S.; Altaf-Ul-Amin, M.; Oshima, T.; Baba, T.; Yamamoto, N.; Kawamura, T.; Ioka-Nakamichi, T.; Kitagawa, M.; Tomita, M.; Kanaya, S.; Wada, C.; Mori, H.; Genome Res. 2006, 16(5), 686-691. Large-scale identification of protein-protein interaction of Escherichia coli K-12. [PDF I PubMed]
Arnold, L.A.; Estebanez-Perpina, E.; Togashi, M.; Shelat, A.; Ocasio, C.A.; McReynolds, A.C.; Nguyen, P.; Baxter, J.D.; Fletterick, R.J.; Webb, P.; Guy, R.K.; Sci. STKE2006, 2006(341), pl3. A high-throughput screening method to identify small molecule inhibitors of thyroid hormone receptor coactivator binding. [PDF I PubMed]
Autin, L.; Steen, M.; Dahlback, B.; Villoutreix, B.O.; Proteins2006, 63(3), 440-450. Proposed structural models of the prothrombinase (FXa-FVa) complex. [PDF I PubMed]
Bader, G.D.; Cary, M.P.; Sander, C.; Nucleic Acids Res. 2006, 34, D504-D506. Pathguide: a pathway resource list. [PDF I PubMed]
Baitaluk, M.; Sedova, M.; Ray, A.; Gupta, A.; Nucleic Acids Res. 2006, 34, W466-W471. BiologicalNetworks: visualization and analysis tool for systems biology. [PubMed]
Balla, S.; Thapar, V.; Verma, S.; Luong, T.; Faghri, T.; Huang, C.H.; Rajasekaran, S.; del Campo, J.J.; Shinn, J.H.; Mohler, W.A.; Maciejewski, M.W.; Gryk, M.R.; Piccirillo, B.; Schiller, S.R.; Schiller, M.R.; Nat. Methods2006, 3(3), 175-177. Minimotif Miner: a tool for investigating protein function. [PDF I PubMed]
Bandyopadhyay, S.; Sharan, R.; Ideker, T.; Genome Res.2006, 16(3), 428-435. Systematic identification of functional orthologs based on protein network comparison. [PDF I PubMed]
Banerjee, A.; Hu, J.; Goss, D.J.; Biochemistry2006, 45(7), 2333-2338. Thermodynamics of protein-protein interactions of cMyc, Max, and Mad: effect of polyions on protein dimerization. [PDF I PubMed]
Banham, J.E.; Timmel, C.R.; Abbott, R.J.; Lea, S.M.; Jeschke, G.; Angew. Chem. Int. Ed. Engl. 2006, 45(7), 1058-1061. The characterization of weak protein-protein interactions: evidence from DEER for the trimerization of a von willebrand factor a domain in solution. [PDF I PubMed]
Bastard, K.; Prevost, C.; Zacharias, M.; Proteins2006, 62(4), 956-969. Accounting for loop flexibility during protein-protein docking. [PDF I PubMed]
Bauch, A.; Superti-Furga, G.; Immunol. Rev. 2006, 210, 187-207. Charting protein complexes, signaling pathways, and networks in the immune system. [PubMed]
Baudot, A.; Martin, D.; Mouren, P.; Chevenet, F.; Guenoche, A.; Jacq, B.; Brun, C.; Bioinformatics2006, 22(2), 248-250. PRODISTIN web site: a tool for the functional classification of proteins from interaction networks. [PDF I PubMed]
Bayraktar, H.; Ghosh, P.S.; Rotello, V.M.; Knapp, M.J.; Chem. Commun. (Camb.) 2006, 13, 1390-1392. Disruption of protein-protein interactions using nanoparticles: inhibition of cytochrome c peroxidase. [PDF I PubMed]
Bedjeguelal, K.; Bienayme, H.; Dumoulin, A.; Poigny, S.; Schmitt, P.; Tam, E.; Bioorg. Med. Chem. Lett. 2006, 16(15), 3998-4001. Discovery of protein-protein binding disruptors using multi-component condensations small molecules. [PDF I PubMed]
Ben-Hur, A.; Noble, W.S.; BMC Bioinformatics2006, 7(Suppl. 1), S1-S2. Choosing negative examples for the prediction of protein-protein interactions. [PDF I PubMed]
Ben-Naim, A.; J. Chem. Phys.2006, 125(2), 24901. On the driving forces for protein-protein association. [PubMed]
Bertsche, U.; Kast, T.; Wolf, B.; Fraipont, C.; Aarsman, M.E.; Kannenberg, K.; von Rechenberg, M.; Nguyen-Disteche, M.; den Blaauwen, T.; Holtje, J.V.; Vollmer, W.; Mol. Microbiol. 2006, 61(3), 675-690. Interaction between two murein (peptidoglycan) synthases, PBP3 and PBP1B, in Escherichia coli. [PubMed]
Bhat, R.A.; Lahaye, T.; Panstruga, R.; Bhat, R.A.; Lahaye, T.; Panstruga, R.; Plant Methods2006, 2(1), 12. The visible touch: in planta visualization of protein-protein interactions by fluorophore-based methods. [PDF I PubMed]
Bidlingmaier, S.; Liu, B.; Mol. Cell Proteomics2006, 5(3), 533-540. Construction and application of a yeast surface-displayed human cDNA library to identify post-translational modification-dependent protein-protein interactions. [PubMed]
Birkland, A.; Yona, G.; Nucleic Acids Res.2006, 34, D235-D242. BIOZON: a hub of heterogeneous biological data. [PDF I PubMed]
Biro, J.C.; Med. Hypotheses2006, 66(1), 137-142. A novel intra-molecular protein-protein interaction code based on partial complementary coding of co-locating amino acids. [PDF I PubMed]
Bonet, J.; Caltabiano, G.; Khan, A.K.; Johnston, M.A.; Corbi, C.; Gomez, A.; Rovira, X.; Teyra, J.; Villa-Freixa, J.; Proteins2006, 63(1), 65-77. The role of residue stability in transient protein-protein interactions involved in enzymatic phosphate hydrolysis. A computational study. [PDF I PubMed]
Borisov, N.M.; Markevich, N.I.; Hoek, J.B.; Kholodenko, B.N.; Biosystems2006, 83(2-3), 152-166. Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains. [PDF I PubMed]
Bradford, J.R.; Needham, C.J.; Bulpitt, A.J.; Westhead, D.R.; J. Mol. Biol.2006, 362(2), 365-386. Insights into protein-protein interfaces using a bayesian network prediction method. [PubMed]
Bravo, J.; Aloy, P.; Curr. Opin. Struct. Biol. 2006, 16(3), 385-392. Target selection for complex structural genomics. [PDF I PubMed]
Bruck, J.; Ebenhöh, O.; Heinrich, R.; Genome Inform.2006, 17(1), 208-218. Patterns of interactions of reaction pairs in metabolic networks. [PubMed]
Burgoyne, N.J.; Jackson, R.M.; Bioinformatics2006, 22(11), 1335-1342. Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. [PDF I PubMed]
Camacho, C.J.; Ma, H.; Champ, P.C.; Proteins2006, 63(4), 868-877. Scoring a diverse set of high-quality docked conformations: A metascore based on electrostatic and desolvation interactions. [PDF I PubMed]
Carlsson, R.; Thorell, K.; Liberg, D.; Leanderson, T.; Biochem. Biophys. Res. Commun. 2006, 344(4), 1155-1160. SPI-C and STAT6 can cooperate to stimulate IgE germline transcription. [PDF I PubMed]
Carmi, S.; Levanon, E.Y.; Havlin, S.; Eisenberg, E.; Phys. Rev. E Stat. Nonlin. Soft Matter. Phys. 2006, 73(3, Pt. 1), 031909. Connectivity and expression in protein networks: Proteins in a complex are uniformly expressed. [PDF I PubMed]
Chang, A.N.; McDermott, J.; Frazier, Z.; Guerquin, M.; Samudrala, R.; BMC Bioinformatics2006, 7(1), 146. INTEGRATOR: interactive graphical search of large protein interactomes over the Web. [PDF I PubMed]
Charbonnier, S.; Zanier, K.; Masson, M.; Trave, G.; Protein Expr. Purif.2006, 50(1), 89-101. Capturing protein-protein complexes at equilibrium: the holdup comparative chromatographic retention assay. [PubMed]
Che, Y.; Brooks, B.R.; Marshall, G.R.; J. Comput. Aided Mol. Des. 2006, 20(2), 109-130. Development of small molecules designed to modulate protein-protein interactions. [PDF I PubMed]
Chelliah, V.; Blundell, T.L.; Fernandez-Recio, J.; J. Mol. Biol.2006, 357(5), 1669-1682. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. [PDF I PubMed]
Chen, J.; Hsu, W.; Lee, M.L.; Ng, S.K.; Bioinformatics2006, 22(16), 1998-2004. Increasing confidence of protein interactomes using network topological metrics. [PDF I PubMed]
Chen, J.; Yuan, B.; Bioinformatics2006, 22(18), 2283-2290. Detecting functional modules in the yeast protein-protein interaction network. [PubMed]
Chen, L.; Wu, L.Y.; Wang, Y.; Zhang, X.S.; Proteins2006, 62(4), 833-837. Inferring protein interactions from experimental data by association probabilistic method. [PDF I PubMed]
Chen, L.; Zhang, S.; Zhang, X.S.; Wang, Y.; Li, Z.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2006, 1(1), 5527-5530. Alignment of protein interaction networks by integer quadratic programming. [PubMed]
Chen, Y.; Lai, M.; Maeno-Hikichi, Y.; Zhang, J.F.; Cell Signal2006, 18(2), 215-224. Essential role of the LIM domain in the formation of the PKCepsilon-ENH-N-type Ca(2+) channel complex. [PDF I PubMed]
Chinnasamy, A.; Mittal, A.; Sung, W.K.; Comput. Biol. Med. 2006, 36(10), 1143-1154. Probabilistic prediction of protein-protein interactions from the protein sequences. [PDF I PubMed]
Chipuk, J.E.; Green, D.R.; Cell Death Differ. 2006, 13(6), 994-1002. Dissecting p53-dependent apoptosis. [PDF I PubMed]
Chou, K.C.; Cai, Y.D.; J. Proteome Res.2006, 5(2), 316-322. Predicting protein-protein interactions from sequences in a hybridization space. [PDF I PubMed]
Chua, H.N.; Sung, W.K.; Wong, L.; Bioinformatics2006, 22(13), 1623-1630. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. [PDF I PubMed]
Chung, J.L.; Wang, W.; Bourne, P.E.; Proteins2006, 62(3), 630-640. Exploiting sequence and structure homologs to identify protein-protein binding sites. [PDF I PubMed]
Cummings, M.D.; Schubert, C.; Parks, D.J.; Calvo, R.R.; Lafrance, L.V.; Lattanze, J.; Milkiewicz, K.L.; Lu, T.; Chem. Biol. Drug Des.2006, 67(3), 201-205.
Substituted 1,4-benzodiazepine-2,5-diones as alpha-helix mimetic antagonists of the HDM2-p53 protein-protein interaction. [PDF I PubMed]
De Bie, P.; van de Sluis, B.; Burstein, E.; Duran, K.J.; Berger, R.; Duckett, C.S.; Wijmenga, C.; Klomp, L.W.; Biochem. J.2006, 398(1), 63-71. Characterization of COMMD protein-protein interactions in NF-kappaB signalling. [PDF I PubMed]
De Filippis, V.; Frasson, R.; Fontana, A.; Protein Sci.2006, 15(5), 976-986. 3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions. [PDF I PubMed]
De Vries, S.J.; Bonvin, A.M.; Bioinformatics2006, 22(17), 2094-2098. Intramolecular surface contacts contain information about protein-protein interface regions. [PDF I PubMed]
De Vries, S.J.; van Dijk, A.D.; Bonvin, A.M.; Proteins2006, 63(3), 479-489. WHISCY: What information does surface conservation yield? Application to data-driven docking. [PDF I PubMed]
Deeds, E.J.; Ashenberg, O.; Shakhnovich, E.I.; Proc. Natl. Acad. Sci. USA2006, 103(2), 311-316. A simple physical model for scaling in protein-protein interaction networks. [PDF I PubMed]
Del Carpio, C.A.; Qiang, P.; Ichiishi, E.; Tsuboi, H.; Koyama, M.; Hatakeyama, N.; Endou, A.; Takaba, H.; Kubo, M.; Miyamoto, A.; Genome Inform. 2006, 17(2), 270-278. Robotic path planning and protein complex modeling considering low frequency intra-molecular loop and domain motions. [PubMed]
Derunes, C.; Burgess, R.; Iraheta, E.; Kellerer, R.; Becherer, K.; Gessner, C.R.; Li, S.; Hewitt, K.; Vuori, K.; Pasquale, E.B.; Woods, V.L.; Ely, K.R.; FEBS Lett.2006, 580(1), 175-178. Molecular determinants for interaction of SHEP1 with Cas localize to a highly solvent-protected region in the complex. [PDF I PubMed]
Deshmukh, V.; Cannings, C.; Thomas, A.; Math. Med. Biol.2006, 23(4), 279-295. Estimating the parameters of a model for protein-protein interaction graphs. [PubMed]
Ding, C.; He, X.; Xiong, H.; Peng, H.; Holbrook, S.R.; Int. J. Data Min. Bioinform. 2006, 1(2), 162-177. Transitive closure and metric inequality of weighted graphs: detecting protein interaction modules using cliques. [PubMed]
Dohkan, S.; Koike, A.; Takagi, T.; In Silico Biol.2006, 6(6), 515-529. Improving the performance of an SVM-based method for predicting protein-protein interactions. [PubMed]
Dong, F.; Zhou, H.X.; Proteins2006, 65(1), 87-102. Electrostatic contribution to the binding stability of protein-protein complexes. [PubMed]
Ebbels, T.M.; Buxton, B.F.; Jones, D.T.; Bioinformatics2006, 22(14), e99-e107. springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an 'information landscape'. [PubMed]
Ehlert, A.; Weltmeier, F.; Wang, X.; Mayer, C.S.; Smeekens, S.; Vicente-Carbajosa, J.; Droge-Laser, W.; Plant J.2006, 46(5), 890-900. Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts: establishment of a heterodimerization map of group C and group S bZIP transcription factors. [PDF I PubMed]
Ekman, D.; Light, S.; Bjorklund, A.K.; Elofsson, A.; Genome Biol.2006, 7(6), R45. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? [PDF I PubMed]
El-Shafey, A.; Tolic, N.; Young, M.M.; Sale, K.; Smith, R.D.; Kery, V.; Protein Sci.2006, 15(3), 429-440. "Zero-length" cross-linking in solid state as an approach for analysis of protein-protein interactions. [PDF I PubMed]
Elion, E.A.; Curr. Protoc. Mol. Biol.2006, Chapter 20, Unit 20.5. Detection of protein-protein interactions by coprecipitation. [PubMed]
Estrada, E.; Proteomics2006, 6(1), 35-40. Virtual identification of essential proteins within the protein interaction network of yeast. [PDF I PubMed]
Ethier, M.; Lambert, J.P.; Vasilescu, J.; Figeys, D.; Anal. Chim. Acta2006, 564(1), 10-18. Analysis of protein interaction networks using mass spectrometry compatible techniques. [PubMed]
Fasan, R.; Dias, R.L.; Moehle, K.; Zerbe, O.; Obrecht, D., Mittl, P.R.; Grutter, M.G.; Robinson, J.A.; Chembiochem. 2006, 7(3), 515-526. Structure-activity studies in a family of beta-hairpin protein epitope mimetic inhibitors of the p53-HDM2 protein-protein interaction. [PDF I PubMed]
Ferraro, E.; Via, A.; Ausiello, G.; Helmer-Citterich, M.; Bioinformatics2006, 22(19), 2333-2339. A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. [PubMed]
Finiguerra, M.G.; Blok, H.; Ubbink, M.; Huber, M.; J. Magn. Reson.2006, 180(2), 197-202. High-field (275GHz) spin-label EPR for high-resolution polarity determination in proteins. [PDF I PubMed]
Fischer, T.B.; Holmes, J.B.; Miller, I.R.; Parsons, J.R.; Tung, L.; Hu, J.C.; Tsai, J.; J. Struct. Biol.2006, 153(2), 103-112. Assessing methods for identifying pair-wise atomic contacts across binding interfaces. [PDF I PubMed]
Fletcher, S.; Hamilton, A.D.; J. R. Soc. Interface2006, 3(7), 215-233. Targeting protein-protein interactions by rational design: mimicry of protein surfaces. [PubMed]
Fujimoto, N.; Terlizzi, J.; Aho, S.; Brittingham, R.; Fertala, A.; Oyama, N.; McGrath, J.A.; Uitto, J.; Exp. Dermatol. 2006, 15(4), 300-307. Extracellular matrix protein 1 inhibits the activity of matrix metalloproteinase 9 through high-affinity protein/protein interactions. [PDF I PubMed]
Gao, Q.; Xue, S.; Doneanu, C.E.; Shaffer, S.A.; Goodlett, D.R.; Nelson, S.D.; Anal. Chem. 2006, 78(7), 2145-2149. Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry. [PDF I PubMed]
Garcia-Foncillas, J.; Bandres, E.; Zarate, R.; Remirez, N.; Clin. Transl. Oncol. 2006, 8(4), 250-261. Proteomic analysis in cancer research: potential application in clinical use. [PubMed]
Gindhart, J.G.; Brief Funct. Genomic Proteomic2006, 5(1), 74-86. Towards an understanding of kinesin-1 dependent transport pathways through the study of protein-protein interactions. [PubMed]
Goede, B.; Naji, S.; von Kampen, O.; Ilg, K.; Thomm, M.; J. Biol. Chem.2006, 281(41), 30581-30592. Protein-protein interactions in the archaeal transcriptional machinery: Binding studies of isolated RNA polymerase subunits and transcription factors. [PubMed]
Gomez, G.E.; Cauerhff, A.; Craig, P.O.; Goldbaum, F.A.; Delfino, J.M.; Protein Sci.2006, 15(4), 744-752. Exploring protein interfaces with a general photochemical reagent. [PDF I PubMed]
Goodrich, T.T.; Wark, A.W.; Corn, R.M.; Lee, H.J.; Methods Mol. Biol.2006, 328, 113-130. Surface plasmon resonance imaging measurements of protein interactions with biopolymer microarrays. [PubMed]
Goryunov, A.S.; Gen. Physiol. Biophys. 2006, 25(3), 303-311. H/D isotope effects on protein hydration and interaction in solution. [PubMed]
Grelle, G.; Kostka, S.; Otto, A.; Kersten, B.; Genser, K.F.; Muller, E.C.; Walter, S.; Boddrich, A.; Stelzl, U.; Hanig, C.; Volkmer-Engert, R.; Landgraf, C.; Alberti, S.; Hohfeld, J.; Strodicke, M.; Wanker, E.E.; Mol. Cell. Proteomics2006, 5(2), 234-244. Identification of VCP/p97, CHIP and amphiphysin II interaction partners using membrane-based human proteome arrays. [PDF I PubMed]
Greenfield, N.J.; Nat. Protoc. 2006, 1(6), 2527-2535. Using circular dichroism collected as a function of temperature to determine the thermodynamics of protein unfolding and binding interactions. [PubMed]
Grigoryan, G.; Keating, A.E.; J. Mol. Biol.2006, 355(5), 1125-1142. Structure-based prediction of bZIP partnering specificity. [PDF I PubMed]
Grimm, V.; Zhang, Y.; Skolnick, J.; Proteins2006, 63(3), 457-465. Benchmarking of dimeric threading and structure refinement. [PDF I PubMed]
Grunberg, R.; Nilges, M.; Leckner, J.; Structure2006, 14(4), 683-693. Flexibility and conformational entropy in protein-protein binding. [PDF I PubMed]
Guerrero, C.; Tagwerker, C.; Kaiser, P.; Huang, L.; Mol. Cell Proteomics2006, 5(2), 366-378. An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. [PDF I PubMed]
Guldener, U.; Munsterkotter, M.; Oesterheld, M.; Pagel, P.; Ruepp, A.; Mewes, H.W.; Stumpflen, V.; Nucleic Acids Res.2006, 34, D436-D441. MPact: the MIPS protein interaction resource on yeast. [PDF I PubMed]
Gully, D.; Bouveret, E.; Proteomics2006, 6(1), 282-293. A protein network for phospholipid synthesis uncovered by a variant of the tandem affinity purification method in Escherichia coli. [PDF I PubMed]
Harris, C.C.; Proc. Natl. Acad. Sci. USA 2006, 103(6), 1659-1660. Protein-protein interactions for cancer therapy. [PDF I PubMed]
He, X.; Zhang, J.; PLoS Genet. 2006, 2(6), e88. Why do hubs tend to be essential in protein networks? [PDF I PubMed]
Hebert, T.E.; Gales, C.; Rebois, R.V.; Cell Biochem. Biophys. 2006, 45(1), 85-109. Detecting and imaging protein-protein interactions during G protein-mediated signal transduction in vivo and in situ by using fluorescence-based techniques. [PubMed]
Horn, S.C.; Lalowski, M.; Goehler, H.; Droge, A.; Wanker, E.E.; Stelzl, U.; J. Neural. Transm. 2006, 113(8), 1081-1090. Huntingtin interacts with the receptor sorting family protein GASP2. [PubMed]
Hoskins, J.; Lovell, S.; Blundell, T.L.; Protein Sci.2006, 15(5), 1017-1029. An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements. [PDF I PubMed]
Howell, J.M.; Winstone, T.L.; Coorssen, J.R.; Turner, R.J.; Proteomics2006, 6(7), 2050-2069. An evaluation of in vitro protein-protein interaction techniques: Assessing contaminating background proteins. [PDF I PubMed]
Hsu, C.M.; Chen, C.Y.; Liu, B.J.; Nucleic Acids Res.2006, 34, W356-W361. MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. [PubMed]
Humbert, S.; Saudou, F.; Cell2006, 125(4), 645-647. The Ataxia-ome: connecting disease proteins of the Cerebellum. [PDF I PubMed]
Issad, T.; Jockers, R.; Methods Mol. Biol. 2006, 332, 195-209. Bioluminescence resonance energy transfer to monitor protein-protein interactions. [PubMed]
Jach, G.; Pesch, M.; Richter, K.; Frings, S.; Uhrig, J.F.; Nat. Methods 2006, 3(8), 597-600. An improved mRFP1 adds red to bimolecular fluorescence complementation. [PubMed]
Jaimovich, A.; Elidan, G.; Margalit, H.; Friedman, N.; J. Comput. Biol.2006, 13(2), 145-164. Towards an integrated protein-protein interaction network: a relational markov network approach. [PDF I PubMed]
Jang, H.; Lim, J.; Lim, J.H.; Park, S.J.; Lee, K.C.; Park, S.H.; Bioinformatics2006, 22(14), e220-e226. Finding the evidence for protein-protein interactions from PubMed abstracts. [PubMed]
Jason-Moller, L.; Murphy, M.; Bruno, J.; Curr. Protoc. Protein Sci.2006, Chapter 19, Unit 19.13. Overview of Biacore systems and their applications. [PubMed]
Jiang, R.; Tu, Z.; Chen, T.; Sun, F.; Proc. Natl. Acad. Sci. USA 2006, 103(25), 9404-9409. Network motif identification in stochastic networks. [PDF I PubMed]
Jin, F.; Hazbun, T.; Michaud, G.A.; Salcius, M.; Predki, P.F.; Fields, S.; Huang, J.; Nat. Methods2006, 3(3), 183-189. A pooling-deconvolution strategy for biological network elucidation. [PDF I PubMed]
Joachimiak, L.A.; Kortemme, T.; Stoddard, B.L.; Baker, D.; J. Mol. Biol.2006, 361(1), 195-208. Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. [PubMed]
Johannessen, M.; Moller, S.; Hansen, T.; Moens, U.; Ghelue, M.V.; Cell Mol. Life Sci. 2006, 63(3), 268-284. The multifunctional roles of the four-and-a-half-LIM only protein FHL2. [PDF I PubMed]
Jones, R.B.; Gordus, A.; Krall, J.A.; Macbeath, G.; Nature2006, 439(7073), 168-174. A quantitative protein interaction network for the ErbB receptors using protein microarrays. [PDF I PubMed]
Jonsson, P.F.; Bates, P.A.; Bioinformatics2006, 22(18), 2291-2297. Global topological features of cancer proteins in the human interactome. [PubMed]
Jonsson, P.F.; Cavanna, T.; Zicha, D.; Bates, P.A.; BMC Bioinformatics2006, 7(1), 2. Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. [PDF I PubMed]
Jordan-Sciutto, K.L.; Montgomery, M.B.; Methods Mol. Biol. 2006, 332, 211-231. Identification of interacting proteins using the yeast two-hybrid screen. [PubMed]
Jothi, R.; Zotenko, E.; Tasneem, A.; Przytycka, T.M.; Bioinformatics2006, 22(7), 779-788. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. [PDF I PubMed]
Julenius, K.; Pedersen, A.G.; Mol. Biol. Evol. 2006, 23(11), 2039-2048. Protein evolution is faster outside the cell. [PubMed]
Junker, B.H.; Koschuetzki, D.; Schreiber, F.; BMC Bioinformatics2006, 7(1), 219. Exploration of biological network centralities with CentiBiN. [PDF I PubMed]
Kaiser, W.J.; Chaudhry, Y.; Sosnovtsev, S.V.; Goodfellow, I.G.; J. Gen. Virol. 2006, 87(Pt. 2), 363-368. Analysis of protein-protein interactions in the feline calicivirus replication complex. [PubMed]
Kanno, A.; Ozawa, T.; Umezawa, Y.; Anal. Chem.2006, 78(2), 556-560. Intein-mediated reporter gene assay for detecting protein-protein interactions in living mammalian cells. [PDF I PubMed]
Karyagina, A.; Ershova, A.; Titov, M.; Olovnikov, I.; Aksianov, E.; Ryazanova, A.; Kubareva, E.; Spirin, S.; Alexeevski, A.; J. Bioinform. Comput. Biol.2006, 4(2), 357-372. Analysis of conserved hydrophobic cores in proteins and supramolecular complexes. [PubMed]
Kaveti, S.; Engen, J.R.; Methods Mol. Biol.2006, 316, 179-197. Protein interactions probed with mass spectrometry. [PubMed]
Kikuchi, A.; Kishida, S.; Yamamoto, H.; Exp. Mol. Med. 2006, 38(1), 1-10. Regulation of Wnt signaling by protein-protein interaction and post-translational modifications. [PDF I PubMed]
Kim, H.S.; Mittenthal, J.E.; Caetano-Anolles, G.; BMC Bioinformatics2006, 7(1), 351. MANET: tracing evolution of protein architecture in metabolic networks. [PubMed]
Kim, J.J.; Zhang, Z.; Park, J.C.; Ng, S.K.; Bioinformatics2006, 22(5), 597-605. BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature. [PDF I PubMed]
Kim, M.; Park, K.; Jeong, E.J.; Shin, Y.B.; Chung, B.H.; Anal. Biochem. 2006, 351(2), 298-304. Surface plasmon resonance imaging analysis of protein-protein interactions using on-chip-expressed capture protein. [PDF I PubMed]
Kim, R.; Choi, C.Y.; Protein Pept. Lett. 2006, 13(1), 29-31. Fragment library-based representation system for protein conformation. [PubMed]
Kim, Y.; Chang, S.; Mol. Neurobiol.2006, 34(2), 129-136. Ever-expanding network of dynamin-interacting proteins. [PubMed]
Kirac, M.; Ozsoyoglu, G.; Yang, J.; Bioinformatics2006, 22(14), e260-e270. Annotating proteins by mining protein interaction networks. [PubMed]
Kiss-Toth, E.; Wyllie, D.H.; Holland, K.; Marsden, L.; Jozsa, V.; Oxley, K.M.; Polgar, T.; Qwarnstrom, E.E.; Dower, S.K.; Cell Signal2006, 18(2), 202-214. Functional mapping and identification of novel regulators for the Toll/Interleukin-1 signalling network by transcription expression cloning. [PDF I PubMed]
Koga, H.; Mol. Biosyst.2006, 2(3-4), 159-164. Establishment of the platform for reverse chemical genetics targeting novel protein-protein interactions. [PubMed]
Kogure, T.; Karasawa, S.; Araki, T.; Saito, K.; Kinjo, M.; Miyawaki, A.; Nat. Biotechnol. 2006, 24(5), 577-581. A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. [PDF I PubMed]
Komatsu, S.; Yano, H.; Proteomics2006, 6(14), 4057-4068. Update and challenges on proteomics in rice. [PDF I PubMed]
Komolov, K.E.; Senin, I.I.; Philippov, P.P.; Koch, K.W.; Anal. Chem. 2006, 78(4), 1228-1234. Surface plasmon resonance study of g protein/receptor coupling in a lipid bilayer-free system. [PDF I PubMed]
Koyuturk, M.; Kim, Y.; Topkara, U.; Subramaniam, S.; Szpankowski, W.; Grama, A.; J. Comput. Biol.2006, 13(2), 182-199. Pairwise alignment of protein interaction networks. [PDF I PubMed]
Krause, F.; Electrophoresis2006, 27(13), 2759-2781. Detection and analysis of protein-protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes. [PubMed]
Kremers, G.J.; Goedhart, J.; van Munster, E.B.; Gadella, T.W.; Biochemistry2006, 45(21), 6570-6580. Cyan and yellow super fluorescent proteins with improved brightness, protein folding, and FRET forster radius. [PDF I PubMed]
Krishnaswamy, S.R.; Williams, E.R.; Kirsch, J.F.; Protein Sci.2006, 15(6), 1465-1475. Free energies of protein-protein association determined by electrospray ionization mass spectrometry correlate accurately with values obtained by solution methods. [PDF I PubMed]
Kroch, A.E.; Fleming, K.G.; J. Mol. Biol. 2006, 357(1), 184-194. Alternate interfaces may mediate homomeric and heteromeric assembly in the transmembrane domains of SNARE proteins. [PDF I PubMed]
Kundrotas, P.J.; Alexov, E.G.; Biophys. J.2006 91(5), 1724-1736. Electrostatic properties of protein-protein complexes. [PDF I PubMed]
Kuroda, K.; Kato, M.; Mima, J.; Ueda, M.; Appl. Microbiol. Biotechnol. 2006, 71(2), 127-136. Systems for the detection and analysis of protein-protein interactions. [PDF I PubMed]
Lata, S.; Gavutis, M.; Tampe, R.; Piehler, J.; J. Am. Chem. Soc.2006, 128(7), 2365-2372. Specific and stable fluorescence labeling of histidine-tagged proteins for dissecting multi-protein complex formation. [PDF I PubMed]
Lee, H.; Tu, Z.; Deng, M.; Sun, F.; Chen, T.; OMICS2006, 10(1), 40-55. Diffusion kernel-based logistic regression models for protein function prediction. [PDF I PubMed]
Lee, T.Y.; Horng, J.T.; Juan, H.F.; Huang, H.D.; Wu, L.C.; Tsai, M.F.; Huang, H.C.; J. Comput. Chem. 2006, 27(9), 1020-1032. An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints. [PDF I PubMed]
Lee, W.P.; Jeng, B.C.; Pai, T.W.; Tsai, C.P.; Yu, C.Y.; Tzou, W.S.; BMC Genomics2006, 7(1), 89. Differential evolutionary conservation of motif modes in a yeast protein interaction network. [PDF I PubMed]
Lehrach, W.P.; Husmeier, D.; Williams, C.K.; Bioinformatics2006, 22(5), 532-540. A regularised discriminative model for the prediction of protein-peptide interactions. [PDF I PubMed]
Lemmens, I.; Lievens, S.; Eyckerman, S.; Tavernier, J.; Nat. Protoc. 2006, 1(1), 92-97. Reverse MAPPIT detects disruptors of protein-protein interactions in human cells. [PubMed]
Levin, A.M.; Coroneus, J.G.; Cocco, M.J.; Weiss, G.A.; Protein Sci. 2006, 15(3), 478-486. Exploring the interaction between the protein kinase A catalytic subunit and caveolin-1 scaffolding domain with shotgun scanning, oligomer complementation, NMR, and docking. [PDF I PubMed]
Li, H.; Li, J.; Wong, L.; Bioinformatics2006, 22(8), 989-996. Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale. [PDF I PubMed]
Li, J.J.; Huang, D.S.; Wang, B.; Chen, P.; Int. J. Biol. Macromol. 2006, 38(3-5), 241-247. Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. [PDF I PubMed]
Li, X.L.; Tan, S.H.; Ng, S.K.; Int. J. Data Min. Bioinform. 2006, 1(2), 138-149. Improving domain-based protein interaction prediction using biologically significant negative datasets. [PubMed]
Li, Z.; Wang, Y.; Wang, S.Z.; Zhang, X.S.; Chen, L.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2006, 1, 5527-5530. Alignment of protein interaction networks by integer quadratic programming. [PubMed]
Liang, Z.; Xu, M.; Teng, M.; Niu, L.; Bioinformatics2006, 22(17), 2175-2177. NetAlign: a web-based tool for comparison of protein interaction networks. [PDF I PubMed]
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.; Cell2006, 125(4), 801-814. A protein-protein interaction network for human inherited ataxias and disorders of purkinje cell degeneration. [PDF I PubMed]
Lim, S.G.; Tan, Y.J.; Goh, P.Y.; Lim, S.P.; Hong, W.J.; Intervirology2006, 49(1-2), 44-50. Use of an in vitro model and yeast two-hybrid system to investigate the pathogenesis of hepatitis C. [PubMed]
Lin, C.Y.; Chen, S.H.; Cho, C.S.; Chen, C.L.; Lin, F.K.; Lin, C.H.; Chen, P.Y.; Lo, C.Z.; Hsiung, C.A.; BMC Bioinformatics2006, 7(Suppl. 5), S18. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. [PubMed]
Lise, S.; Walker-Taylor, A.; Jones, D.T.; BMC Bioinformatics2006, 7(1), 310. Docking protein domains in contact space. [PDF I PubMed]
Liu, B.F.; Liang, J.J.; J. Biol. Chem.2006, 281(5), 2624-2630. Domain interaction sites of human lens beta B2-crystallin. [PubMed]
Liu, J.; Zheng, Q.; Deng, Y.; Kallenbach, N.R.; Lu, M.; J. Mol. Biol.2006, 361(1), 168-179. Conformational transition between four and five-stranded phenylalanine zippers determined by a local packing interaction. [PubMed]
Liu, R.; Hu, D.; Tan, X.; Lu, H.P.; J. Am. Chem. Soc. 2006, 128(31), 10034-10042. Revealing two-state protein-protein interactions of calmodulin by single-molecule spectroscopy. [PubMed]
Liu, S.; Li, Q.; Lai, L.; Proteins2006, 64(1), 68-78. A combinatorial score to distinguish biological and nonbiological protein-protein interfaces. [PDF I PubMed]
Liu, S.; Rauhut, R.; Vornlocher, H.P.; Luhrmann, R.; RNA2006, 12(7), 1418-1430. The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP. [PDF I PubMed]
Liu, Y.; Scolari, M.; Im, W.; Woo, H.J.; Proteins2006, 64(1), 156-166. Protein-protein interactions in actin-myosin binding and structural effects of R405Q mutation: a molecular dynamics study. [PDF I PubMed]
Lubovac, Z.; Gamalielsson, J.; Olsson, B.; Proteins2006, 64(4), 948-959. Combining functional and topological properties to identify core modules in protein interaction networks. [PubMed]
Lundholt, B.K.; Heydorn, A.; Bjorn, S.P.; Praestegaard, M.; Assay Drug Dev. Technol.2006, 4(6), 679-688. A simple cell-based HTS assay system to screen for inhibitors of p53-Hdm2 protein-protein interactions. [PubMed]
Magliery, T.J.; Regan, L.; Methods Biochem. Anal. 2006, 47, 391-405. Reassembled GFP: detecting protein-protein interactions and protein expression patterns. [PubMed]
Makino, T.; Gojobori, T.; Mol. Biol. Evol. 2006, 23(4), 784-789. The evolutionary rate of a protein is influenced by features of the interacting partners. [PDF I PubMed]
Mansuy-Schlick, V.; Delage-Mourroux, R.; Jouvenot, M.; Boireau, W.; Biosens. Bioelectron.2006, 21(9), 1830-1837. Strategy of macromolecular grafting onto a gold substrate dedicated to protein-protein interaction measurements. [PDF I PubMed]
Mathivanan, S; Periaswamy, B.; Gandhi, T.; Kandasamy, K.; Suresh, S.; Mohmood, R.; Ramachandra, Y.; Pandey, A.; BMC Bioinformatics2006, 7(Suppl. 5), S19. An evaluation of human protein-protein interaction data in the public domain. [PubMed]
Mewes, H.W.; Frishman, D.; Mayer, K.F.; Munsterkotter, M.; Noubibou, O.; Pagel, P.; Rattei, T.; Oesterheld, M.; Ruepp, A.; Stumpflen, V.; Nucleic Acids Res. 2006, 34, D169-D172. MIPS: analysis and annotation of proteins from whole genomes in 2005. [PDF I PubMed]
Mika, S.; Rost, B.; PLoS Comput. Biol.2006, 2(7), e79. Protein-protein interactions more conserved within species than across species. [PubMed]
Mikula, M.; Dzwonek, A.; Karczmarski, J.; Rubel, T.; Dadlez, M.; Wyrwicz, L.S.; Bomsztyk, K.; Ostrowski, J.; Proteomics2006, 6(8), 2395-2406. Landscape of the hnRNP K protein-protein interactome. [PDF I PubMed]
Minopoli, G.; Zambrano, N.; Russo, T.; Ital. J. Biochem. 2006, 55(3-4), 205-211. The cytosolic domain of APP and its possible role in the pathogenesis of Alzheimer's disease. [PubMed]
Moffet, D.A.; Khosla, C.; Cane, D.E.; Bioorg. Med. Chem. Lett. 2006, 16(1), 213-216. Modular polyketide synthases: investigating intermodular communication using 6 deoxyerythronolide B synthase module 2. [PDF I PubMed]
Monecke, P.; Borosch, T.; Brickmann, J.; Kast, S.M.; Biophys. J.2006, 90(3), 841-850. Determination of the interfacial water content in protein-protein complexes from free energy simulations. [PubMed]
Montañez, R.; Navas-Delgado, I.; Medina, M.A.; Aldana-Montes, J.F.; Sánchez-Jiménez, F.; Cell Immunol.2006, 244(2), 84-86. Information integration of protein-protein interactions as essential tools for immunomics. [PubMed]
Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.; J. Phys. Chem. B Condens. Matter. Mater. Surf. Interfaces Biophys. 2006, 110(22), 10962-10969. Unraveling the importance of protein-protein interaction: application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex. [PDF I PubMed]
Moreira, I.S.; Fernandes, P.A.; Ramos, M.J.; Proteins2006, 63(4), 811-821. Detailed microscopic study of the full zipA:FtsZ interface. [PDF I PubMed]
Moroziewicz, D.N.; Ju, W.; Zhong, R.; Znong, N.; Beijing Da Xue Xue Bao2006, 38(1), 38-40. N-terminal segments are the functional domains of CLN3-encoded battenin for protein interactions. [PubMed]
Morrison, J.L.; Breitling, R.; Higham, D.J.; Gilbert, D.R.; Bioinformatics2006, 22(16), 2012-2019. A lock-and-key model for protein-protein interactions. [PDF I PubMed]
Mougeot, J.L.; Bahrani-Mostafavi, Z.; Vachris, J.C.; McKinney, K.Q.; Gurlov, S.; Zhang, J.; Naumann, R.W.; Higgins, R.V.; Hall, J.B.; J. Mol. Biol. 2006, 358(1), 310-329. Gene expression profiling of ovarian tissues for determination of molecular pathways reflective of tumorigenesis. [PDF I PubMed]
Moza, B.; Buonpane, R.A.; Zhu, P.; Herfst, C.A.; Rahman, A.K.; McCormick, J.K.; Kranz, D.M.; Sundberg, E.J.; Proc. Natl. Acad. Sci. USA 2006, 103(26), 9867-9872. Long-range cooperative binding effects in a T cell receptor variable domain. [PDF I PubMed]
Müller, W.; Horstmann, N.; Hillen, W.; Sticht, H.; FEBS J.2006, 273(6), 1251-1261. The transcription regulator RbsR represents a novel interaction partner of the phosphoprotein HPr-Ser46-P in Bacillus subtilis. [PDF I PubMed]
Muppidi, J.R.; Lobito, A.A.; Ramaswamy, M.; Yang, J.K.; Wang, L.; Wu, H.; Siegel, R.M.; Cell Death Differ.2006, 13(10), 1641-1650. Homotypic FADD interactions through a conserved RXDLL motif are required for death receptor-induced apoptosis. [PDF I PubMed]
Murakami, Y.; Jones, S.; Bioinformatics2006, 22(14), 1794-1795. SHARP2: protein-protein interaction predictions using patch analysis. [PDF I PubMed]
Muresanu, L.; Pristovsek, P.; Lohr, F.; Maneg, O.; Mukrasch, M.D.; Ruterjans, H.; Ludwig, B.; Lucke, C.; J. Biol. Chem.2006, 281(20), 14503-14513. The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase - a combined NMR and computational approach. [PDF I PubMed]
Murphy, M.; Jason-Moller, L.; Bruno, J.; Curr. Protoc. Protein Sci.2006, Chapter 19, Unit 19.14. Using Biacore to measure the binding kinetics of an antibody-antigen interaction. [PubMed]
Nanni, L.; Lumini, A.; Bioinformatics2006, 22(10), 1207-1210. An ensemble of K-local hyperplanes for predicting protein-protein interactions. [PDF I PubMed]
Nazabal, A.; Wenzel, R.J.; Zenobi, R.; Anal. Chem. 2006, 78(11), 3562-3570. Immunoassays with direct mass spectrometric detection. [PDF I PubMed]
Ng, A.; Bursteinas, B.; Gao, Q.; Mollison, E.; Zvelebil, M.; Nucleic Acids Res. 2006, 34, D527-D534. pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. [PDF I PubMed]
Nguyen, T.P.; Ho, T.B.; Genome Inform.2006, 17(2), 35-45. Discovering signal transduction networks using signaling domain-domain interactions. [PubMed]
Oender, K.; Niedermayr, P.; Hintner, H.; Richter, K.; Koller, L.; Trost, A.; Bauer, J.W.; Hundsberger, H.; Assay Drug Dev. Technol.2006, 4(6), 709-719. Relative quantitation of protein-protein interaction strength within the yeast two-hybrid system via fluorescence beta-galactosidase activity detection in a high-throughput and low-cost manner. [PubMed]
Ortuso, F.; Langer, T.; Alcaro, S.; Bioinformatics2006, 22(12), 1449-1455. GBPM: GRID based pharmacophore model. Concept and application studies to protein-protein recognition. [PDF I PubMed]
Oti, M.; Snel, B.; Huynen, M.A.; Brunner, H.G.; J. Med. Genet. 2006, 43(8), 691-698. Predicting disease genes using protein-protein interactions. [PubMed]
Oyama, R.; Takashima, H.; Yonezawa, M.; Doi, N.; Miyamoto-Sato, E.; Kinjo, M.; Yanagawa, H.; Nucleic Acids Res. 2006, 34(14), e102. Protein-protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy. [PubMed]
Pal, G.; Kouadio, J.L.; Artis, D.R.; Kossiakoff, A.A.; Sidhu, S.S.; J. Biol. Chem. 2006, 281(31), 22378-22385. Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning. [PDF I PubMed]
Park, J.; Choi, J.; Yang, J.; Park, S.J.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2006, 1, 5810-5813. A rule-based detection of functional modules in protein-protein interaction networks. [PubMed]
Parks, D.J.; Lafrance, L.V.; Calvo, R.R.; Milkiewicz, K.L.; Jose Marugan, J.; Raboisson, P.; Schubert, C.; Koblish, H.K.; Zhao, S.; Franks, C.F.; Lattanze, J.; Carver, T.E.; Cummings, M.D.; Maguire, D.; Grasberger, B.L.; Maroney, A.C.; Lu, T.; Bioorg. Med. Chem. Lett. 2006, 16(12), 3310-3314. Enhanced pharmacokinetic properties of 1,4-benzodiazepine-2,5-dione antagonists of the HDM2-p53 protein-protein interaction through structure-based drug design. [PDF I PubMed]
Paschalidis, I.Ch.; Shen, Y.; Vakili, P.; Vajda, S.; Conf. Proc. IEEE Eng. Med. Biol. Soc. 2006, 1, 5330-5333. Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels. [PubMed]
Patargias, G.; Zitzmann, N.; Dwek, R.; Fischer, W.B.; J. Med. Chem. 2006, 49(2), 648-655. Protein-protein interactions: modeling the hepatitis C virus ion channel p7. [PDF I PubMed]
Patil, A.; Nakamura, H.; FEBS Lett. 2006, 580(8), 2041-2045. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. [PDF I PubMed]
Patton, W.F.; Biotechnol. J.2006, 1(3), 351. Protein-protein interactions: methods and applications. By Haian Fu (Ed.). [PubMed]
Peltier, J.B.; Cai, Y.; Sun, Q.; Zabrouskov, V.; Giacomelli, L.; Rudella, A.; Ytterberg, A.J.; Rutschow, H.; van Wijk, K.J.; Mol. Cell Proteomics2006, 5(1), 114-133. The oligomeric stromal proteome of A. thaliana chloroplasts. [PDF I PubMed]
Perry, J.; BMC Genomics2006, 7(1), 6. The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins. [PDF I PubMed]
Pfleger, K.D.; Dromey, J.R.; Dalrymple, M.B.; Lim, E.M.; Thomas, W.G.; Eidne, K.A.; Cell Signal2006, 18(10), 1664-16670. Extended bioluminescence resonance energy transfer (eBRET) for monitoring prolonged protein-protein interactions in live cells. [PDF I PubMed]
Pfleger, K.D.; Eidne, K.A.; Nat. Methods2006, 3(3), 165-174. Illuminating insights into protein-protein interactions using bioluminescence resonance energy transfer (BRET). [PDF I PubMed]
Pfleger, K.D.; Seeber, R.M.; Eidne, K.A.; Nat. Protoc. 2006, 1(1), 337-345. Bioluminescence resonance energy transfer (BRET) for the real-time detection of protein-protein interactions. [PubMed]
Phee, B.K.; Shin, D.H.; Cho, J.H.; Kim, S.H.; Kim, J.I.; Lee, Y.H.; Jeon, J.S.; Bhoo, S.H.; Hahn, T.R.; Proteomics2006, 6(12), 3671-3680. Identification of phytochrome-interacting protein candidates in Arabidopsis thaliana by co-immunoprecipitation coupled with MALDI-TOF MS. [PDF I PubMed]
Pitre, S.; Dehne, F.; Chan, A.; Cheetham, J.; Duong, A.; Emili, A.; Gebbia, M.; Greenblatt, J.; Jessulat, M.; Krogan, N.; Luo, X.; Golshani, A.; BMC Bioinformatics2006, 7(1), 365. PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. [PubMed]
Plake, C.; Schiemann, T.; Pankalla, M.; Hakenberg, J.; Leser, U.; Bioinformatics2006, 22(19), 2444-2445. ALIBABA: PubMed as a graph. [PubMed]
Pommier, Y.; Weinstein, J.N.; Aladjem, M.I.; Kohn, K.W.; Clin. Cancer Res.2006, 12(9), 2657-2661. Chk2 molecular interaction map and rationale for Chk2 inhibitors.[PubMed]
Pocklington, A.J.; Cumiskey, M.; Armstrong, J.D.; Grant, S.G.; Mol. Syst. Biol.2006, 2, 2006.0023. The proteomes of neurotransmitter receptor complexes form modular networks with distributed functionality underlying plasticity and behaviour. [PDF I PubMed]
Powell, D.W.; Merchant, M.L.; Link, A.J.; Expert Rev. Proteomics2006, 3(1), 63-74. Discovery of regulatory molecular events and biomarkers using 2D capillary chromatography and mass spectrometry. [PDF I PubMed]
Prachumwat, A.; Li, W.H.; Mol. Biol. Evol.2006, 23(1), 30-39. Protein function, connectivity, and duplicability in yeast. [PDF I PubMed]
Prieto, C.; De Las Rivas, J.; Nucleic Acids Res. 2006, 34, W298-W302. APID: agile protein interaction dataAnalyzer. [PubMed]
Prinz, A.; Diskar, M.; Erlbruch, A.; Herberg, F.W.; Cell Signal. 2006, 18(10), 1616-1625. Novel, isotype-specific sensors for protein kinase A subunit interaction based on bioluminescence resonance energy transfer (BRET). [PDF I PubMed]
Przulj, N.; Corneil, D.G.; Jurisica, I.; Bioinformatics2006, 22(8), 974-980. Efficient estimation of graphlet frequency distributions in protein-protein interaction networks. [PDF I PubMed]
Pyysalo, S.; Ginter, F.; Pahikkala, T.; Boberg, J.; Jarvinen, J.; Salakoski, T.; Int. J. Med. Inform. 2006, 75(6), 430-442. Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. [PDF I PubMed]
Qi, Y.; Bar-Joseph, Z.; Klein-Seetharaman, J.; Proteins2006, 63(3), 490-500. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. [PDF I PubMed]
Qu, E.; Guo, H.; Xu, C.; Liu, C.; Li, Z.; Cheng, B.; Zhang, D.; J. Biomed. Opt. 2006, 11(6), 064035. Method used to measure interaction of proteins with dual-beam optical tweezers. [PubMed]
Radaev, S.; Li, S.; Sun, P.D.; Acta Crystallogr. D Biol. Crystallogr. 2006, 62(Pt. 6), 605-612. A survey of protein-protein complex crystallizations. [PubMed]
Ramos, A.; Hollingworth, D.; Adinolfi, S.; Castets, M.; Kelly, G.; Frenkiel, T.A.; Bardoni, B.; Pastore, A.; Structure2006, 14(1), 21-31. The structure of the N-terminal domain of the fragile X mental retardation protein: a platform for protein-protein interaction. [PDF I PubMed]
Ro, H.S.; Koh, B.H.; Jung, S.O.; Park, H.K.; Shin, Y.B.; Kim, M.G.; Chung, B.H.; Proteomics2006, 6(7), 2108-2111. Surface plasmon resonance imaging protein arrays for analysis of triple protein interactions of HPV, E6, E6AP, and p53. [PDF I PubMed]
Robinette, D.; Neamati, N.; Tomer, K.B.; Borchers, C.H.; Expert. Rev. Proteomics2006, 3(4), 399-408. Photoaffinity labeling combined with mass spectrometric approaches as a tool for structural proteomics. [PubMed]
Roche, P.; Brown, J.; Denley, A.; Forbes, B.E.; Wallace, J.C.; Jones, E.Y.; Esnouf, R.M.; Proteins2006, 64(3), 758-768. Computational model for the IGF-II/IGF2r complex that is predictive of mutational and surface plasmon resonance data. [PubMed]
Rohila, J.S.; Chen, M.; Chen, S.; Chen, J.; Cerny, R.; Dardick, C.; Canlas, P.; Xu, X.; Gribskov, M.; Kanrar, S.; Zhu, J.K.; Ronald, P.; Fromm, M.E.; Plant J. 2006, 46(1), 1-13. Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice. [PDF I PubMed]
Roy, S.; Schnell, S.; Radivojac, P.; Comput. Biol. Chem. 2006, 30(4), 241-248. Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. [PubMed]
Rubinsztein, D.C.; Genome Biol.2006, 7(8), 229. Protein-protein interaction networks in the spinocerebellar ataxias. [PubMed]
Ruepp, A.; Doudieu, O.N.; van den Oever, J.; Brauner, B.; Dunger-Kaltenbach, I.; Fobo, G.; Frishman, G.; Montrone, C.; Skornia, C.; Wanka, S.; Rattei, T.; Pagel, P.; Riley, L.; Frishman, D.; Surmeli, D.; Tetko, I.V.; Oesterheld, M.; Stumpflen, V.; Mewes, H.W.; Nucleic Acids Res.2006, 34, D568-D571. The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. [PDF I PubMed]
Russell, M.; Berardi, P.; Gong, W.; Riabowol, K.; Exp. Cell. Res. 2006, 312(7), 951-961. Grow-ING, Age-ING and Die-ING: ING proteins link cancer, senescence and apoptosis. [PDF I PubMed]
Saeed, R.; Deane, C.M.; BMC Bioinformatics2006, 7(1), 128. Protein protein interactions, evolutionary rate, abundance and age. [PDF I PubMed]
Saha, R.P.; Bahadur, R.P.; Pal, A.; Mandal, S.; Chakrabarti, P.; BMC Struct. Biol. 2006, 6(1), 11. ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces. [PDF I PubMed]
Saitoh, T.; Ikegami, T.; Nakayama, M.; Teshima, K.; Akutsu, H.; Hase, T.; J. Biol. Chem. 2006, 281(15), 10482-10488. NMR study of the electron transfer complex of plant ferredoxin and sulfite reductase: mapping the interaction sites of ferredoxin. [PubMed]
Salazar, C.; Hofer, T.; Biosystems2006, 83(2-3), 195-206. Kinetic models of phosphorylation cycles: a systematic approach using the rapid-equilibrium approximation for protein-protein interactions. [PDF I PubMed]
Salgado, H.; Santos-Zavaleta, A.; Gama-Castro, S.; Peralta-Gil, M.; Peñaloza-Spínola, M.I.; Martínez-Antonio, A.; Karp, P.D.; Collado-Vides, J.; BMC Bioinformatics2006, 7, 5. The comprehensive updated regulatory network of Escherichia coli K-12. [PubMed]
Saluja, A.; Badkar, A.V.; Zeng, D.L.; Nema, S.; Kalonia, D.S.; J. Pharm. Sci. 2006, 95(9), 1967-1983. Application of high-frequency rheology measurements for analyzing protein-protein interactions in high protein concentration solutions using a model monoclonal antibody (IgG(2)). [PubMed]
Sarrouilhe, D.; di Tommaso, A.; Metaye, T.; Ladeveze, V.; Biochimie2006, 88(9), 1099-1113. Spinophilin: from partners to functions. [PDF I PubMed]
Sato, T.; Yamanishi, Y.; Horimoto, K.; Kanehisa, M.; Toh, H.; Bioinformatics2006, 22(20), 2488-2492. Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. [PubMed]
Sen, T.Z.; Kloczkowski, A.; Jernigan, R.L.; BMC Bioinformatics2006, 7(1), 355. Functional clustering of yeast proteins from the protein-protein interaction network. [PubMed]
Seshasayee, A.S.; In Silico Biol.2006, 6(1-2), 0012. Social behavior of the yeast protein-protein interaction network. [PubMed]
Shannon, P.T.; Reiss, D.J.; Bonneau, R.; Baliga, N.S.; BMC Bioinformatics2006, 7(1), 176. Gaggle: An open-source software system for integrating bioinformatics software and data sources. [PDF I PubMed]
Shatsky, M.; Nussinov, R.; Wolfson, H.J.; Proteins2006, 62(1), 209-217. Optimization of multiple-sequence alignment based on multiple-structure alignment. [PDF I PubMed]
Shi, Y.Y.; Miller, G.A.; Qian, H.; Bomsztyk, K.; Proc. Natl. Acad. Sci. USA 2006, 103(31), 11527-11532. Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences. [PubMed]
Shimura, K.; Waki, T.; Okada, M.; Toda, T.; Kimoto, I.; Kasai, K.I.; Electrophoresis2006, 27(10), 1886-1894. Analysis of protein-protein interactions with a multi-capillary electrophoresis instrument. [PDF I PubMed]
Shlomi, T.; Segal, D.; Ruppin, E.; Sharan, R.; BMC Bioinformatics2006, 7(1), 199. QPath: a method for querying pathways in a protein-protein interaction network. [PDF I PubMed]
Sielaff, I.; Arnold, A.; Godin, G.; Tugulu, S.; Klok, H.A.; Johnsson, K.; Chembiochem. 2006, 7(1), 194-202. Protein function microarrays based on self-immobilizing and self-labeling fusion proteins. [PDF I PubMed]
Sinz, A.; Mass Spectrom. Rev.2006, 25(4), 663-682. Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. [PDF I PubMed]
Sivasubramanian, A.; Chao, G.; Pressler, H.M.; Wittrup, K.D.; Gray, J.J.; Structure2006, 14(3), 401-414. Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. [PDF I PubMed]
Song, E.; Gao, S.; Tian, R.; Ma, S.; Huang, H.; Guo, J.; Li, Y.; Zhang, L.; Gao, Y.; Mol. Cell Proteomics2006, 5(8), 1368-1381. A high-efficiency strategy for binding property characterization of peptide-binding domains. [PDF I PubMed]
Soyer, O.S.; Salathe, M.; Bonhoeffer, S.; J. Theor. Biol.2006, 238(2), 416-425. Signal transduction networks: topology, response and biochemical processes. [PDF I PubMed]
Stiffler, M.A.; Grantcharova, V.P.; Sevecka, M.; Macbeath, G.; J. Am. Chem. Soc.2006, 128(17), 5913-5922. Uncovering quantitative protein interaction networks for mouse PDZ domains using protein microarrays. [PDF I PubMed]
Stoevesandt, O.; Brock, R.; Nat. Protoc. 2006, 1(1), 223-229. One-step analysis of protein complexes in microliters of cell lysate using indirect immunolabeling & fluorescence cross-correlation spectroscopy. [PubMed]
Su, Y.; Ding, Y.; Jiang, M.; Jiang, W.; Hu, X.; Zhang, Z.; Mol. Cell. Biochem. 2006, 289(1-2), 159-166. Associations of protein 4.2 with band 3 and ankyrin. [PDF I PubMed]
Sun, S.; Zhao, Y.; Jiao, Y.; Yin, Y.; Cai, L.; Zhang, Y.; Lu, H.; Chen, R., Bu, D.; FEBS Lett.2006, 580(7), 1891-1896. Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm. [PDF I PubMed]
Susanna, K.A.; Fusetti, F.; Thunnissen, A.M.; Hamoen, L.W.; Kuipers, O.P.; Microbiology2006, 152(Pt. 2), 473-483. Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. [PDF I PubMed]
Suthram, S.; Shlomi, T.; Ruppin, E.; Sharan, R.; Ideker, T.; BMC Bioinformatics2006, 7, 360. A direct comparison of protein interaction confidence assignment schemes. [PubMed]
Suzuki, H.; J. Physiol.2006, 575(Pt. 2), 373-377. Protein-protein interactions in the mammalian brain. [PubMed]
Takahashi, H.; Miyazawa, M.; Ina, Y.; Fukunishi, Y.; Mizukoshi, Y.; Nakamura, H.; Shimada, I.; J. Biomol. NMR2006, 34(3), 167-177. Utilization of methyl proton resonances in cross-saturation measurement for determining the interfaces of large protein-protein complexes. [PDF I PubMed]
Takeda-Shitaka, M.; Terashi, G.; Chiba, C.; Takaya, D.; Umeyama, H.; Med. Chem. 2006, 2(2), 191-201. FAMS complex: a fully automated homology modeling system for protein complex structures. [PubMed]
Teyra, J.; Doms, A.; Schroeder, M.; Pisabarro, M.T.; BMC Bioinformatics2006, 7(1), 104. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. [PDF I PubMed]
Thom, G.; Cockroft, A.C.; Buchanan, A.G.; Joberty Candotti, C.; Cohen, E.S.; Lowne, D.; Monk, P.; Shorrock-Hart, C.P.; Jermutus, L.; Minter, R.R.; Proc. Natl. Acad. Sci. USA2006, 103(20), 7619-7624. Probing a protein-protein interaction by in vitro evolution. [PDF I PubMed]
Tobi, D.; Bahar, I.; Proteins2006, 62(4), 970-981. Optimal design of protein docking potentials: efficiency and limitations. [PDF I PubMed]
Topinka, C.; Shyu, C.R.; AMIA Annu. Symp. Proc. 2006, 1123. Predicting cancer interaction networks using text-mining and structure understanding. [PubMed]
Torres, G.E.; J. Neurochem. 2006, [epub ahead of print]. The dopamine transporter proteome. [PDF I PubMed]
Tovchigrechko, A.; Vakser, I.A.; Nucleic Acids Res. 2006, 34, W310-W314. GRAMM-X public web server for protein-protein docking. [PubMed]
Trosset, J.Y.; Dalvit, C.; Knapp, S.; Fasolini, M.; Veronesi, M.; Mantegani, S.; Gianellini, L.M.; Catana, C.; Sundstrom, M.; Stouten, P.F.; Moll, J.K.; Proteins2006, 64(1), 60-67. Inhibition of protein-protein interactions: the discovery of druglike beta-catenin inhibitors by combining virtual and biophysical screening. [PDF I PubMed]
Truant, R.; Atwal, R.; Burtnik, A.; Biochem. Cell. Biol. 2006, 84(6), 912-917. Hypothesis: Huntingtin may function in membrane association and vesicular trafficking. [PubMed]
Tu, K.; Yu, H.; Li, Y.X.; J. Biotechnol.2006, 124(3), 475-485. Combining gene expression profiles and protein-protein interaction data to infer gene functions. [PDF I PubMed]
Tutar, Y.; Protein Pept. Lett. 2006, 13(3), 307-311. Target peptide recognition by S100P protein and role of central linker region and dimer interface. [PubMed]
Uhrig, J.F.; Planta2006, 224(4), 771-781. Protein interaction networks in plants. [PDF I PubMed]
Umezawa, Y.; Chem. Asian J.2006, 1(3), 304-312. Illuminating molecular processes in living cells. [PubMed]
Valente, A.X.; Cusick, M.E.; Nucleic Acids Res. 2006, 34(9), 2812-2819. Yeast protein interactome topology provides framework for coordinated-functionality. [PDF I PubMed]
van Delft, M.F.; Huang, D.C.; Cell Res. 2006, 16(2), 203-213. How the Bcl-2 family of proteins interact to regulate apoptosis. [PDF I PubMed]
Van Dijk, A.D.; Bonvin, A.M.; Bioinformatics2006, 22(19), 2340-2347. Solvated docking: introducing water into the modelling of biomolecular complexes. [PubMed]
van Dijk, A.D.; Kaptein, R.; Boelens, R.; Bonvin, A.M.; J. Biomol. NMR2006, 34(4), 237-244. Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. [PDF I PubMed]
van Driel, M.A.; Bruggeman, J.; Vriend, G.; Brunner, H.G.; Leunissen, J.A.; Eur. J. Hum. Genet.2006, 14(5), 535-542. A text-mining analysis of the human phenome. [PDF I PubMed]
Vasilescu, J.; Figeys, D.; Curr. Opin. Biotechnol.2006, 17(4), 394-399. Mapping protein-protein interactions by mass spectrometry. [PubMed]
Vaynberg, J.; Qin, J.; Trends Biotechnol.2006, 24(1), 22-27. Weak protein-protein interactions as probed by NMR spectroscopy. [PDF I PubMed]
Waharte, F.; Spriet, C.; Heliot, L.; Cytometry A2006, 69A(4), 299-306. Setup and characterization of a multiphoton FLIM instrument for protein-protein interaction measurements in living cells. [PDF I PubMed]
Walsh, E.P.; Lamont, D.J.; Beattie, K.A.; Stark, M.J.; Methods Mol. Biol. 2006, 365, 235-246. Proteins interacting with Saccharomyces cerevisiae type 1 protein phosphatase catalytic subunit identified by single-step affinity purification and mass spectrometry. [PubMed]
Wang, B.; Chen, P.; Huang, D.S.; Li, J.J.; Lok, T.M.; Lyu, M.R.; FEBS Lett.2006, 580(2), 380-384. Predicting protein interaction sites from residue spatial sequence profile and evolution rate. [PDF I PubMed]
Wang, B.; Wong, H.S.; Huang, D.S.; Protein Pept. Lett.2006, 13(10), 999-1005. Inferring protein-protein interacting sites using residue conservation and evolutionary information. [PubMed]
Wang, H.J.; Tannukit, S.; Wen, X.; Shapiro, J.L.; Snead, M.L.; Paine, M.L.; Eur. J. Oral. Sci.2006, 114(Suppl. 1), 276-279. Using the yeast two-hybrid assay to discover protein partners for the leucine-rich amelogenin peptide and for tuftelin-interacting protein 11. [PubMed]
Wang, Y.; Hanley, R.; Klemke, R.L.; J. Proteome Res. 2006, 5(4), 907-915. Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer. [PDF I PubMed]
Wang, Y.E.; DeLisi, C.; Genome Inform.2006, 17(1), 23-35. Inferring protein-protein interactions in viral proteins by co-evolution of conserved side chains. [PubMed]
Warringer, J.; Blomberg, A.; BMC Evol. Biol. 2006, 6(1), 61. Evolutionary constraints on yeast protein size. [PubMed]
Weissman, K.J.; Hong, H.; Popovic, B.; Meersman, F.; Chem. Biol. 2006, 13(6), 625-636. Evidence for a protein-protein interaction motif on an acyl carrier protein domain from a modular polyketide synthase. [PDF I PubMed]
Whitty, A.; Kumaravel, G.; Nat. Chem. Biol.2006, 2(3), 112-118. Between a rock and a hard place? [PubMed]
Willis, R.C.; Hogue, C.W.; Curr. Protoc. Bioinformatics2006, Chapter 8, Unit 8.9. Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). [PubMed]
Winter, C.; Henschel, A.; Kim, W.K.; Schroeder, M.; Nucleic Acids Res. 2006, 34, D310-D314. SCOPPI: a structural classification of protein-protein interfaces. [PDF I PubMed]
Wu, X.; Zhu, L.; Guo, J.; Zhang, D.Y.; Lin, K.; Nucleic Acids Res. 2006, 34(7), 2137-2150. Prediction of yeast protein-protein interaction network: insights from the Gene Ontology and annotations. [PDF I PubMed]
Wuchty, S.; Barabasi, A.L.; Ferdig, M.T.; BMC Evol. Biol.2006, 6, 8. Stable evolutionary signal in a yeast protein interaction network. [PDF I PubMed]
Xia, Y.; Lu, L.J.; Gerstein, M.; J. Mol. Biol.2006, 357(1), 339-349. Integrated prediction of the helical membrane protein interactome in yeast. [PDF I PubMed]
Xirasagar, S.; Gustafson, S.F.; Huang, C.C.; Pan, Q.; Fostel, J.; Boyer, P.; Merrick, B.A.; Tomer, K.B.; Chan, D.D.; Yost, K.J.; Choi, D.; Xiao, N.; Stasiewicz, S.; Bushel, P.; Waters, M.D.; Bioinformatics2006, 22(7), 874-882. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application. [PDF I PubMed]
Xu, Y.; Lu, H.; Kennedy, J.P.; Yan, X.; McAllister, L.A.; Yamamoto, N.; Moss, J.A.; Boldt, G.E.; Jiang, S.; Janda, K.D.; J. Comb. Chem. 2006, 8(4), 531-539. Evaluation of "credit card" libraries for inhibition of HIV-1 gp41 fusogenic core formation. [PubMed]
Xu, Y.; Shi, J.; Yamamoto, N.; Moss, J.A.; Vogt, P.K.; Janda, K.D.; Bioorg. Med. Chem. 2006, 14(8), 2660-2673. A credit-card library approach for disrupting protein-protein interactions. [PDF I PubMed]
Yaffe, M.B.; Sci. STKE2006, 2006(340), pe28. "Bits" and pieces. [PDF I PubMed]
Yang, L.; Tan, C.H.; Hsieh, M.J.; Wang, J.; Duan, Y.; Cieplak, P.; Caldwell, J.; Kollman, P.A.; Luo, R.; J. Phys. Chem. B Condens. Matter. Mater. Surf. Interfaces Biophys. 2006, 110(26), 13166-13176. New-generation Amber united-atom force field. [PDF I PubMed]
Yang, Q.; Siganos, G.; Faloutsos, M.; Lonardi, S.; Comput. Syst. Bioinformatics Conf. 2006, 299-310. Evolution versus "intelligent design": comparing the topology of protein-protein interaction networks to the Internet. [PubMed]
Yap, K.L.; Zhou, M.M.; Results Probl. Cell. Differ. 2006, 41, 1-23. Structure and function of protein modules in chromatin biology. [PubMed]
Yeats, C.; Maibaum, M.; Marsden, R.; Dibley, M.; Lee, D.; Addou, S.; Orengo, C.A.; Nucleic Acids Res. 2006, 34, D281-D284. Gene3D: modelling protein structure, function and evolution. [PDF I PubMed]
Yoder, N.C.; Kumar, K.; J. Am. Chem. Soc. 2006, 128(1), 188-191. Selective protein-protein interactions driven by a phenylalanine interface. [PDF I PubMed]
Yu, H.; Paccanaro, A.; Trifonov, V.; Gerstein, M.; Bioinformatics2006, 22(7), 823-829. Predicting interactions in protein networks by completing defective cliques. [PDF I PubMed]
Yu, J.; Fotouhi, F.; J. Med. Syst. 2006, 30(1), 39-44. Computational approaches for predicting protein-protein interactions: a survey. [PubMed]
Yu, X.; Lin, J.; Masuda, T.; Esumi, N.; Zack, D.J.; Qian, J.; Nucleic Acids Res.2006, 34(3), 917-927. Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae. [PDF I PubMed]
Yuk, J.S.; Kim, H.S.; Jung, J.W.; Jung, S.H.; Lee, S.J.; Kim, W.J.; Han, J.A.; Kim, Y.M.; Ha, K.S.; Biosens. Bioelectron. 2006, 21(8), 1521-1528. Analysis of protein interactions on protein arrays by a novel spectral surface plasmon resonance imaging. [PDF I PubMed]
Zhang, D.; Martyniuk, C.J.; Trudeau, V.L.; Bioinformatics2006, 22(20), 2459-2462. SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation. [PubMed]
Zhang, L.; Shao, C.; Zheng, D.; Gao, Y.; Mol. Cell Proteomics2006, 5(7), 1224-1232. An integrated machine learning system to computationally screen protein databases for protein binding peptide ligands. [PDF I PubMed]
Zhou, Y.; Wang, R.; Li, L.; Xia, X.; Sun, Z.; J. Mol. Biol.2006, 359(4), 1150-1159.
Inferring functional linkages between proteins from evolutionary scenarios. [PDF I PubMed]