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J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. Conservation and structural analysis of the Xenopus laevis phospho-proteome. submitted. J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J. Fernandez, A. Sali, J. Kilmartin, T. Davis, D. Agard. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol 22, 132-137, 2015. PMCID4318760 A. Politis, C. Schmidt, E. Tjioe, A. Sandercock, K. Lasker, Y. Gordiyenko, D. Russel, A. Sali, C. Robinson. Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex. Chem Biol 22, 117-128, 2015. PMCID4306531 E. Verschueren, J. VonDollen, P. Cimermancic, A. Sali, N. Gulbahce, N. Krogan. Analyzing AP-MS data with Mass Spectrometry Interaction Statistics (MIST). Curr Protoc Bioinformatics 49, 8.19.1-8.19.16, 2015. PMCID TBD by Journal B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. In: Current Protocols in Bioinformatics, John Wiley and Sons, 2014. Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M. Rout, B. Chait. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics 13, 2927-2943, 2014. PMCID4223482 S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T. Weiss, A. Markina-Inarrairaegui, J. Bonanno, M. Sauder, S. Burley, B.T. Chait, S. Almo, M. Rout, A. Sali. Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. Mol Cell Proteomics 13, 2911-2926, 2014. PMCID4223481 M.H. Medema, P. Cimermancic, A. Sali, E. Takano, M. Fischbach. A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis. PLoS Comput Biol 10, e1004016, 2014. PMCID4256081 P. Cimermancic, M.H. Medema, J. Claesen, K. Kurita, L. Wieland Brown, K. Mavrommatis, A. Pati, P.A. Godfrey, M. Koehrsen, J. Clardy, B.W. Birren, E. Takano, A. Sali, R.G. Linington, M. Fischbach. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158, 412-421, 2014. PMCID4123684 D. Schneidman-Duhovny, R. Pellarin, A. Sali. Uncertainty in Integrative Structural Modeling. Curr Opin Struct Biol 28, 96-104, 2014. PMCID4252396 J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex. Cell 158, 1125-1135, 2014. PMCID4151992 X. Zeng-Elmore, X. Gao, R. Pellarin, D. Schneidman-Duhovny, X. Zhang, K. Kozacka, Y. Tang, A. Sali, R. Chalkley, R. Cote, F. Chu. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol 426, 3713-3728, 2014. PMCID4253074 T. Street, X. Zeng, R. Pellarin, M. Bonomi, A. Sali, M. Kelly, F. Chu, D. Agard. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol 12, 2393-2404, 2014. PMCID TBD by Journal R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B. Chait, M. Rout, S. Dokudovskaya. Molecular Architecture and Function of the SEA Complex - a Modulator of the TORC1 Pathway. Mol Cell Proteomics 13, 2855-2870, 2014. PMCID4223477 G.Q. Dong, S. Calhoun, H. Fan, C. Kalyanaraman, N. London, M. Branch, S. Mashiyama, M. Jacobson, B. Shoichet, P. Babbitt, R. Armstrong, A. Sali. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 6, 1687-1699, 2014. PMCID4068255 Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat 21, 203-208, 2014. PMCID3874021 B. Webb, K. Lasker, J. Velazquez-Muriel, D. Schneidman-Duhovny, R. Pellarin, M. Bonomi, C. Greenberg, B. Raveh, E. Tjioe, D. Russel, A. Sali. Modeling of proteins and their assemblies with the Integrative Modeling Platform. In: Structural Genomics. Ed: Y. Chen, pp. 277-295, Humana Press, London, UK, 2014. K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ. Structure 22, 1239-1251, 2014. PMCID4322757 U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 42, 336-346, 2014. PMCID3965011 M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. Determining protein complex structures based on a Bayesian model of in vivo FRET data. Mol Cell Proteomics 13, 2812-2823, 2014. PMCID4223474 B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Methods in Molecular Biology. Ed: D. Kihara, 1137, pp. 1-15, Springer, New York, 2014.