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Topic: Proteomics

MF Lensink, IH Moal, PA Bates, PL Kastritis, AS Melquiond, E Karaca, C Schmitz, M Van Dijk, AM Bonvin, M Eisenstein, B Jimenez-Garcia, S Grosdidier, A Solernou, L Perez-Cano, C Pallara, J Fernandez-Recio, J Xu, P Muthu, KP Kilambi, JJ Gray, S Grudinin, G Derevyanko, JC Mitchell, J Wieting, E Kanamori, Y Tsuchiya, Y Murakami, J Sarmiento, DM Standley, M Shirota, K Kinoshita, H Nakamura, M Chavent, DW Ritchie, H Park, J Ko, H Lee, C Seok, Y Shen, D Kozakov, S Vajda, PJ Kundrotas, IA Vakser, BG Pierce, H Hwang, T Vreven, Z Weng, I Buch, E Farkash, HJ Wolfson, M Zacharias, S Qin, HX Zhou, SY Huang, X Zou, JA Wojdyla, C Kleanthous, SJ Wodak, "Blind Prediction of Interfacial Water Positions in CAPRI", Proteins, 82: 620–632. doi: 10.1002/prot.24439  (Journal Publication)  [More Details]  [Online]

Yang Shen, Michael D. Altman, Akbar Ali, Madhavi N. L. Nalam, Hong Cao, Tariq M. Rana, Celia A. Schiffer, and Bruce Tidor, "Testing the Substrate-Envelope Hypothesis with Designed Pairs of Compounds", ACS Chemical Biology 2013 8 (11), 2433-2441  (Journal Publication)  [More Details]  [Online]

Yang Shen, "Improved flexible refinement of protein docking in CAPRI rounds 22–27", Proteins, 81: 2129–2136. doi: 10.1002/prot.24404  (Journal Publication)  [More Details]  [Online]

Yang Shen, Michael K. Gilson, and Bruce Tidor, "Charge Optimization Theory for Induced-Fit Ligands", Journal of Chemical Theory and Computation 2012 8 (11), 4580-4592  (Journal Publication)  [More Details]  [Online]

Y. Sun, U.M. Braga-Neto and E.R. Dougherty, "A systematic model of the LC-MS proteomics pipeline", BMC Genomics, GENSIPS'2011 Special Issue, Vol. 13, Suppl. 6, October 2012, p. S2, doi:10.1186/1471-2164-13-S6-S2  (Journal Publication)  [More Details]  [Online]

Y. Sun, J. Zhang, U.M. Braga-Neto and E.R. Dougherty,, "BPDA2d — A 2D global optimization based Bayesian peptide detection algorithm for LC-MS", Bioinformatics, Vol. 28, No. 4, February 2012, pp. 564-572  (Journal Publication)  [More Details]  [Online]

Kozakov, D., Hall, D. R., Beglov, D., Brenke, R., Comeau, S. R., Shen, Y., Li, K., Zheng, J., Vakili, P., Paschalidis, I. Ch. and Vajda, S, "Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19", Proteins, 78: 3124–3130. doi: 10.1002/prot.22835 (2010)  (Journal Publication)  [More Details]  [Online]

Dmitri Beglov, Ryan Brenke, Gwo-Yu Chuang, David Hall, Melissa Landon, Chi Ho Ngan, Yang Shen, Spencer Thiel, Brandon Zerbe, Dima Kozakov, Sandor Vajda, "Identification of Druggable Hot Spots on Proteins and in Protein–Protein Interfaces", In D Beglov, R Brenke, GY Chuang, D Hall, M Landon eds., Computational Protein-Protein Interactions, 2010, CRC Press  (Book Chapter)  [More Details]

Yang Shen, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, "Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes", PLoS Comput Biol 4(10): e1000191. doi: 10.1371/journal.pcbi.1000191 (2008)  (Journal Publication)  [More Details]  [Online]

Shen, Y., Brenke, R., Kozakov, D., Comeau, S. R., Beglov, D. and Vajda, S. , "Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI", Proteins, 69: 734–742. doi: 10.1002/prot.21754  (Journal Publication)  [More Details]  [Online]

IC Paschalidis, Y Shen, P Vakili, S Vajda, "SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking", Automatic Control, IEEE Transactions on 52 (4), 664-676   (Journal Publication)  [More Details]  [Online]

Comeau, S. R., Kozakov, D., Brenke, R., Shen, Y., Beglov, D. and Vajda, S, "ClusPro: Performance in CAPRI rounds 6–11 and the new server", Proteins, 69: 781–785. doi: 10.1002/prot.21795  (Journal Publication)  [More Details]  [Online]