======== GPS (Group-based Phosphorylation Scoring) Web server release note (ver 1.10)==== Date : Jan. 10. 2005 Version : 1.10 Author of this document : Yu Xue, Fengfeng Zhou, Minjie Zhu, Guoliang Chen, Xuebiao Yao, , Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, PR China School of Life Science, University of Science and Technology of China, Hefei 230027, PR China Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA Yu Xue, Fengfeng Zhou and Minjie Zhu are members of Cuckoo Workgroup, LCD, USTC *** Contents of this distribution : 71 protein kinase (PK) groups; 216 unique PKs; BLOSUM62 matrix is used. Materials & Data preparation: We get the data set of phosphorylation sites from Phospho.ELM which also includes the data of PhosphoBase. After removing the phosphorylation sites with ambiguous information of PKs, we get 1404 items. We also manually checked the recent publications and got 597 more items. After clustering some homology PKs (protein kinases) with too few known phosphorylation sites into a unique group, we got 52 PK groups with 177 unique PKs, including ABL, ALK, AMPK, ATM, AURORA-A, AURORA-B, BTK, CAK, CaM-I/IV, CaM-II, CDKs, Chk1/Chk2, CK1, CK2, DAPK, DNA-PK, EGFR, EPHA/B, FAK, Fer, Fes, FGFR, Fms, Fgr, Fyn/Yes, GRK, GSK3, Hck, IGFR, IKK, ILK, IPL1(yeast), IR, JAK, KIS, KIT, LCK, LYN, MAPKK, MAPK, MAPKAPK2, MAPKK, MAPKKK, MET/RON, MLCK, MTOR, NIMA, P34CDC2, PAK, PDGFR, PDK, PHK, PKA, PKB, PKC, PKG, PKR, PLK, RAF1, RET, RLK, ROCK, S6K, SGK, SRC, SYK, TIE2, TYK2, TRK, VEGFR, and ZAP70, etc. The kinases with few verified phosphorylation sites are excluded. Updation (compring to 1.0): 1. NEK -> NIMA; 2. CHK -> Chk1/Chk2; 3. Adding 19 more PK groups. *** How to use the web server : * Please refer to http://973-proteinweb.ustc.edu.cn/gps/gps_web/faq.php, the web server is easy-to-use. *** Copyright and license : Copyright (C) 2004 LCD,USTC, All Rights Reserved *** Acknowledgments : We would like to thank Dr. T.J. Gibson and Dr. F. Diella for providing the data set of Phospho.ELM for this work. The work was supported by grants from Chinese Natural Science Foundation (39925018 and 30121001), Chinese Academy of Science (KSCX2-2-01), Chinese 973 project (2002CB713700), and American Cancer Society (RPG-99-173-01) to X. Yao. X. Yao is a GCC Distinguished Cancer Research Scholar. ======== end of release note ======== ======== GPS (Group-based Phosphorylation Scoring) Web server release note (ver 1.0)==== Date : Oct. 06. 2004 Version : 1.0 Author of this document : Yu Xue, Fengfeng Zhou, Minjie Zhu, Guoliang Chen, Xuebiao Yao, , Department of Computer Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, PR China School of Life Science, University of Science and Technology of China, Hefei 230027, PR China Department of Physiology, Morehouse School of Medicine, Atlanta, GA 30310, USA Yu Xue, Fengfeng Zhou and Minjie Zhu are members of Cuckoo Workgroup, LCD, USTC *** Contents of this distribution : 52 protein kinase (PK) groups; 177 unique PKs; Materials & Data preparation: We get the data set of phosphorylation sites from Phospho.ELM which also includes the data of PhosphoBase. After removing the phosphorylation sites with ambiguous information of PKs, we get 1404 items. We also manually checked the recent publications and got 597 more items. After clustering some homology PKs (protein kinases) with too few known phosphorylation sites into a unique group, we got 52 PK groups with 177 unique PKs, including ABL, ALK, AMPK, ATM, AURORA-B, BTK, CAK, CAM-II, CDK, CHK, CK1, CK2, DAPK, DNA-PK, EGFR, EPHA, FAK, FGFR, FYN, GRK, GSK3, IGFR, IKK, IR, JAK, LCK, LYN, MAPKK, MAPK, MAPKAPK2, MET, MTOR, NEK, P34CDC2, PAK, PDGFR, PDK, PHK, PKA, PKB, PKC, PKG, PKR, PLK, ROCK, S6K, SGK, SRC, SYK, TRK, VEGFR, and ZAP70, etc. The kinases with less than ten verified phosphorylation sites are excluded. *** How to use the web server : * Please refer to http://973-proteinweb.ustc.edu.cn/gps/gps_web/faq.php, the web server is easy-to-use. *** Copyright and license : Copyright (C) 2004 LCD,USTC, All Rights Reserved *** Acknowledgments : We would like to thank Dr. T.J. Gibson and Dr. F. Diella for providing the data set of Phospho.ELM for this work. The work was supported by grants from Chinese Natural Science Foundation (39925018 and 30121001), Chinese Academy of Science (KSCX2-2-01), Chinese 973 project (2002CB713700), and American Cancer Society (RPG-99-173-01) to X. Yao. X. Yao is a GCC Distinguished Cancer Research Scholar. ======== end of release note ========