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Publications
- Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM. 2009.
Survey of large protein complexes in D. vulgaris reveals great structural diversity. PNAS doi: 10.1073/pnas.0813068106. [PDF]|[Supporting information]
- Kim SH, Shin DH, Kim R, Adams P, Chandonia JM. 2008. Structural genomics of minimal organisms: pipeline and results.
Methods Mol Biol. 426:475-96.
[PDF]|[PubMed]
- Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP,
Chothia C, Murzin AG. 2008. Data growth and its impact on the
SCOP database: new developments.
Nucleic Acids Res
Jan;36(Database issue):D419-25. Epub 2007 Nov 13.
[PDF]|[PubMed]
- Chandonia JM. 2007. StrBioLib: a Java library for development of custom computational structural biology applications. Bioinformatics 23: 2018-20. [Preprint PDF]|[PubMed]|[abstract]
- Lowery TJ, Pelton JG, Chandonia JM, Kim R, Yokota H, Wemmer DE. 2007. NMR structure of the N-terminal domain of the replication initiator protein DnaA. J Struct Funct Genomics [PDF]|[PubMed]|[abstract]
- Shin DH, Hou J, Chandonia JM, Das D, Choi IG, Kim R, Kim SH. 2007. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center. J Struct Funct Genomics [PDF]|[PubMed]|[abstract]
- Yooseph S, ... (13 authors) ..., Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, ... (6 authors) ..., Brenner SE, ... (6 authors) ..., Venter JC. 2007. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biol 5:e16. [PDF]|[PubMed]|[abstract]
- Chandonia JM, Brenner SE. 2006. The impact of structural genomics: expectations and outcomes. Science 311:347-51. [PDF]|[Supplementary Info]|[TOC PDF]|[PubMed]|[abstract]
- Chandonia JM, Kim SH, Brenner SE. 2006. Target selection and deselection at the Berkeley Structural Genomics Center. Proteins 62:356-370. [PDF]|[Supplementary Info]|[PubMed]|[abstract]
- Chandonia JM, Kim SH. 2006. Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications. BMC Struct Biol 6:7. [PDF]|[PubMed]
- Smith A, Chandonia JM, Brenner SE. 2006. ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics 22:618-620. [PDF]|[Supplementary Info]|[PubMed]|[abstract]
- Chandonia JM, Brenner SE. 2005. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets. Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, Shanghai, China [PDF]|[abstract]
- Chandonia JM, Brenner SE. 2005. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches. Proteins 58:166-79. [PDF]|[Supplementary data]|[PubMed]|[abstract]
- Zhang Y, Chandonia JM, Ding C, Holbrook SR. 2005. Comparative mapping of sequence-based and structure-based protein domains. BMC Bioinformatics 6: 77. [PDF]|[PubMed]|[abstract]
- Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IC, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, Kim R. 2005. Structural Genomics of Minimal Organisms and Protein Fold Space. J Struct Funct Genomics 6:63-70. [PDF]|[PubMed]
- Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2004. The ASTRAL Compendium in 2004. Nucleic Acids Res 32 Database issue:D189-92. [PDF]|[PubMed]|[abstract]
- Chandonia JM, Earnest TN, Brenner SE. 2004. Structural genomics and structural biology: compare and contrast. Genome Biology 5:343. [PDF]|[PubMed]
- Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res 14:1188-90. [PDF]|[PubMed]|[abstract]
- Chandonia JM, Cohen FE. 2003. New local potential useful for genome annotation and 3D modeling. J Mol Biol 332:835-50. [PDF]|[abstract]
- Chandonia JM, Walker NS, Lo Conte L, Koehl P, Levitt M, Brenner SE. 2002. ASTRAL compendium enhancements. Nucleic Acids Res 30:260-3. [PDF]|[PubMed]|[abstract]
- Chandonia JM, Karplus M. 1999. New methods for accurate prediction of protein secondary structure. Proteins 35:293-306. [PDF]|[abstract]
- Schwartz HL, Chandonia JM, Kash SF, Kanaani J, Tunnell E, ... Richter W, Baekkeskov S. 1999. High-resolution autoreactive epitope mapping and structural modeling of
the 65 kDa form of human glutamic acid decarboxylase. J Mol Biol 287:983-99. [PDF]|[abstract]
- Chandonia JM, Karplus M. 1996. The importance of larger data sets for protein secondary structure
prediction with neural networks. Protein Sci 5:768-74. [OCR PDF]|[PDF]|[abstract]
- Chandonia JM, Karplus M. 1995. Neural networks for secondary structure and structural class predictions. Protein Sci 4:275-85. [OCR PDF]|[PDF]|[abstract]
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Research
Publications