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2P455 Web service of the Protein Data Bank Japan (PDBj)(48. Bioinformatics, genomics and proteomics (II),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Takashi Kosada, Reiko Igarashi, Yumiko Kengaku, Yasuyo Morita, Kanna Matsuura, Masami Kusunoki, Yukiko Shimizu, Reiko Yamashita, Haruki Nakamura
2006 Seibutsu Butsuri  
One of thc most vital fimctions in organisms ;s Lhe ]'egulation of gene cxpressien achieved by a network of transcription facLors and their turget genes. In recent years, 1argc amuunts of sequenee and struetura] infurmation for genes and proteins have emcrged imm various ongotng .genome projccts, However, the functions of many genes and proteins T:main te be clurified. Also, the mechanisms by which the transcriptlon factors identify their target genes are stilt not well undcrstood, Ib achieve
more » ... tter undcrstanding of the gene Tegulation mecbanjsm, it is vital to idcntil'y pruteins thut bind to DNA and RNA, and target sites of transcription fuctors. Wb have dcveloped the nietheds to predict DNAIRNA-binding proteins based on atnino-aeid compositio", sequence centext aligmnent and structural information, and to prcdict targets of transctiption factors based on str-cniral information and computer sinlulations, In order to apply tliese methocls to a genomc-wide prcdiction, vve conducted a pilot study fbr thc Yeusr genome. For this purpose, we havc eonstrueted a database, which purs togcthcr various kinds ef datu related to gene regulatjon in the yeast ge]{)me, including ORF, trmiscription facLor sequences and featurcs, structural information. known binding sites. We haye integraled the predicted DNA binding probability and binding sit:s For euch transcriptaon t'aetor intu the database. and analyzcd thc rclationship u,ith other annotaLieii data in the databasc, These iesults wi]1 provide insight into the meehanisrn of gene regulation network in Ydast. Ljniversity BiomedicalEnginceri]gReseurchOrgunization We havc becn working on deyelopingtcenstructing crystallization suppoft system fer 1arge-scale srmcmiral bie]og}, studies as a purt ef Ibotein 3000 preject A huge database has been organized to rccord al1 results: cloning, expressien, purification, crystallizaLitm und summary of structure determination, ImbrmaLien of eueh target in a]l stcps is connected and viewed i'ia a bi'owsing interface. We prescnt hcre eur perfoTmancc of crystallizarion system atid discuss th: prneedure based on actual results. It woutd be helpfu1 fnr pLamning oi' a laboratory use and this systeTn is being develepedtimpioved fi}T wide-ranging uscrs, {D Crystallization Order sysLem: A person can ordcr a screening or refinement eiperinient by sclcetjng a kiL or a foiiuatted reagent. (2) Analysis for sample qualiLy, Native PAGE, Dynaniic Light ScatteTing, mass spcctrometry (MALDI-MS), N-tem]i-al sequenee, peptide unalysis CrystallizationJImaging system: A regutar scrccning is performed with 96-vs,ell sitting drop prate and jmaged rer 2 menths by Crystai Farm (tsexlls). Mlcro-hatch hy TERA (RTKEN), 96-wcll hanging drop CKajixx) and micrp-ci},staLtjzation by Musguite (Tl'P) are atsn uscd. (4) Soim:are developmen[ for crystallization, All iirtages and experimentat information are exported from any imaging system to a dtttabasc scrver in a simple tbrniat. The]i users can access thc databnsc to look im'ough and score all crystals togethcr. Teols tu figure out the next condition and to make a forniuLati on are under devclopmcnt. 2P455Web service of the Protein Data Bank Japan (PDBj) KannaHaruki Osaka The world wide Protein Data Bunk (wwPDB) is the sole internatiellal p-blic repository for thrcc ditnensional srructure data ef bielegical macromoleculcs, and it serves for supporting cssential bielugicul sciences, The PDBj. RCSB and MSD-EBI have formed the wwPDB on 2003 te m2Lintain a single archjve of macromeleeular struetural data[4], The PDBj has enhanced the capabiljties and has pcrformcd the following activiLies since it wus formed in 200U, at the lnsLiLuLc tbr Protein Research, Osaka University. 1. PDB search web site [1]. 2. PDB depesition siLe [1], 3. FTP download sLtc [1]. 4, Process and ReLeuse of Deposited entries. 5. Eiploiting an XML formal database[2], a 3D viewcr, and secollclary databases[31. Convenient methods of finding partictLlur e]tries from sueh many cntries and the deposjtion mcthod ineluding the abov: list 1. to 5. will be presented here. Also thc eulltribution of PDBj deposition and precessing PDB ennies wM be showii. The nuniber of depssniolls and processipg through the PDBj are increasing, The PDBj provides timely scrviccs Eor users a}id depesitors of Asian and Oceaniuii regions. 11he PDBj would 1ikc to solicit you te depesit your entries throvgh the PDBj deposition sitc, Retcrcnccs
doi:10.2142/biophys.46.s409_3 fatcat:h3gxm3c3bvbe5m5jzftflissom

Announcing mandatory submission of PDBx/mmCIF format files for crystallographic depositions to the Protein Data Bank (PDB)

Paul D. Adams, Pavel V. Afonine, Kumaran Baskaran, Helen M. Berman, John Berrisford, Gerard Bricogne, David G. Brown, Stephen K. Burley, Minyu Chen, Zukang Feng, Claus Flensburg, Aleksandras Gutmanas (+23 others)
2019 Acta Crystallographica Section D: Structural Biology  
doi:10.1107/s2059798319004522 pmid:30988261 pmcid:PMC6465986 fatcat:lfqllnbmuzapnc4cv2r4za3ncy

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

Jasmine Y Young, John D Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M Berrisford, G Jawahar Swaminathan, Thomas J Oldfield, Aleksandras Gutmanas, Reiko Igarashi (+39 others)
2018 Database: The Journal of Biological Databases and Curation  
Citation details: Young,J.Y., Westbrook,J.D., Feng,Z. et al. Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The V C The Author(s) worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability,
more » ... ccessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a highquality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/
doi:10.1093/database/bay002 pmid:29688351 pmcid:PMC5804564 fatcat:pymncvy65zghjgdhleavnz7oce

Protein Data Bank: the single global archive for 3D macromolecular structure data

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh, David S Goodsell (+70 others)
2018 Nucleic Acids Research  
The Protein Data Bank (PDB) is the single global archive of experimentally determined three-dimensional (3D) structure data of biological macromolecules. Since 2003, the PDB has been managed by the Worldwide Protein Data Bank (wwPDB; wwpdb.org), an international consortium that collaboratively oversees deposition, validation, biocuration, and open access dissemination of 3D macromolecular structure data. The PDB Core Archive houses 3D atomic coordinates of more than 144 000 structural models of
more » ... proteins, DNA/RNA, and their complexes with metals and small molecules and related experimental data and metadata. Structure and experimental data/metadata are also stored in the PDB Core Archive using the readily extensible wwPDB PDBx/mmCIF master data format, which will continue to evolve as data/metadata from new experimental techniques and structure determination methods are incorporated by the wwPDB. Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific wwPDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans.
doi:10.1093/nar/gky949 pmid:30357364 pmcid:PMC6324056 fatcat:ca3xenxsdzgvnb7vcwi2gtomoa

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
2016 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors thank the PDBj annotators, Reiko Igarashi, Yumiko Kengaku, Hasumi Cho, Junko Sato for their constant effort that makes the wwPDB possible at all, and Reiko Yamashita and Takahiro  ... 
doi:10.1093/nar/gkw962 pmid:27789697 pmcid:PMC5210648 fatcat:pan6qdrpe5bknfgkot6blgnp6u

Abstracts for the 29th Annual Meeting of the Japan Neuroscience Society (Neuroscience2006)

2006 Neuroscience research  
PS1A-E062 Role of PTP in the morphogenesis of Purkinje cell dendrites in the cerebellum Nobuna Fukazawa 1 , Mineko Kengaku 2 , Nobuaki Maeda 1 1 Dept. of Dev. Neurosci., Tokyo Metro.  ...  PS1A-E061 Developmental change and function of chondroitin sulfate deposited around Purkinje cells Nobuaki Maeda 1 , Maki Ishii 1 , Isao Nagata 2 , Yumiko Shimazaki 1 1 Dept. of Dev.  ...  Research funds: Grant C1 from Kansai Medical University PS3P-H103 Unusually folded SOD1 species sequester specific motor molecules and inhibit the axonal transport of their cargos Minako Tateno 1 , Yumiko  ... 
doi:10.1016/j.neures.2006.04.004 fatcat:mja5yvu2tbcjrmfx3a7abvvicm