Journal of structural and functional genomics最新文献

Structural Genomics: General Applications 结构基因组学:一般应用

Journal of structural and functional genomics Pub Date : 2021-01-01 DOI: 10.1007/978-1-0716-0892-0

Yu Wai Chen, C. Yiu

引用次数: 6

Classification of ligand molecules in PDB with graph match-based structural superposition 基于图匹配结构叠加的PDB配体分子分类

Journal of structural and functional genomics Pub Date : 2016-12-23 DOI: 10.1007/s10969-016-9209-x

C. Shionyu-Mitsuyama, A. Hijikata, T. Tsuji, T. Shirai

引用次数: 1

Special issue: big data analyses in structural and functional genomics 特刊:结构和功能基因组学中的大数据分析

Journal of structural and functional genomics Pub Date : 2016-12-01 DOI: 10.1007/s10969-016-9213-1

S. Yokoyama, K. Yura

引用次数: 3

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix 利用敏感矩阵的启发式算法加速蛋白质序列相似性搜索

Journal of structural and functional genomics Pub Date : 2016-12-01 DOI: 10.1007/s10969-016-9210-4

Kyungtaek Lim, Kazunori D. Yamada, M. Frith, K. Tomii

引用次数: 1

Toward the next step in G protein-coupled receptor research: a knowledge-driven analysis for the next potential targets in drug discovery 迈向G蛋白偶联受体研究的下一步:为药物发现的下一个潜在靶点进行知识驱动分析

Journal of structural and functional genomics Pub Date : 2016-12-01 DOI: 10.1007/s10969-016-9212-2

K. Nagata, Y. Katayama, Tomomi Sato, Yeondae Kwon, T. Kawabata

引用次数: 5

HOMCOS: an updated server to search and model complex 3D structures. HOMCOS:一个更新的服务器来搜索和建模复杂的3D结构。

Journal of structural and functional genomics Pub Date : 2016-12-01 Epub Date: 2016-08-13 DOI: 10.1007/s10969-016-9208-y

Takeshi Kawabata

{"title":"HOMCOS: an updated server to search and model complex 3D structures.","authors":"Takeshi Kawabata","doi":"10.1007/s10969-016-9208-y","DOIUrl":"https://doi.org/10.1007/s10969-016-9208-y","url":null,"abstract":"The HOMCOS server ( http://homcos.pdbj.org ) was updated for both searching and modeling the 3D complexes for all molecules in the PDB. As compared to the previous HOMCOS server, the current server targets all of the molecules in the PDB including proteins, nucleic acids, small compounds and metal ions. Their binding relationships are stored in the database. Five services are available for users. For the services \"Modeling a Homo Protein Multimer\" and \"Modeling a Hetero Protein Multimer\", a user can input one or two proteins as the queries, while for the service \"Protein-Compound Complex\", a user can input one chemical compound and one protein. The server searches similar molecules by BLAST and KCOMBU. Based on each similar complex found, a simple sequence-replaced model is quickly generated by replacing the residue names and numbers with those of the query protein. A target compound is flexibly superimposed onto the template compound using the program fkcombu. If monomeric 3D structures are input as the query, then template-based docking can be performed. For the service \"Searching Contact Molecules for a Query Protein\", a user inputs one protein sequence as the query, and then the server searches for its homologous proteins in PDB and summarizes their contacting molecules as the predicted contacting molecules. The results are summarized in \"Summary Bars\" or \"Site Table\"display. The latter shows the results as a one-site-one-row table, which is useful for annotating the effects of mutations. The service \"Searching Contact Molecules for a Query Compound\" is also available.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-016-9208-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34307029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 37

NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. NLDB:酶促反应中三维蛋白质-配体相互作用的数据库。

Journal of structural and functional genomics Pub Date : 2016-12-01 Epub Date: 2016-08-16 DOI: 10.1007/s10969-016-9206-0

Yoichi Murakami, Satoshi Omori, Kengo Kinoshita

{"title":"NLDB: a database for 3D protein-ligand interactions in enzymatic reactions.","authors":"Yoichi Murakami, Satoshi Omori, Kengo Kinoshita","doi":"10.1007/s10969-016-9206-0","DOIUrl":"https://doi.org/10.1007/s10969-016-9206-0","url":null,"abstract":"NLDB (Natural Ligand DataBase; URL: http://nldb.hgc.jp ) is a database of automatically collected and predicted 3D protein-ligand interactions for the enzymatic reactions of metabolic pathways registered in KEGG. Structural information about these reactions is important for studying the molecular functions of enzymes, however a large number of the 3D interactions are still unknown. Therefore, in order to complement such missing information, we predicted protein-ligand complex structures, and constructed a database of the 3D interactions in reactions. NLDB provides three different types of data resources; the natural complexes are experimentally determined protein-ligand complex structures in PDB, the analog complexes are predicted based on known protein structures in a complex with a similar ligand, and the ab initio complexes are predicted by docking simulations. In addition, NLDB shows the known polymorphisms found in human genome on protein structures. The database has a flexible search function based on various types of keywords, and an enrichment analysis function based on a set of KEGG compound IDs. NLDB will be a valuable resource for experimental biologists studying protein-ligand interactions in specific reactions, and for theoretical researchers wishing to undertake more precise simulations of interactions.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-016-9206-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34656283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

VaProS: a database-integration approach for protein/genome information retrieval. VaProS：蛋白质/基因组信息检索的数据库整合方法。

Journal of structural and functional genomics Pub Date : 2016-12-01 Epub Date: 2016-12-23 DOI: 10.1007/s10969-016-9211-3

Takashi Gojobori, Kazuho Ikeo, Yukie Katayama, Takeshi Kawabata, Akira R Kinjo, Kengo Kinoshita, Yeondae Kwon, Ohsuke Migita, Hisashi Mizutani, Masafumi Muraoka, Koji Nagata, Satoshi Omori, Hideaki Sugawara, Daichi Yamada, Kei Yura

{"title":"VaProS: a database-integration approach for protein/genome information retrieval.","authors":"Takashi Gojobori, Kazuho Ikeo, Yukie Katayama, Takeshi Kawabata, Akira R Kinjo, Kengo Kinoshita, Yeondae Kwon, Ohsuke Migita, Hisashi Mizutani, Masafumi Muraoka, Koji Nagata, Satoshi Omori, Hideaki Sugawara, Daichi Yamada, Kei Yura","doi":"10.1007/s10969-016-9211-3","DOIUrl":"10.1007/s10969-016-9211-3","url":null,"abstract":"Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein-protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts' knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/ .","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5274651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77807969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Successful completion of a semi-automated enzyme-free cloning method. 成功完成半自动化无酶克隆方法。

Journal of structural and functional genomics Pub Date : 2016-09-01 Epub Date: 2016-08-09 DOI: 10.1007/s10969-016-9207-z

Stefano Bonacci, Scilla Buccato, Domenico Maione, Roberto Petracca

{"title":"Successful completion of a semi-automated enzyme-free cloning method.","authors":"Stefano Bonacci, Scilla Buccato, Domenico Maione, Roberto Petracca","doi":"10.1007/s10969-016-9207-z","DOIUrl":"https://doi.org/10.1007/s10969-016-9207-z","url":null,"abstract":"Nowadays, in scientific fields such as Structural Biology or Vaccinology, there is an increasing need of fast, effective and reproducible gene cloning and expression processes. Consequently, the implementation of robotic platforms enabling the automation of protocols is becoming a pressing demand. The main goal of our study was to set up a robotic platform devoted to the high-throughput automation of the polymerase incomplete primer extension cloning method, and to evaluate its efficiency compared to that achieved manually, by selecting a set of bacterial genes that were processed either in the automated platform (330) or manually (94). Here we show that we successfully set up a platform able to complete, with high efficiency, a wide range of molecular biology and biochemical steps. 329 gene targets (99 %) were effectively amplified using the automated procedure and 286 (87 %) of these PCR products were successfully cloned in expression vectors, with cloning success rates being higher for the automated protocols respect to the manual procedure (93.6 and 74.5 %, respectively). ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-016-9207-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34356165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Structural mapping of Kelch13 mutations associated with artemisinin resistance in malaria. 疟疾中与青蒿素耐药性相关的Kelch13突变的结构定位。

Journal of structural and functional genomics Pub Date : 2016-09-01 Epub Date: 2016-07-11 DOI: 10.1007/s10969-016-9205-1

Gajinder Pal Singh, Preeti Goel, Amit Sharma

引用次数: 18