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The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family

M. Fischer, M. Knoll, D. Sirim, F. Wagner, S. Funke, J. Pleiss
2007 Bioinformatics  
The Cytochrome P450 Engineering Database (CYPED) has been designed to serve as a tool for a comprehensive and systematic comparison of protein sequences and structures within the vast and diverse family  ...  of cytochrome P450 monooxygenases (CYPs).  ...  We further are grateful for the unknown reviewer's comments which contributed greatly to the improvement of data content and the user interface of the CYPED.  ... 
doi:10.1093/bioinformatics/btm268 pmid:17510166 fatcat:epgwi5p74vcjdiskqwpe3rllcy

The Cytochrome P450 Engineering Database: integration of biochemical properties

Demet Sirim, Florian Wagner, Andrey Lisitsa, Jürgen Pleiss
2009 BMC Biochemistry  
For the comprehensive and systematic comparison of protein sequences and structures the Cytochrome P450 Engineering Database (CYPED) was established.  ...  Description: The new version of the CYPED contains information on sequences and structures of 8613 and 47 proteins, respectively, which strictly follow Nelson's classification rules for homologous families  ...  Acknowledgements This work was supported by the German Research Foundation (SFB 706).  ... 
doi:10.1186/1471-2091-10-27 pmid:19909539 pmcid:PMC2779185 fatcat:6iwbgy75ejcx3l5jghzknlayh4

Phylogenomics databases for facilitating functional genomics in rice

Ki-Hong Jung, Peijian Cao, Rita Sharma, Rashmi Jain, Pamela C Ronald
2015 Rice  
hydrolases, kinases, transcription factors, transporters, and cytochrome P450 monooxygenases.  ...  To more accurately analyze functional redundancy in the rice genome, we have developed a phylogenomics databases for six large gene families in rice, including those for glycosyltransferases, glycoside  ...  Other features are similar to those of the GT database. Rice Cytochrome P450 database Cytochrome P450 monooxygenases belong to the superfamily of proteins containing a heme cofactor.  ... 
doi:10.1186/s12284-015-0060-7 pmid:26223238 pmcid:PMC4519439 fatcat:7dmdbqkjyva47p2jlzzu75el5m

DetoxiProt: an integrated database for detoxification proteins

Zhen Yang, Ying Yu, Lei Yao, Guangui Li, Lin Wang, Yiyao Hu, Haibin Wei, Li Wang, Riadh Hammami, Roxanne Razavi, Yang Zhong, Xufang Liang
2011 BMC Genomics  
Results: To store, retrieve and analyze the information related to their features and functions, we developed the DetoxiProt, a comprehensive database for annotation of these proteins.  ...  This database would be a valuable source for toxicologists, pharmacologists and medicinal chemists. DetoxiProt database is freely available at  ...  At the gene-family level, the cytochrome P450 family and the glutathione S-transferase family are the most abundant groups, with 68 and 48 members identified in humans, respectively.  ... 
doi:10.1186/1471-2164-12-s3-s2 pmid:22369658 pmcid:PMC3333179 fatcat:3nxy4in3zfearmzbdki6qfqalu

SorghumFDB: sorghum functional genomics database with multidimensional network analysis

Tian Tian, Qi You, Liwei Zhang, Xin Yi, Hengyu Yan, Wenying Xu, Zhen Su
2016 Database: The Journal of Biological Databases and Curation  
SorghumFDB integrated knowledge of sorghum gene family classifications (transcription regulators/factors, carbohydrate-active enzymes, protein kinases, ubiquitins, cytochrome P450, monolignol biosynthesis  ...  We further constructed a dynamic network of multidimensional biological relationships, comprised of the coexpression data, protein-protein interactions and miRNA-target pairs.  ...  It contains eight gene family categories, super families for transcription factors/regulators (TFs/TRs), carbohydrate-active enzymes (CAZymes), protein kinases (PKs), ubiquitins (UBs), cytochrome P450  ... 
doi:10.1093/database/baw099 pmid:27352859 pmcid:PMC4921789 fatcat:oohnxb2pqzazjki4ljbykmeot4

The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis

Karel Miettinen, Sabrina Iñigo, Lukasz Kreft, Jacob Pollier, Christof De Bo, Alexander Botzki, Frederik Coppens, Søren Bak, Alain Goossens
2017 Nucleic Acids Research  
The database can be accessed by direct browsing or through convenient search tools including keyword, BLAST, plant species and substructure options.  ...  Given that the number of characterized triterpene biosynthesis enzymes has been growing fast recently, the need for a database specifically focusing on triterpene enzymology became eminent.  ...  ACKNOWLEDGEMENTS We thank Annick Bleys for help with preparing the article and all TriForC consortium partners for contributing to and curating the database content.  ... 
doi:10.1093/nar/gkx925 pmid:29045755 pmcid:PMC5753214 fatcat:6azzybvovfh7jaug2tqmb2mrxe

Prediction and analysis of the modular structure of cytochrome P450 monooxygenases

Demet Sirim, Michael Widmann, Florian Wagner, Jürgen Pleiss
2010 BMC Structural Biology  
Cytochrome P450 monooxygenases (CYPs) form a vast and diverse family of highly variable sequences.  ...  Description: This systematic comparison of CYPs based on the Cytochrome P450 Engineering Database (CYPED) involved sequence and structure analysis of more than 8000 sequences. 31 structures have been applied  ...  MW contributed to the analysis and to the manuscript. FW carried out the annotation and generated the web interface. JP supervised the project and finalized the manuscript.  ... 
doi:10.1186/1472-6807-10-34 pmid:20950472 pmcid:PMC3224734 fatcat:w4r6nphj6ncwvdwcaof4iofju4

MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes

A. Braun, B. Halwachs, M. Geier, K. Weinhandl, M. Guggemos, J. Marienhagen, A. J. Ruff, U. Schwaneberg, V. Rabin, D. E. Torres Pazmino, G. G. Thallinger, A. Glieder
2012 Database: The Journal of Biological Databases and Curation  
To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases.  ...  MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner.  ...  Acknowledgements We would like to thank Andrea Camattari, Peter Remler, Norbert Klempier, Kurt Faber, Peter Macheroux, Helmut Schwab and the whole OXYGREEN team for assistance and fruitful discussions.  ... 
doi:10.1093/database/bas028 pmid:22730453 pmcid:PMC3381223 fatcat:ofcgk7iedzh65i5cvt23ssuoyq

Deciphering protein evolution and fitness landscapes with latent space models

Xinqiang Ding, Zhengting Zou, Charles L. Brooks III
2019 Nature Communications  
and stability and hence are well-suited to help guide protein engineering efforts.  ...  Moreover, the model is also useful in predicting protein mutational stability landscapes and quantifying the importance of stability in shaping protein evolution.  ...  Troy Wymore for insightful discussions and also for reading the manuscript. X.D. is supported by the NIH grant GM037554 and the Rackham Predoctoral Fellowship Program from the University of Michigan.  ... 
doi:10.1038/s41467-019-13633-0 pmid:31822668 pmcid:PMC6904478 fatcat:7tzyk2nee5gtfpugn2mnqymufe

The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases

Michael Knoll, Thomas M Hamm, Florian Wagner, Virginia Martinez, Jürgen Pleiss
2009 BMC Bioinformatics  
Results: The PHA Depolymerase Engineering Database (DED, http://www.ded.uni-stuttgart.de) has been established as a tool for systematic analysis of this enzyme family.  ...  Conclusion: The DED is a valuable tool which can be applied to identify new PHA depolymerase sequences from complete genomes in silico, to classify PHA depolymerases, to predict their biochemical properties  ...  Conclusion The PHA Depolymerase Engineering Database (DED) has been designed to serve as a navigation and analysis tool of PHA depolymerases.  ... 
doi:10.1186/1471-2105-10-89 pmid:19296857 pmcid:PMC2666664 fatcat:lfrfjzvkijbepia2ykvlljo7am

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

Trupti Joshi, Kapil Patil, Michael R Fitzpatrick, Levi D Franklin, Qiuming Yao, Jeffrey R Cook, Zheng Wang, Marc Libault, Laurent Brechenmacher, Babu Valliyodan, Xiaolei Wu, Jianlin Cheng (+3 others)
2012 BMC Genomics  
ML, LB, BV and XW performed experiments, generated data and provided feedback. ZW and JC predicted protein structures for all genes. DX provided overall guidance.  ...  Methods: SoyKB has many useful tools such as Affymetrix probe ID search, gene family search, multiple gene/ metabolite search supporting co-expression analysis, and protein 3D structure viewer as well  ...  Acknowledgements The authors wish to thank all researchers who have contributed data to the database. The  ... 
doi:10.1186/1471-2164-13-s1-s15 pmid:22369646 pmcid:PMC3303740 fatcat:5aepmj5je5c5tjozf2fja4e6ze

CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes

Jaeyoung Choi, Kyeongchae Cheong, Kyongyong Jung, Jongbum Jeon, Gir-Won Lee, Seogchan Kang, Sangsoo Kim, Yin-Won Lee, Yong-Hwan Lee
2012 Nucleic Acids Research  
CFGP also introduced Favorite, a personalized virtual space for data storage and analysis with these six tools.  ...  The Taxonomy Browser of CFGP 2.0 allows users to interactively navigate through a large number of genomes according to their taxonomic positions.  ...  ://ftfd.snu.ac.kr/) (34), (iii) Fungal Cytochrome P450 Database (FCPD; http://p450.riceblast .snu.ac.kr/) (35), (iv) Fungal Secretome Database (FSD; http://fsd.snu.ac.kr/) (39), (v) Eukaryotic DNAJ and  ... 
doi:10.1093/nar/gks1163 pmid:23193288 pmcid:PMC3531191 fatcat:476qr3rejfempg6uubbtywejp4

OPM database and PPM web server: resources for positioning of proteins in membranes

Mikhail A. Lomize, Irina D. Pogozheva, Hyeon Joo, Henry I. Mosberg, Andrei L. Lomize
2011 Nucleic Acids Research  
The database offers downloadable coordinates of proteins and peptides with membrane boundaries. A gallery of protein images and several visualization tools are provided.  ...  The Orientations of Proteins in Membranes (OPM) database is a curated web resource that provides spatial positions of membrane-bound peptides and proteins of known three-dimensional structure in the lipid  ...  For example, secretory phospolipases A2 and cytochromes P450 were taken in the physologically relevant monomeric state, even though PISA identifies some of them as stable dimers.  ... 
doi:10.1093/nar/gkr703 pmid:21890895 pmcid:PMC3245162 fatcat:kkm24rsl4rfenklrkfhjcyynfy

Using Gene Expression to Study Specialized Metabolism—A Practical Guide

Riccardo Delli-Ponti, Devendra Shivhare, Marek Mutwil
2021 Frontiers in Plant Science  
Many of the specialized metabolites are expressed in a narrow range of organs, tissues, and cell types, suggesting a tight regulation of the responsible biosynthetic pathways.  ...  Finally, we analyze the performance of co-expression networks and show that they are a valuable addition to elucidating multiple the biosynthetic pathways of specialized metabolism.  ...  P450, family 703, subfamily A, polypeptide 2 Biosynthesis of medium-chain hydroxy fatty acids Morant et al., 2007 AT1G69500 CYP704B1 Cytochrome P450, family 704, subfamily B, polypeptide 1  ... 
doi:10.3389/fpls.2020.625035 pmid:33510763 pmcid:PMC7835209 fatcat:mtruldeqpzbk3cszsceh6fbxcq

The Medium-Chain Dehydrogenase/Reductase Engineering Database: A systematic analysis of a diverse protein family to understand sequence-structure-function relationship

Michael Knoll, Jürgen Pleiss
2008 Protein Science  
The Medium-Chain Dehydrogenase/Reductase Engineering Database (MDRED, http://www.mdred. uni-stuttgart.de) has been established to serve as an analysis tool for a systematic investigation of sequence-structure-function  ...  The length of the QSDL is predictive for tetramer (short QSDL) and dimer (long QSDL) formation. The class of medium QSDL includes both tetrameric and dimeric MDRs.  ...  Acknowledgments Valuable contributions by Ima Avalos Vizcarra and Florian Wagner are acknowledged. This work was financially supported by the Deutsche Bundesstiftung Umwelt.  ... 
doi:10.1110/ps.035428.108 pmid:18614751 pmcid:PMC2548362 fatcat:mavbojwb4fchnnmfmyvimv2amu
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