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BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

Ida Schomburg, Antje Chang, Sandra Placzek, Carola Söhngen, Michael Rother, Maren Lang, Cornelia Munaretto, Susanne Ulas, Michael Stelzer, Andreas Grote, Maurice Scheer, Dietmar Schomburg
2012 Nucleic Acids Research  
KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts.  ...  The supplemental database DRENDA provides more than 910 000 new EC numberdisease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information  ...  ACKNOWLEDGEMENTS The authors wish to express their thanks to all collaborating scientists, who performed the literature annotation and created the ligand structures.  ... 
doi:10.1093/nar/gks1049 pmid:23203881 pmcid:PMC3531171 fatcat:xzcsbi44aff7vdhbcyxpn4ww5m

BRENDA in 2015: exciting developments in its 25th year of existence

Antje Chang, Ida Schomburg, Sandra Placzek, Lisa Jeske, Marcus Ulbrich, Mei Xiao, Christoph W. Sensen, Dietmar Schomburg
2014 Nucleic Acids Research  
Functional and structural data of more than 190 000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented.  ...  The EnzymeDetector genome annotation tool and the reaction database BKM-react including reactions from BRENDA, KEGG and MetaCyc were improved. The website was redesigned providing new query options.  ...  With the fast growing number of data and knowledge in the 'OMICS' area, the continuous integration of new data and new developments in BRENDA has to meet the expectations as an enzyme and enzyme function  ... 
doi:10.1093/nar/gku1068 pmid:25378310 pmcid:PMC4383907 fatcat:sdwv66mdaffetnkky63xabh3jm

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0 [article]

Iván Domenzain, Benjamín Sánchez, Mihail Anton, Eduard J. Kerkhoven, Aarón Millán-Oropeza, Céline Henry, Verena Siewers, John P. Morrissey, Nikolaus Sonnenschein, Jens Nielsen
2021 bioRxiv   pre-print
Streamlined integration of enzyme constraints and proteomics data into GEMs was first enabled by the GECKO method, allowing the study of phenotypes constrained by protein limitations.  ...  Here, we upgraded the GECKO toolbox in order to enhance models with enzyme and proteomics constraints for any organism with an available GEM reconstruction.  ...  Additionally, several utility functions were integrated into the toolbox in order to enable basic simulation purposes, accessible retrieval of enzyme parameters, integration of proteomics data as constraints  ... 
doi:10.1101/2021.03.05.433259 fatcat:eqbqt5gww5bpbotkpe6ibu4f2a

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
In section 3, we discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in Big Data era.  ...  We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.  ...  Acknowledgments This work was supported by grants from the National Institutes of Health: U41HG007822 and Delaware-INBRE (P20GM103446).  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics

Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck
2013 BMC Bioinformatics  
To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (  ...  This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small  ...  , Syngenta and DuPont.  ... 
doi:10.1186/1471-2105-14-103 pmid:23514033 pmcid:PMC3623738 fatcat:lq4k3fmy45fsdmf5c7vjhxdt6u

Improving prediction fidelity of cellular metabolism with kinetic descriptions

Anupam Chowdhury, Ali Khodayari, Costas D Maranas
2015 Current Opinion in Biotechnology  
22 developed keeping pace with the rapid development in high-throughput data generation and 23 advances in metabolic engineering techniques.  ...  7 Kinetic model development requires knowledge of stoichiometry, kinetic rate laws, and 8 fluxomic/metabolomics data to support parameter estimation.  ...  Acknowledgement 31 The authors gratefully acknowledge funding from the DOE ( grant 32 numbers DE-SC0008091 and DE-SC0012377, and the NSF ( award number  ... 
doi:10.1016/j.copbio.2015.08.011 pmid:26318076 fatcat:q3owgtvvdfdgziul3ayqgzvgxy

Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway

Helen E Benson, Steven Watterson, Joanna L Sharman, Chido P Mpamhanga, Andrew Parton, Christopher Southan, Anthony J Harmar, Peter Ghazal
2017 British Journal of Pharmacology  
Abbreviations API, Application Programme Interface; BPS, British Pharmacological Society; BRENDA, Braunschweig Enzyme Database; CID, compound identifier; FDA, US Food and Drug Administration; FDFT1, farnesyl-diphosphate  ...  KEY RESULTS We describe serious impediments to systems pharmacology studies arising from limitations in the data, incomplete coverage and inconsistent reporting.  ...  Author contributions This work was conceived by H.B., S.W., P.G. and A.H. The analysis and data compilation was undertaken by H.B., S. W., J.S. and A.P.  ... 
doi:10.1111/bph.14037 pmid:28910500 pmcid:PMC5715582 fatcat:zybcxh3tyfesxo3hjuuobbv5kq

2013 Canadian Stroke Congress Abstracts

2013 Stroke  
In volunteers PI and CS techniques were evaluated individually and in combination.  ...  Critical hypoperfusion was well depicted by relative pCT in acute and subacute ischemic stroke.  ...  Methods: Data was derived from a population of 919 patients receiving care from the Community Stroke Rehabilitation Teams (CSRT) in Ontario.  ... 
doi:10.1161/01.str.0000438095.11293.72 fatcat:wuapkkr73zcvbga266lrkjwdwy

International Journal of Medical Students - Year 2013 - Volume 2 - Supplement

Executive Committee of IJMS
2014 International Journal of Medical Students  
Abstracts of the 20th Academic Medical Congress of Piaui, Brazil, COMAPI 2013Abstracts of the 15th International Congress for Medical Students and Young Health Professionals, Romania, Medicalis 2014Abstracts  ...  of the 25th Colombian Student Congress of Medical Research, Armenia, Colombia, CECIM 2014Abstracts of the 6th International Student Medical Congress in Košice, Slovak Republic, ISMCK 2014Abstracts of  ...  MUNI/A/0951/2013.  ... 
doi:10.5195/ijms.2014.53 fatcat:gmijj74eqfhqlniiiehnptd7dm

Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics

Elena Zaikova, David S. Goerlitz, Scott W. Tighe, Nicole Y. Wagner, Yu Bai, Brenda L. Hall, Julie G. Bevilacqua, Margaret M. Weng, Maya D. Samuels-Fair, Sarah Stewart Johnson
2019 Frontiers in Ecology and Evolution  
., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.  ...  A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.  ... 
doi:10.3389/fevo.2019.00001 fatcat:leqoc3iso5beral3bvyilssqg4

Structure and dynamics of molecular networks: A novel paradigm of drug discovery

Peter Csermely, Tamás Korcsmáros, Huba J.M. Kiss, Gábor London, Ruth Nussinov
2013 Pharmacology and Therapeutics  
Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design.  ...  Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of  ...  Acknowledgments Authors thank Aditya Barve and Andreas Wagner (University of Zürich, Switzerland) for sharing the human homology of enzymes encoding superessential metabolic reactions, Haiyuan Yu, Xiujuan  ... 
doi:10.1016/j.pharmthera.2013.01.016 pmid:23384594 pmcid:PMC3647006 fatcat:osjkz6kpr5gzxomqlyenla2fvq

BioModels: Content, Features, Functionality, and Use

N Juty, R Ali, M Glont, S Keating, N Rodriguez, MJ Swat, SM Wimalaratne, H Hermjakob, N Le Novère, C Laibe, V Chelliah
2015 CPT: Pharmacometrics & Systems Pharmacology  
This tutorial presents BioModels' content, features, functionality, and usage.  ...  The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources.  ...  This work received support from the Biotechnology and Biological Sciences Research Council (BioModels, BB/J019305/  ... 
doi:10.1002/psp4.3 pmid:26225232 pmcid:PMC4360671 fatcat:4ki3pd2zdze5pdvtqo4qhjbi3a

Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome [article]

Kentaro Kawata, Katsuyuki Yugi, Atsushi Hatano, Masashi Fujii, Yoko Tomizawa, Toshiya Kokaji, Takanori Sano, Kaori Y. Tanaka, Shinsuke Uda, Hiroyuki Kubota, Yutaka Suzuki, Masaki Matsumoto (+7 others)
2017 bioRxiv   pre-print
The concentration and temporal pattern of insulin selectively regulate multiple cellular functions.  ...  This integrated analysis enables molecular insight into how cells interpret physiologically fed and fasting insulin signals.  ...  The computational analysis of this work was performed in part with support of the super computer system of National Institute of  ... 
doi:10.1101/187088 fatcat:mt5qnaxrpvg4nj4xujhlakqzdu

Computational Approaches in Preclinical Studies on Drug Discovery and Development

Fengxu Wu, Yuquan Zhou, Langhui Li, Xianhuan Shen, Ganying Chen, Xiaoqing Wang, Xianyang Liang, Mengyuan Tan, Zunnan Huang
2020 Frontiers in Chemistry  
In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling).  ...  Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction.  ...  Users can search for classification, metabolic reactions, and kinetics-related information about compounds by structure or substructure.  ... 
doi:10.3389/fchem.2020.00726 pmid:33062633 pmcid:PMC7517894 fatcat:eaowpr56dbccbdpovcpm7t23se

Standard methods for virus research inApis mellifera

Joachim R de Miranda, Lesley Bailey, Brenda V Ball, Philippe Blanchard, Giles E Budge, Nor Chejanovsky, Yan-Ping Chen, Laurent Gauthier, Elke Genersch, Dirk C de Graaf, Magali Ribière, Eugene Ryabov (+2 others)
2013 Journal of Apicultural Research  
associated with virus infection and disease.  ...  Secondly, that viruses operate in an exponential world, while the host operates in a linear world and that much of the understanding and management of viruses hinges on reconciling these fundamental mathematical  ...  epigenetic data to better understand how the breakdown in the homeostasis between host and pathogen results in disease.  ... 
doi:10.3896/ibra. fatcat:tsc4zlw7xnbttpu3men2rd5yam
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