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PDBWiki: added value through community annotation of the Protein Data Bank

H. Stehr, J. M. Duarte, M. Lappe, J. Bhak, D. M. Bolser
2010 Database: The Journal of Biological Databases and Curation  
The authors would like to thank Maryana Bhak for help proofreading and correcting a draft of the article.  ...  Conflict of interest.  ...  Introduction The number of protein structures deposited in the Protein Data Bank (PDB) (1) has recently surpassed 60 000 and continues to grow at an increasing rate (2, 3) .  ... 
doi:10.1093/database/baq009 pmid:20624717 pmcid:PMC2911844 fatcat:wfjmw6seavb3lghiegphrrvhg4

TOPSAN: a collaborative annotation environment for structural genomics

Dana Weekes, S. SRI Krishna, Constantina Bakolitsa, Ian A Wilson, Adam Godzik, John Wooley
2010 BMC Bioinformatics  
Results: To address this issue we have developed TOPSAN, The Open Protein Structure Annotation Network, a web-based platform that combines the openness of the wiki model with the quality control of scientific  ...  Because of this they are not accessible by the standard tools of literature searches, remaining underutilized by the broad biological community.  ...  This work was supported by the NIH Protein Structure Initiative grants U54 GM074898 (JCSG) and P20 GM076221 (JCMM) from the National Institute of General Medical Sciences.  ... 
doi:10.1186/1471-2105-11-426 pmid:20716366 pmcid:PMC2936398 fatcat:tlvv5eouzvgvrpmfglsuwbi36y

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jose C. Jimenez-Lopez, Emma W. Gachomo, Sweta Sharma, Simeon O. Kotchoni
2013 American Journal of Molecular Biology  
Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification  ...  We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks.  ...  annotation (http://en.wikipedia.org/wiki/Gene), and 5) PDBWiki (a scientific wiki for the community annotation of protein structures (http://pdbwiki.org/wiki/Main_Page).  ... 
doi:10.4236/ajmb.2013.32016 fatcat:qqfycymt2fh6pl6ifudliybm2q

Data Integration in Bioinformatics: Current Efforts and Challenges [chapter]

Zhang Zhang, Vladimir B., Jun Yu, Kei-Hoi Cheung, Jeffrey P.
2011 Bioinformatics - Trends and Methodologies  
) and PDBWiki (a scientific wiki for the community annotation of protein structures; Stehr, et al., 2010) .  ...  on proteins, structures and annotations.  ...  Because of the rapid development of new technologies in molecular biology, new bioinformatic techniques emerge accordingly to keep the pace of in silico development of life science.  ... 
doi:10.5772/21654 fatcat:zaiy3lxhgrdwhgqdqnjrqg3gbm

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody
2015 Bioinformatics  
Among the main challenges for the future are better addressing of weak interfaces and the application of interface classification concepts to prediction problems like protein-protein docking.  ...  A key issue linked to protein interface classification is the identification of the biological assembly of a crystal structure and the analysis of its symmetry.  ...  Research Program of the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (support to S.B.). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btv622 pmid:26508758 pmcid:PMC4743631 fatcat:y5taf2mmlfgtxjjqjb7ghiqvxu

The Sentinel Initiative as a Knowledge Commons [chapter]

Ryan Abbott, Katherine J. Strandburg, Brett M. Frischmann, Michael J. Madison
Governing Medical Knowledge Commons  
The editors' previous volume, Governing Knowledge Commons, demonstrated the framework's power through case studies in a diverse range of areas.  ...  a practical introduction to the knowledge commons framework and a synthesis of conclusions and lessons.  ...  Interestingly, in a system built on openness and designed to avoid intellectual property claims, this centralized structure establishes something of a proprietary interest in the data on the part of the  ... 
doi:10.1017/9781316544587.007 fatcat:lefya2gjp5hwnfdvl4fnjqdrvq

Protein interfaces in crystal structures: insights from evolution

Jose Manuel Duarte Gamero
2013
A necessary step in this analysis was to compile a validated set of transmembrane protein-protein interfaces from the known set of membrane structures deposited in the Protein Data Bank.  ...  Through it we have tried to establish the principles of how interfaces assemble in the transmembrane region and how they compare to those of soluble proteins.  ...  Acknowledgements Financial support from the Research Committee of the Paul Scherrer Institut and the SNF to GC (grant numbers FK-05.08.1, FK-04.09.1 and 140879, respectively) is gratefully acknowledged  ... 
doi:10.5167/uzh-164288 fatcat:hvbdjoqunna5nptkwtwzs6oxze