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Building a Structured PDB: The RS-PDB Database
2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 2006A method for automatically analyzing structures deposited in the Protein Data Bank is presented. The method is capable to detect missing atoms, bond length deviations, atom bumps and to correctly identify protein-ligand complexes. The results are organized into a database, called the Rich Structure PDB (RS-PDB in short) from which one can easily select
Zoltan Szabadka, Vince Grolmusz
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Nature Biotechnology, 2007
The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
Schierz, Amanda C. +2 more
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The Brookhaven Protein Data Bank was once a pioneering database, but its organization of structural data is now outdated and in need of an upgrade.
Schierz, Amanda C. +2 more
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2006 International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation.
Yan Chao Wang, Rajshekhar Sunderraman
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In this paper, we propose two architectures for curating PDB data to improve its quality. The first one, PDB Data Curation System, is developed by adding two parts, Checking Filter and Curation Engine, between User Interface and Database. This architecture supports the basic PDB data curation.
Yan Chao Wang, Rajshekhar Sunderraman
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PDB@: An offline toolkit for exploration and analysis of PDB files
Journal of Structural and Functional Genomics, 2013Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually.
Udayakumar, Mani +2 more
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Parallel PDB data retriever “PDB diving booster”
1997A powerful PDB-data-retrieval system “PDB Diving Booster,” which is a collection of functions/methods for data-retrieval and datatransmission, will enhances high-performance parallel-distributed programming in the field of structural biology. This system provides with 1) functions for reading whatever irregular data in PDB file, 2) methods to access ...
Kentaro Onizuka +3 more
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Structural changes of homodimers in the PDB
Journal of Structural Biology, 2018Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods.
Ryotaro, Koike +3 more
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Journal of Molecular Biology, 2023
Molecular modeling and simulation play important roles in biomedical research as they provide molecular-level insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI (https://charmm-gui.org) is a web-based cyberinfrastructure that is widely used to generate various molecular ...
Sang-Jun Park +4 more
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Molecular modeling and simulation play important roles in biomedical research as they provide molecular-level insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI (https://charmm-gui.org) is a web-based cyberinfrastructure that is widely used to generate various molecular ...
Sang-Jun Park +4 more
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Proceedings of the 45th annual southeast regional conference, 2007
The Protein Data Bank (PDB) was established in 1971 as a repository for macromolecular crystal structure data. Recent development of high throughput structural genomic technologies has produced massive quantities of data, and the amount of macromolecular structure data is increasing exponentially.
Edward E. Pryor Jr., Jacquelyn S. Fetrow
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The Protein Data Bank (PDB) was established in 1971 as a repository for macromolecular crystal structure data. Recent development of high throughput structural genomic technologies has produced massive quantities of data, and the amount of macromolecular structure data is increasing exponentially.
Edward E. Pryor Jr., Jacquelyn S. Fetrow
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<p><span style="font-size:12pt"><span calibri="" style="font-family:"><b><span arial="" style="font-family:">ASBMB Learning Objectives</span></b> </span></span></p> <p><span style="font-size:12pt"><span calibri="" style="font-family:"><span arial="" style="font-family ...
Johnson, Keith, Dutta, Shuchismita
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Johnson, Keith, Dutta, Shuchismita
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PDB-REPRDB: a database of representative protein chains in PDB (Protein Data Bank).
Proceedings. International Conference on Intelligent Systems for Molecular Biology, 1997We propose a novel set of 'representative' protein chains in PDB, where not only sequential but also structural similarities are taken into account. Hobohm et al. have already proposed "PDB_SELECT", which eliminates redundant chains based solely on sequence similarity.
Tamotsu Noguchi +3 more
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