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Iditis: Protein Structure Database

Stephen Gardner, Janet Thornton
1998 Acta Crystallographica Section D: Biological Crystallography  
TheIditisprotein structure database has been designed to allow the widest possible range of queries to be performed across all available protein structures.  ...  TheIditisdatabase is the most comprehensive protein structure resource currently available, and contains over 500 fields of information describing all publicly deposited protein structures.  ...  Order in a pseudo-relational database Many queries on protein structure data re¯ect the fact that protein structures are made up of a series of serially linked amino acids.  ... 
doi:10.1107/s0907444998007112 pmid:10089482 fatcat:nwgagdcczfc6dldx6tokqsnteu

Structural Propensity Database Of Proteins [article]

Kamil Tamiola, Matthew Michael Heberling, Jan Domanski
2017 bioRxiv   pre-print
Thus, to expand our understanding of intrinsic protein disorder, we have created a database of secondary structure (SS) propensities for proteins (dSPP) as a reference resource for experimental research  ...  An overwhelming amount of experimental evidence suggests that elucidations of protein function, interactions, and pathology are incomplete without inclusion of intrinsic protein disorder and structural  ...  Computational analysis of public protein 27 databases, especially the Protein Data Bank (PDB) (Varadi et al., 2015), has played an integral role in 28 shaping our fundamental understanding of protein structure  ... 
doi:10.1101/144840 fatcat:ly2u3epjxjbs5drfrimwrdzp2y

VPDB: Viral Protein Structural Database

Om Prakash Sharma, Ankush Jadhav, Afzal Hussain, Muthuvel Suresh Kumar
2011 Bioinformation  
Database Volume 6(8) ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation 6(8): 324-326 (2011) 324 Abstract: Viral Protein Database is an interactive database for three dimensional viral proteins.  ...  Currently, VPDB includes ~1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search.  ...  Although there exists numerous databases and resources for virus structure information, a comprehensive viral protein structural database is unavailable till the date which can provide detailed sequential  ... 
doi:10.6026/97320630006324 pmid:21769196 pmcid:PMC3134783 fatcat:tb7fmcf6cbgoppbmh52hs62vsm

Circularly permuted proteins in the protein structure database

Jongsun Jung, Byungkook Lee
2001 Protein Science  
Here we report the result of a systematic search for all protein pairs in the SCOP 90% id domain database that become structurally superimposable when the sequence of one of the pairs is circularly permuted  ...  Using a reasonable set of criteria, we find that 47% of all protein domains are superimposable to at least one other protein domain in the database after their sequence is circularly permuted.  ...  Detecting repeated sequence segments and circularly permuted proteins from a sequence database has been reported recently (Marcotte et al. 1999; Uliel et al. 1999 ).  ... 
doi:10.1110/ps.05801 pmid:11514679 pmcid:PMC2253205 fatcat:5h4ruolvhzar7nwiul3ygwtrlm

Defining a protein: mining the protein structure database

B. Stec, B.V.L.S. Prasad, Y. Zhang, A. Godzik
2008 Acta Crystallographica Section A Foundations of Crystallography  
We constructed a database of redundant protein structures by application of sequence-based methods (CD-HIT).  ...  Keywords: redundant structure database, distribution of conformational states, protein folding P24.06.08 Acta Cryst. (2008) .  ... 
doi:10.1107/s0108767308079804 fatcat:vb4sv2pipnhthkfx3l7nxlkpda

Protein structural databases in computational biology

Raut AS, Patil AM, Shinde SS, Sarode DK, Shinde NA
2022 International journal of computing, programming and database management  
This review covers some basic of protein structure and associated databases and it is more advanced topic of protein structural bioinformatics.  ...  Searching database is a first step of study to find new protein. We introduce the basics of protein structural bioinformatics.  ...  The use of database helps to understand the structure and function of protein.  ... 
doi:10.33545/27076636.2022.v3.i1a.33 fatcat:2v772mup65f3njqfzi6d2sm3t4

Database of Structural Motifs in Proteins

K. Guruprasad, M. S. Prasad, G. R. Kumar
2000 Bioinformatics  
The database of structural motifs in proteins (DSMP) contains data relevant to helices, β-turns, γ -turns, β-hairpins, ψ-loops, β-α-β motifs, β-sheets, β-strands and disulphide bridges extracted from all  ...  This data is available for a representative data set of 1028 protein chains and also for all 10 213 proteins in the Protein Data Bank.  ...  These databases also encompass domains in the protein (Holm and Sander, 1998) .  ... 
doi:10.1093/bioinformatics/16.4.372 pmid:10869035 fatcat:ywz4tkjac5ashh72obm2bduwvu

PrePPI: a structure-informed database of protein–protein interactions

Qiangfeng Cliff Zhang, Donald Petrey, José Ignacio Garzón, Lei Deng, Barry Honig
2012 Nucleic Acids Research  
PrePPI (http://bhapp.c2b2.columbia.edu/PrePPI) is a database that combines predicted and experimentally determined protein-protein interactions (PPIs) using a Bayesian framework.  ...  The PrePPI database constitutes an integrated resource that enables users to examine aggregate information on PPIs, including both known and potentially novel interactions, and that provides structural  ...  database (21) , the database of interacting proteins [DIP, (22) ], the protein interaction database [IntAct, (23) ], the molecular interaction database [MINT, (24) ], the Human Protein Reference Database  ... 
doi:10.1093/nar/gks1231 pmid:23193263 pmcid:PMC3531098 fatcat:fzlanecbm5frjmj4expsxy5diy

SCOP: a Structural Classification of Proteins database

T. J. P. Hubbard, A. G. Murzin, S. E. Brenner, C. Chothia
1997 Nucleic Acids Research  
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures.  ...  The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures.  ...  To facilitate access to this information, we have constructed the Structural Classification of Proteins (SCOP) database (2) .  ... 
doi:10.1093/nar/25.1.236 pmid:9016544 pmcid:PMC146380 fatcat:7n6fydvqzvg2zcwr2apmeilc7u

SCOP: a Structural Classification of Proteins database

L. Lo Conte
2000 Nucleic Acids Research  
The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of known protein structures.  ...  , or selections of, protein structures.  ...  To facilitate access to this information, we constructed the Structural Classification of Proteins (SCOP) database (2) .  ... 
doi:10.1093/nar/28.1.257 pmid:10592240 pmcid:PMC102479 fatcat:k4nmwxisxbadvhfwen4a3rxryq

Protein structure database search and evolutionary classification

J.-M. Yang
2006 Nucleic Acids Research  
Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural  ...  database.  ...  The authors are grateful to both the hardware and software supports of the Structural Bioinformatics Core Facility at National Chiao Tung University.  ... 
doi:10.1093/nar/gkl395 pmid:16885238 pmcid:PMC1540718 fatcat:vkbeipthoffphi5hxrpdbixode

The RESID Database of protein structure modifications

J. S. Garavelli
1999 Nucleic Acids Research  
Because the number of post-translational modifications requiring standardized annotation in the PIR-International Protein Sequence Database was large and steadily increasing, a database of protein structure  ...  The RESID Database can be used to predict atomic masses for peptides, and is being enhanced to provide molecular structures for graphical presentation on the PIR Web site using widely available molecular  ...  ACKNOWLEDGEMENTS Enhancement of the RESID Database is supported by NSF grant DBI-9808414. The RESID Database is copyrighted by the National Biomedical Research Foundation.  ... 
doi:10.1093/nar/27.1.198 pmid:9847179 pmcid:PMC148134 fatcat:miynu6p5afdfrmmycnmhvcql6i

Protein Structure Evolution and the Scop Database [chapter]

Boojala V. B. Reddy, Philip E. Bourne
2005 Methods of biochemical analysis  
Proteins that have descended from the same ancestor retain memory of that ancestor through the sequence, structure, and function.  ...  Murzin (1998) discussed various aspects of the evolution of sequence, structure, fold, and function with specific examples. Strong sequence Structural Bioinformatics, Second Edition Edited  ...  The appearance of such proteins in the structural databases often help to identify more distant relationships between protein domains and lead to a classification rearrangement that unifies distinct protein  ... 
doi:10.1002/0471721204.ch12 fatcat:wdhvob3bjzdcndzggcwo3rufuy

Database searching by flexible protein structure alignment

Yuzhen Ye, Adam Godzik
2004 Protein Science  
We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures.  ...  One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases.  ...  On the basis of this, a new database protein structural similarity searching tool, FATCAT-search, has been developed by extending a flexible protein structure alignment algorithm, FATCAT.  ... 
doi:10.1110/ps.03602304 pmid:15215527 pmcid:PMC2279924 fatcat:hie7lyudlbffjdhpietk3ztzky

3Dee: a database of protein structural domains

A. S. Siddiqui, U. Dengler, G. J. Barton
2001 Bioinformatics  
The 3Dee database is a repository of protein structural domains.  ...  It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies, contains non-redundant set(s) of sequences and structures, multiple structure  ...  The domain is an important intermediate in the protein structural hierarchy.  ... 
doi:10.1093/bioinformatics/17.2.200 pmid:11238081 fatcat:uds7neb3nzenndv25witx5z7yy
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