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Real time structural search of the protein data bank

Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte, Charlotte M Deane
2020 PLoS Computational Biology  
This fact, together with recent growth of oligomeric structures in the Protein Data Bank (PDB), demands more efficient approaches to oligomeric assembly alignment/retrieval.  ...  Similarity searching with this approach enables real-time retrieval of proteins/protein assemblies resembling a target, from PDB or user input, together with resulting alignments (  ...  Based on these principles, we have developed a search system that enables real-time retrieval of similar protein assemblies to a target assembly, obtained from the PDB or uploaded by a user, together with  ... 
doi:10.1371/journal.pcbi.1007970 pmid:32639954 fatcat:b76xqbstibegpbjmjmvivircfq

RCSB PDB next-generation data delivery and search services

Christine Zardecki, Jose M. Duarte, Chunxiao Bi, Charmi Bhikadiya, Sebastian Bittrich, Li Chen, Dmytro Guzenko, Robert Lowe, Joan Segura, Yana Valasatava, John Westbrook, Stephen Burley
2020 Acta Crystallographica Section A: Foundations and Advances  
RCSB Protein Data Bank (PDB) provides tools for analysis and visualization of 3D structures of biological macromolecules stored in the PDB archive.  ...  Examples of the searches integrated by the aggregator are mmseqs2 sequence search (1), BioZernike structure shape search (2), and sequence motif search.  ...  Real time structural search of the Protein Data Bank (2020) bioRxiv doi: 1 RCSB Protein Data Bank (PDB) provides tools for analysis and visualization of 3D structures of  ... 
doi:10.1107/s0108767320099298 fatcat:yvixhxqrt5aofi45w4iuldmyty

ProteinDBS: a real-time retrieval system for protein structure comparison

C.-R. Shyu, P.-H. Chi, G. Scott, D. Xu
2004 Nucleic Acids Research  
We have developed a web server (ProteinDBS) for the life science community to search for similar protein tertiary structures in real time.  ...  ProteinDBS provides two types of query method: query by Protein Data Bank protein chain ID and by new structures uploaded by users. The system is hosted at  ...  (15) , which generates ribboned protein images, the Kinemage graphic packages for presenting 3D interactive protein structures, the SCOP database for ground truth testing, and the Protein Data Bank  ... 
doi:10.1093/nar/gkh436 pmid:15215453 pmcid:PMC441574 fatcat:fhkca5oscbdt7hi5k5wgc3ph4q

A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment [article]

Barış Ekim
2017 arXiv   pre-print
With the exponential increase of structural proteomics data, the methods that scale with the rate of increase of data lose efficiency.  ...  The resulting method replicates the results of the current gold standard with a minimal loss in sensitivity in a significantly shorter amount of time, while ameliorating the existing web workspace of protein  ...  Noah Daniels at Computer Science and Artificial Intelligence Laboratory (CSAIL) at the Massachusetts Institute of Technology (MIT) for their mentorship and guidance, Dr.  ... 
arXiv:1701.01975v1 fatcat:3cpsxcimnngm7pqh5liqwjmmpu

ProteinDBS v2.0: a web server for global and local protein structure search

C.-R. Shyu, B. Pang, P.-H. Chi, N. Zhao, D. Korkin, D. Xu
2010 Nucleic Acids Research  
The experimental results show that our system is able to return results of global comparisons in seconds from a complete Protein Data Bank (PDB) database of 152 959 protein chains and that it takes much  ...  It provides two comparison methods, global-to-global and local-to-local, to facilitate the searches of protein structures or substructures.  ...  /), which generates view of aligned proteins, the SCOP database for ground truth testing (15) , and the PDB ( for maintaining the tertiary structures.  ... 
doi:10.1093/nar/gkq522 pmid:20538653 pmcid:PMC2896110 fatcat:myvtwck4kbavteguopix7negbq

A Real-Time All-Atom Structural Search Engine for Proteins

Gabriel Gonzalez, Brett Hannigan, William F. DeGrado, Andreas Prlic
2014 PLoS Computational Biology  
To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system.  ...  Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds.  ...  Conceived and designed the experiments: GG BH WFD. Performed the experiments: GG BH. Analyzed the data: GG BH WFD. Contributed reagents/materials/analysis tools: GG BH WFD. Wrote the paper: GG BH WFD.  ... 
doi:10.1371/journal.pcbi.1003750 pmid:25079944 pmcid:PMC4117414 fatcat:6alijvev2zd27iufhdswivw5xm

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K

J. Lee, A. Liwo, H. A. Scheraga
1999 Proceedings of the National Academy of Sciences of the United States of America  
It appears that the CSA method with the UNRES force field, which is based on the thermodynamic hypothesis, can be used in prediction of protein structures in real time.  ...  Although the potential was not calibrated with these two proteins, the native-like structures were found among the low-energy conformations, without the use of threading or secondary-structure predictions  ...  of proteins possible in real time.  ... 
doi:10.1073/pnas.96.5.2025 pmid:10051588 pmcid:PMC26730 fatcat:wdgbjxopl5gd7n5uoc3lqpf2de

New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)

Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata (+4 others)
2017 Protein Science  
The Protein Data Bank Japan (PDBj), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined biological macromolecular structures.  ...  surfaces, the extensions of the Omokage search for molecular shape similarity, and the integration of PDBj and BMRB searches.  ...  Introduction The Protein Data Bank Japan (PDBj, https://pdbj. org/) 1,2 accepts and annotates biological macromolecular structure data in collaboration with the other worldwide Protein Data Bank (wwPDB  ... 
doi:10.1002/pro.3273 pmid:28815765 pmcid:PMC5734392 fatcat:7ttn55ucxvcjfjkmivznvmet34

New Hashing Techniques for Three-Dimensional Protein Structures

Tatsuya Akutsu, Kentaro Onizuka, Masato Ishikawa
1994 Genome Informatics Series  
Using the hash vectors, searching for similar protein structures can be done quickly. The methods were compared with the previous methods using PDB data, and were shown to be much faster.  ...  This paper describes new methods to evaluate the structural similarity of proteins.  ...  Each item in DATA denotes a filename (denoting a protein structure) of PDB data, where chain A is used in the case of 4HHB.  ... 
doi:10.11234/gi1990.5.1 fatcat:vzllmdor35fzhic6xmp724jcau

Protein Structure Annotation Resources [chapter]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
in the Protein Data Bank archive (v. 2014-03-25) (3, 4).  ...  Since the 3-D structure of proteins are ultimately responsible for most actions in the cell, this review will focus on protein structure annotation resources that aim to explain a  ...  Acknowledgments The authors are grateful to B. Coimbatore Narayanan, G. Gabanyi  ... 
doi:10.1007/978-1-4939-2230-7_1 pmid:25502191 pmcid:PMC5586544 fatcat:n4wrlx7rtvfy7mya7w457ppwca

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte, Shuchismita Dutta, Zukang Feng (+26 others)
2020 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership  ...  , serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of users around  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (  ... 
doi:10.1093/nar/gkaa1038 pmid:33211854 pmcid:PMC7779003 fatcat:dkqo54quqjgovp7y4v67b635zu

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

Stephen K Burley, Helen M Berman, Charmi Bhikadiya, Chunxiao Bi, Li Chen, Luigi Di Costanzo, Cole Christie, Ken Dalenberg, Jose M Duarte, Shuchismita Dutta, Zukang Feng, Sutapa Ghosh (+28 others)
2018 Nucleic Acids Research  
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB,, the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania  ...  in support of a 'Structural View of Biology.'  ...  ACKNOWLEDGEMENTS RCSB PDB is a member of the Worldwide Protein Data Bank (  ... 
doi:10.1093/nar/gky1004 pmid:30357411 pmcid:PMC6324064 fatcat:clctmqo6ujaifm7s27vk3s2h7i

Disordered Residues and Patterns in the Protein Data Bank

Mikhail Yu Lobanov, Ilya V Likhachev, Oxana V Galzitskaya
2020 Molecules  
Using this database, the user can: (1) find homologues in the entire Protein Data Bank; (2) perform a statistical analysis of disordered residues in protein structures; (3) search for disordered patterns  ...  We created a new library of disordered patterns and disordered residues in the Protein Data Bank (PDB).  ...  That is, in the real proteins, AC2 sequences were 100 times more than in the random ones.  ... 
doi:10.3390/molecules25071522 pmid:32230759 pmcid:PMC7180803 fatcat:ex4wmiamgvg5dcqndic5fcbhya

The Homeodomain Resource: sequences, structures and genomic information

S. Banerjee-Basu, E. S. Ferlanti, J. F. Ryan, A. D. Baxevanis
1999 Nucleic Acids Research  
The Homeodomain Resource is a comprehensive collection of sequence, structure and genomic information on the homeodomain protein family.  ...  Available through the Resource are both full-length and domain-only sequence data, as well as X-ray and NMR structural data for proteins and protein-DNA complexes.  ...  A link is also provided to NCBI Entrez for real-time queries against the protein databases; results of this search will yield a complete but unrefined set of all homeodomain sequences.  ... 
doi:10.1093/nar/27.1.336 pmid:9847220 pmcid:PMC148175 fatcat:zj73c2ekqzgsdgwxi4kpgvylfm

Protein structure databases with new web services for structural biology and biomedical research

D. M. Standley, A. R. Kinjo, K. Kinoshita, H. Nakamura
2008 Briefings in Bioinformatics  
The Protein Data Bank Japan (PDBj) curates, edits and distributes protein structural data as a member of the worldwide Protein Data Bank (wwPDB) and currently processes $25^30% of all deposited data in  ...  Structural information is enhanced by the addition of biological and biochemical functional data as well as experimental details extracted from the literature and other databases.  ...  Acknowledgements The authors would like to thank the PDBj staff for technical support, in particular, Mr Atsuro Yoshihara and Ms Reiko Yamashita.  ... 
doi:10.1093/bib/bbn015 pmid:18430752 fatcat:rmlvhckicrcn7m4b2yvzniiaq4
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