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DBAli tools: mining the protein structure space

M. A. Marti-Renom, U. Pieper, M. S. Madhusudhan, A. Rossi, N. Eswar, F. P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali
2007 Nucleic Acids Research  
Thus, the DBAli tools, which are freely accessible via the World Wide Web at, allow users to mine the protein structure space by establishing relationships between protein structures  ...  The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB).  ...  ACKNOWLEDGEMENTS We are grateful to Dr Angel Ortiz for the MAMMOTH program. We would also like to thank the JMol team, Erik Bosrup and Stijn van Dongen for JMol, overLib and MCL, respectively.  ... 
doi:10.1093/nar/gkm236 pmid:17478513 pmcid:PMC1933139 fatcat:uimvsv7rgrajlczypwgi6jfnyy

Identification of similar regions of protein structures using integrated sequence and structure analysis tools

Brandon Peters, Charles Moad, Eunseog Youn, Kris Buffington, Randy Heiland, Sean Mooney
2006 BMC Structural Biology  
With structural genomics initiatives determining structures with little, if any, functional characterization, development of protein structure and function analysis tools are a necessary endeavor.  ...  environments that make that match using a suite of sequence and structure analysis tools.  ...  The DBAli tools provide CATH, SCOP, EC, GO and keyword annotations for a protein structure [21] . ProFunc uses sequence, structure and residue templates to characterize proteins of interest [22] .  ... 
doi:10.1186/1472-6807-6-4 pmid:16526955 pmcid:PMC1435900 fatcat:pjjbmcg5gfcclgcpwuyqb234hy

The AnnoLite and AnnoLyze programs for comparative annotation of protein structures

Marc A Marti-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali
2007 BMC Bioinformatics  
Acknowledgements: This work is funded by an RO1 from the NHGRI and by a Presidential Early Career Award for Scientists and Engineers from the National Science Foundation.  ...  Given a query structure, the AnnoLite program searches DBAli for structurally similiar proteins and collects their known annotations.  ...  Structural Genomics aims to cover the structural space by selecting targets from groups of proteins of unknown structure [4] .  ... 
doi:10.1186/1471-2105-8-s4-s4 pmid:17570147 pmcid:PMC1892083 fatcat:o5p5c46emzbhxlmq27vqibskdi

Medium- and short-chain dehydrogenase/reductase gene and protein families

R. Ladenstein, J.-O. Winberg, J. Benach
2008 Cellular and Molecular Life Sciences (CMLS)  
DBAIi tools: mining the protein structure space. Nucleic Acids Res. 35, W393-397 Ramaswamy, S., Scholze, M. and Plapp, B. V. (1997). Binding of formamides to liver alcohol dehydrogenase.  ...  Secondary-structure matching (SSM), a new tool for fast protein structure align- ment in three dimensions. Acta Crystallogr. 60, 2256-2268. Emsley, P. and Cowtan, K. (2004).  ... 
doi:10.1007/s00018-008-8590-4 pmid:19011748 fatcat:ltvbhexxdnchvj74hlw4hbfcha

Abstracts from the 9th Meeting of The European Association of NeuroOncology, September 16-19, 2010, Maastricht, The Netherlands

2010 Neuro-Oncology  
Furthermore, the levels of MGMT, MLH1, MSH2, MSH6, and PMS2 proteins were analyzed semiquantitatively by immunohistochemistry (IHC) in 43 patients.  ...  However, immunohistochemical expression scores for MLH1, MSH2, MSH6, and PMS2 proteins were frequently reduced in the recurrent tumor when compared with the corresponding primary tumor.  ...  A spontaneous speech analysis might be a more sensitive tool to detect language problems than structured language tasks, such as naming, all linguistic levels are involved.  ... 
doi:10.1093/neuonc/noq085 fatcat:gjf6gsrup5derot25vxenj6tvy

Wolne oprogramowanie QGIS i jego możliwości wykorzystania w edukacji

Paulina Pokojska, Wojciech Pokojski
2017 Edukacja – Technika – Informatyka  
proteins.  ...  compositions and structures of preparations of tissues of wheat rich by proteins,  to determine the rational quantity of nutritional fibers to be put in canned meat products,  to identify the technological  ...  With this proposed technology enterprises can save money and space by combining multiple authentication tools such as 'valid' ID to be embedded in a barcode or NFC target into a single label.  ... 
doi:10.15584/eti.2017.4.45 fatcat:7ktfbpdmprcklkhx2jfnj66j2i