نتایج جستجو برای: protein families

تعداد نتایج: 1343866  

Journal: :Biochimica et biophysica acta 2012
Wenji Ma Craig McAnulla Lusheng Wang

With the development of high-throughput methods for identifying protein-protein interactions, large scale interaction networks are available. Computational methods to analyze the networks to detect functional modules as protein complexes are becoming more important. However, most of the existing methods only make use of the protein-protein interaction networks without considering the structural...

2010
S. Sri Krishna L. Aravind Constantina Bakolitsa Jonathan Caruthers Dennis Carlton Mitchell D. Miller Polat Abdubek Tamara Astakhova Herbert L Axelrod Hsiu-Ju Chiu Thomas Clayton Marc C. Deller Lian Duan Julie Feuerhelm Joanna C. Grant Gye Won Han Lukasz Jaroszewski Kevin K. Jin Heath E. Klock Mark W. Knuth Abhinav Kumar David Marciano Daniel McMullan Andrew T. Morse Edward Nigoghossian Linda Okach Ron Reyes Christopher L. Rife Henry van den Bedem Dana Weekes Qingping Xu Keith O. Hodgson John Wooley Marc-André Elsliger Ashley M. Deacon Adam Godzik Scott A. Lesley Ian A. Wilson

SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein-protein inter...

2014
Amel Ghouila Isabelle Florent Fatma Zahra Guerfali Nicolas Terrapon Dhafer Laouini Sadok Ben Yahia Olivier Gascuel Laurent Bréhélin

Identification of protein domains is a key step for understanding protein function. Hidden Markov Models (HMMs) have proved to be a powerful tool for this task. The Pfam database notably provides a large collection of HMMs which are widely used for the annotation of proteins in sequenced organisms. This is done via sequence/HMM comparisons. However, this approach may lack sensitivity when searc...

Journal: :Nucleic acids research 2016
Robert D. Finn Penny C. Coggill Ruth Y. Eberhardt Sean R. Eddy Jaina Mistry Alex L. Mitchell Simon C. Potter Marco Punta Matloob Qureshi Amaia Sangrador-Vegas Gustavo A. Salazar John G. Tate Alex Bateman

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website res...

2017
Ameya Dipak Bendre Sureshkumar Ramasamy C G Suresh Hyun Kyu Song

Kunitz type trypsin inhibitor (KTI) family is one of the most versatile families of protease inhibitors. Their exact natural physiological role in plants is still unclear. According to some reports, KTIs are involved in proper growth and development of plants. Some researchers suggested their role in recovery from physical damage, while others have shown their applications in plant’s defence fr...

Journal: :Biochemical Society transactions 2010
Michael R Dyson

Proteins can contain multiple domains each of which is capable of possessing a separate independent function and three-dimensional structure. It is often useful to clone and express individual protein domains to study their biochemical properties and for structure determination. However, the annotated domain boundaries in databases such as Pfam or SMART are not always accurate. The present revi...

2009
Roman A. Laskowski

PDBsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the Protein Data Bank (PDB). Here we describe some of its most recent features, including figures from the structure's key reference, citation data, Pfam domain diagrams, topology diagrams and protein-protein interactions. Furthermore, it now accepts users' own PDB format f...

Journal: :Molecular biology and evolution 2001
S Wuchty

Several technical, social, and biological networks were recently found to demonstrate scale-free and small-world behavior instead of random graph characteristics. In this work, the topology of protein domain networks generated with data from the ProDom, Pfam, and Prosite domain databases was studied. It was found that these networks exhibited small-world and scale-free topologies with a high de...

Journal: :Genetics 2011
Danny A Bitton Valerie Wood Paul J Scutt Agnes Grallert Tim Yates Duncan L Smith Iain M Hagan Crispin J Miller

Genome annotation is a synthesis of computational prediction and experimental evidence. Small genes are notoriously difficult to detect because the patterns used to identify them are often indistinguishable from chance occurrences, leading to an arbitrary cutoff threshold for the length of a protein-coding gene identified solely by in silico analysis. We report a systematic reappraisal of the S...

2013
Jaina Mistry Edda Kloppmann Burkhard Rost Marco Punta

High-resolution structural knowledge is key to understanding how proteins function at the molecular level. The number of entries in the Protein Data Bank (PDB), the repository of all publicly available protein structures, continues to increase, with more than 8000 structures released in 2012 alone. The authors of this article have studied how structural coverage of the protein-sequence space ha...

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