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Literature DB >> 23563419

ProtoNet: charting the expanding universe of protein sequences.

Nadav Rappoport, Nathan Linial, Michal Linial.

Abstract

Mesh：

Substances：
Proteins

Year: 2013 PMID： 23563419 DOI： 10.1038/nbt.2553

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

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7 in total

1. The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.

Authors: Alison L Cuff; Ian Sillitoe; Tony Lewis; Oliver C Redfern; Richard Garratt; Janet Thornton; Christine A Orengo
Journal: Nucleic Acids Res Date: 2008-11-07 Impact factor: 16.971

2. Reorganizing the protein space at the Universal Protein Resource (UniProt).

Authors:
Journal: Nucleic Acids Res Date: 2011-11-18 Impact factor: 16.971

3. ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.

Authors: Nadav Rappoport; Solange Karsenty; Amos Stern; Nathan Linial; Michal Linial
Journal: Nucleic Acids Res Date: 2011-11-25 Impact factor: 16.971

4. Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

Authors: Yaniv Loewenstein; Elon Portugaly; Menachem Fromer; Michal Linial
Journal: Bioinformatics Date: 2008-07-01 Impact factor: 6.937

5. SCOP database in 2004: refinements integrate structure and sequence family data.

Authors: Antonina Andreeva; Dave Howorth; Steven E Brenner; Tim J P Hubbard; Cyrus Chothia; Alexey G Murzin
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

6. InterPro: the integrative protein signature database.

Authors: Sarah Hunter; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Ujjwal Das; Louise Daugherty; Lauranne Duquenne; Robert D Finn; Julian Gough; Daniel Haft; Nicolas Hulo; Daniel Kahn; Elizabeth Kelly; Aurélie Laugraud; Ivica Letunic; David Lonsdale; Rodrigo Lopez; Martin Madera; John Maslen; Craig McAnulla; Jennifer McDowall; Jaina Mistry; Alex Mitchell; Nicola Mulder; Darren Natale; Christine Orengo; Antony F Quinn; Jeremy D Selengut; Christian J A Sigrist; Manjula Thimma; Paul D Thomas; Franck Valentin; Derek Wilson; Cathy H Wu; Corin Yeats
Journal: Nucleic Acids Res Date: 2008-10-21 Impact factor: 16.971

7. The Pfam protein families database.

Authors: Robert D Finn; John Tate; Jaina Mistry; Penny C Coggill; Stephen John Sammut; Hans-Rudolf Hotz; Goran Ceric; Kristoffer Forslund; Sean R Eddy; Erik L L Sonnhammer; Alex Bateman
Journal: Nucleic Acids Res Date: 2007-11-26 Impact factor: 16.971

7 in total

6 in total

ProtoNet: charting the expanding universe of protein sequences.

1. The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.

2. Reorganizing the protein space at the Universal Protein Resource (UniProt).

3. ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.

4. Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space.

5. SCOP database in 2004: refinements integrate structure and sequence family data.

6. InterPro: the integrative protein signature database.

7. The Pfam protein families database.

1. NeuroPID: a classifier of neuropeptide precursors.

Review 2. Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.

3. Trends in genome dynamics among major orders of insects revealed through variations in protein families.

4. ProtoBug: functional families from the complete proteomes of insects.

5. Entropy-driven partitioning of the hierarchical protein space.

Review 6. Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.