Command List (ls)
pdb
Searches the PDB (Protein Databank at http://www.pdb.org) by accession code. Brings you to the protein structure summary page. For example, to find the structure of Arabidopsis Tom20 by it's PDB accession code, use: pdb 1ZU2
2173 uses
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Created 2008-01-10 04:04:23
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Last used
2024-04-16 02:37:25
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Description
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http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s
uniprot
Uniprot protein knowledgebase keyword search.
1368 uses
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Created 2008-08-26 07:11:58
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Last used
2024-03-16 11:51:43
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Description
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http://www.uniprot.org/uniprot/?query=%s&sort=score
kegg
KEGG Search. Kegg is a great biological resource. To find entries connected with glycolysis in KEGG kegg glycolysis To find entries with given protein knowing id kegg y1313 To find entries for gene with given id kegg glk
280 uses
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Created 2009-10-16 08:24:09
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Last used
2022-11-14 05:04:07
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Description
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http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=kegg&keywords=%s
plantcyc
NAME PlantCyc - search the plant metabolism database maintained by the Plant Metabolic Network (PMN) PlantCyc is a very useful database containing pathways and their catalytic enzymes and genes, as well as compounds from many plant species. Extracted from the plant literature, either supported by experimental evidence or based on expert hypotheses. Both experimentally-verified and computationally-predicted enzymes and genes are assigned to pathways. Evidence codes are attached to pathways and t…
122 uses
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Created 2013-04-11 14:38:54
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Last used
2022-02-01 09:54:57
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Description
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http://pmn.plantcyc.org{ifThen -value1 %s -value2 -test NOTEQUAL -then /PLANT/substring-search?type=NIL&object=%s}
ihop
Searches the iHOP (Information Hyperlinked over Proteins) service, which uses gene networks to help navigate the biomedical literature.
105 uses
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Created 2008-11-11 06:21:47
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Last used
2023-04-27 08:42:43
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Description
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http://www.ihop-net.org/UniPub/iHOP/?search=%s
rcsb
Search the RSCB Protein Data Bank
101 uses
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Created 2021-02-04 15:49:29
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Last used
2024-03-04 06:48:13
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Description
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https://www.rcsb.org/structure/%s
genome
UCSC Genome Browser, Human Genome, March 2006 (hg18) assembly Can search by Gene names, symbols, chromosome number or region, keywords, database ID's (NP, NM, OMIM, etc.) Examples: chr7 Displays all of chromosome 7 20p13 Displays region for band p13 on chr 20 chr3:1-1000000 Displays first million bases of chr 3, counting from p arm telomere chr3:1000000+2000 Displays a region of chr3 that spans 2000 bases, starting with position 1000000 D16S3046 Displays region around STS marker D16S3046 from t…
74 uses
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Created 2007-08-14 19:36:52
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Last used
2025-05-26 15:37:19
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Description
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http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=96205306&clade=vertebrate&org=Human&db=hg18&position=%s&pix=620&hgsid=96205306&hgt.dummyEnterButton.x=0&hgt.dummyEnterButton.y=0
protein
Protein OS The system from which we operate
53 uses
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Created 2006-04-21 17:02:15
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Last used
2020-04-21 16:07:34
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Description
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http://www.proteinos.com
pfam
query the Sanger center protein family database for a specific protein family. Protein families start with PF to find a protein just type protein family Example:pfam PF02574
46 uses
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Created 2007-12-06 19:40:51
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Last used
2021-09-23 10:21:12
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Description
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http://pfam.sanger.ac.uk/family?acc=%s
prosite
Searching PROSITE database. Intended to use for finding descriptions of functional protein motifs.
14 uses
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Created 2008-10-01 13:55:07
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Last used
2013-10-03 05:52:07
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Description
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http://expasy.org/cgi-bin/prosite-search-ful?SEARCH=%s
