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Topic: Protein motif

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	BioMed Central \| Full text \| Automatic annotation of protein motif function with Gene Ontology terms
		If one regards protein sequences as "sentences" of the biological language with amino acids as the alphabet, then protein motifs can be considered as words or phrases of that language and determining the function of a motif is equivalent to determining the sense of a word.
		These databases are usually constructed by studying the set of protein sequences that are known to have certain functions and extracting the conserved sequence motifs that are believed to be responsible for their functions.
		With the advent of algorithms and programs that can automatically discover sequence motifs from any given set of sequences [1,2,7-9], it is possible to mine a large number of sequences to find novel motifs without necessarily knowing their functions and to compile a dictionary of biological language accordingly.
	www.biomedcentral.com /1471-2105/5/122 (6053 words)

	Structural motif - Wikipedia, the free encyclopedia
		Motifs exhibit both tertiary and secondary structure, and may be regarded as a configuration of secondary structures.
		In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" structure.
		Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene.
	en.wikipedia.org /wiki/Protein_motif (449 words)

	Motif - Wikipedia, the free encyclopedia
		Sequence motif, a pattern in a DNA sequence.
		Structural motif, a pattern in a protein structure.
		Motif (widget toolkit), a graphical user interface toolkit used in software development.
	en.wikipedia.org /wiki/Motif (125 words)

	244p
		The first characterization of the C2H2ZF motif was done by Aaron Klug at MRC, Cambridge University, in 1985 [1] The motif was found in the TFIIIA transcription factor for the 5S ribosomal RNA gene from Xenopus laevis, a protein that has the distinction of being the first known eukaryotic transcription factor.
		Inspection of the protein revealed the presence of 9 repeats of a 30 residue pattern and an abundance of zinc.
		The protein sequences used for the project were obtained for the October 7, 2000 version of genome database using annotation "genieKnownPep" These are 8243 protein sequences of known genes.
	www.cse.ucsc.edu /~afyfe/244p2.htm (2574 words)

	Computing Papers on Motif (Site not responding. Last check: )
		The protein sequence data generated this way will be used to construct a decision tree, which after testing, can be used to predict the family of an unknown protein.
		ABSTRACT: The GXXXG Motif is a frequently occurring sequence of residues that is known to favor helix-helix interactions in membrane proteins.
		Protein structure may be modeled using a variety of graph representations [6].
	computing.breinestorm.net /Motif (2697 words)

	regular expression and protein motif (Site not responding. Last check: )
		Protein motifs gets their importance when it becomes too difficult to detect the unknown protein's resemblance by aligning it to the protein of known structure.
		These motifs can be created by clustering of a family of proteins and identifying the conserved positions.
		Since these motifs can be represented as regular expressions, it is important to understand about regular expressions in general, and how to use them with the Python language in particular (see Appendix).
	www.embl-heidelberg.de /~chenna/elm_2.html (1164 words)

	Bioinformatics Software on the Web (Site not responding. Last check: )
		Motifs in protein databases program determines if a protein motif is present in a database of protein sequences.
		This program allows the user to define a protein motif and then determine if a DNA sequence might encode them or if they are present in a protein database.
		PATTINPROT scans a protein sequence or a protein database for one or several patterns.
	www.cs.jhu.edu /~salzberg/appendixa.html (4417 words)

	The Angiotensin II-dependent Nuclear Translocation of Stat1 Is Mediated by the Jak2 Protein Motif 231YRFRR -- Sayeski ... (Site not responding. Last check: )
		YRFRR protein motif, to coprecipitate with the AT receptor in
		This protein is a substrate of Jak2 and is
		The proteins were transferred onto a nitrocellulose membrane and blotted with anti-Stat1 mAb to assess Stat1 nuclear translocation.
	www.jbc.org /cgi/content/full/276/13/10556 (4845 words)

	GFScan: A Gene Family Search Tool at Genomic DNA Level -- Xuan et al. 12 (7): 1142 -- Genome Research
		First, based on the locations of the protein motif in protein sequences, the corresponding mRNA regions were extracted and aligned to reveal the consensus pattern.
		In the final Genomic DNA Motif, the two numbers separated by a comma in the parentheses (34, 105467) are the minimum and maximum lengths of the intron in this position.
		For an intron-containing motif, the genomic DNA motif was separated into several submotifs, and the longest one was used to search the genome first.
	www.genome.org /cgi/content/full/12/7/1142 (3159 words)

	The Protein Motif Search Problem
		The set of proteins to be searched is pre-processed to determine the frequency of occurrence of each of the characters representing the amino acids.
		The search algorithm has three levels of major choice-points: selection of a protein, selection of a pattern and the selection of a position within the protein where the matching is attempted.
		Consequently, if a larger protein is processed towards the end of the computation, the system may run out of other proteins to process in parallel before the longer computation is finished.
	www-fp.mcs.anl.gov /~lusk/aurora/aurora.app/subsection3.5.2.html (1485 words)

	Bioinformatics project-Junmin Liu (Site not responding. Last check: )
		Structural studies on one member of the protein family revealed that the structure core is formed by a three-helix bundle, and beta-turn between the helices.Those beta-turns are called wing.
		Biologist present the structural evidence supporting the hypothesis that the binding specificity of the winged helix DNA binding motif is mediated by residues adjacent to the alpha-helix (H3), the moiety which is primarily involved in the interaction with DNA.
		As known, one hypothesis about this protein family is that the binding specificity of the winged helix DNA binding motif is mediated by residues adjacent to the third helix, here the multiple alignment result gives another evidence for the hypothesis.
	www.msci.memphis.edu /~giri/compbio/f99/junmin/Project.htm (1808 words)

	SWBIC - Motif, Domain, Profile, Pattern, & Repeat Searches (Site not responding. Last check: )
		The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the results as an intutive graphical summary.
		It also runs BLAST2 for the input PDB chain sequence against all protein sequences in the ExInt* database and maps the intron positions and phases of aligned search results on the input protein's 3D structure.
		XdomView is a useful visualization tool for scientists working on gene and protein evolution and structural modeling and classification.
	www.swbic.org /links/1.10.php (1601 words)

	Protein List
		functions as a scaffold protein within the SCF complex which functions as ubiquitin E3 ligase
		a helix-loop-helix protein lacking a basic motif shown to be involved in the control of cell proliferation in the wing
		novel protein - downstream of DPP - Smad family members convey TGF¨ signals from their receptors to the nucleus
	www.biochem.northwestern.edu /holmgren/Glossary/Protein_list.html (337 words)

	Protein Pattern, Motif, and Domain Databases
		However, one of your proteins is the Caenorhabditis elegans dUTPase, and the combination of the known dUTPase quaternary structure in E. coli and domain analysis of the nematode sequence immediately makes a pretty strong prediction about its quaternary structure...
		And worse, if domain A is the real heart of protein 1 (say, the catalytic domain), and domain B is just some auxiliary domain (say, a common generic protein-protein interaction domain), I screwed up 2's annotation too.
		One of your proteins is a receptor tyrosine kinase, containing an intracellular kinase domain and extracellular fibronectin type III domains.
	www.people.virginia.edu /~wrp/cshl00/domain-lecture.html (1656 words)

	ISREC Protein domains page
		In the framework of the PROSITE project, we are constructing generalized profiles in order to describe local homology regions in proteins and make them searchable.
		A duplicated sequence motif occuring in phospholipases D and related phosphatidyltransferases, as well as in several other proteins using a ping-pong phosphotransferase mechanism.
		A sequence motif of unknown function, associated with UBA domains and ub-related proteins.
	www.isrec.isb-sib.ch /domains (504 words)

	MEME - Overview (Site not responding. Last check: )
		A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences.
		MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern.
		MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested.
	meme.sdsc.edu /meme/website/meme-intro.html (125 words)

	Predicting Subcellular Localization via Protein Motif Co-Occurrence -- Scott et al. 14 (10): 1957 -- Genome Research
		proteins to the mitochondria or elsewhere in the cell.
		of the proteins predicted by PSLT to be peroxisomal and by the
		all mouse proteins from SWISS-PROT release 42.10 that are annotated
	www.genome.org /cgi/content/full/14/10a/1957 (6228 words)

	InterPro: Home (Site not responding. Last check: )
		PROSITE is a database of protein families and domains.
		SCOP: a structural classification of proteins database for the investigation of sequences and structures.
		InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
	www.ebi.ac.uk /interpro (379 words)

	BLAST: Basic Local Alignment and Search Tool
		The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
		BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
		Search protein database using a translated nucleotide query
	www.ncbi.nlm.nih.gov /BLAST (251 words)

	Identification and Preliminary Characterization of a Protein Motif Related to the Zinc Finger -- Lovering et al. 90 ...
		We have identified a protein motif, related to the zinc finger, which defines a newly discovered family of proteins.
		The motif was found in the sequence of the human RING1 gene, which is proximal to the major histocompatibility complex region on chromosome six.
		We propose naming this motif the "RING finger" and it is found in 27 proteins, all of which have putative DNA binding functions.
	www.pnas.org /cgi/content/abstract/90/6/2112 (1454 words)

	EMBOSS: patmatdb (Site not responding. Last check: )
		Takes a protein motif and compares it to a set of protein sequences.
		It returns the number of matches there were between the motif and each matched sequence, length of match, start and end positions of match, and writes out an alignment.
		Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional.
	emboss.sourceforge.net /apps/patmatdb.html (827 words)

	Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction -- ...
		The three-protein motif of a mixed-feedback loop between coregulating proteins (Table 2, motif E) was not included here, because by itself it is a combination of two other three-protein motifs.
		Dangling motifs, where a fourth node is connected to only one of the nodes of the three-protein motif, are not presented.
		of protein pairs and triplets that recur in motifs.
	www.pnas.org /cgi/content/full/101/16/5934?ck=nck (3798 words)

	Protein Motif Recognition (ResearchIndex)
		We present a method for nding simple protein motifs in such sequences, building upon the standard dynamic programming sequence alignment algorithm.
		The commonly used frameshift penalty is replaced by a probabilistic model of the indel rate, providing both a means of controlling selectivity and a guide for...
		6 Comparison of DNA sequences with protein sequences (context) - Pearson, Wood et al.
	citeseer.ist.psu.edu /630148.html (331 words)

	ExPASy - PROSITE
		It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs [More details / References / Disclaimer].
		InterProScan - Scan a sequence against all the motif databases in InterPro
		PRATT - Interactively generates conserved patterns from a series of unaligned proteins
	www.expasy.ch /prosite (263 words)

	Motif-based Protein Sequence Classification Using Neural (ResearchIndex)
		39 A discriminative framework for detecting remote protein homo..
		1 Motif identification neural design for rapid and sensitive p..
		1 Protein family classification based on searching a database..
	citeseer.ist.psu.edu /719608.html (427 words)

	Protein Pattern, Motif, and Domain Databases
		There are a plethora of protein domain databases.
		"Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments", Proteins 28:405-420, 1997.
		Below are two predicted protein sequences from the Caenorhabditis elegans genome sequencing project, including the semi-automated annotation that was added by the genome sequencing teams following a routine BLAST analysis.
	www.people.virginia.edu /~wrp/cshl97/domain-lecture.html (606 words)

	[No title] (Site not responding. Last check: )
		#!/usr/bin/perl # # Exercise 9.4 # # Modify Example 5-3 to report on the locations of the motifs that it finds, even if # motif appears multiple times in the sequence data.
		# # Answer to Exercise 9.4 use strict; use warnings; # Searching for motifs # Ask the user for the filename of the file containing # the protein sequence data, and collect it from the keyboard print "Please type the filename of the protein sequence data: "; my $proteinfilename =
		; # Remove the newline at the end of $motif chomp $motif; # Look for the motif ################################################## # # Here is the modification to Exercise 5.3 # ################################################## my @locations = (); while($protein =~ /$motif/g) { # The pos function returns the position in the sequence following the match.
	www.sci.csuhayward.edu /~dlo/exercises/exer09.04 (211 words)

	Pattern Search (Site not responding. Last check: )
		Select the output type, matching domain or whole protein sequence, to view only the domain or the whole protein sequence in Fasta format.
		Example 2: To search for the ATP/GTP-binding site (motif A, P-loop) using the Prosite pattern (see PDOC00017) [AG]-x(4)-G-K-[ST], enter the pattern into the pattern textbox, check the Prosite pattern checkbox, choose an output format then select submit.
		Example 3: To search for the same motif of example 2 using a Perl regular expression, enter [AG].{4}GK[ST], check the Perl regular expression checkbox, choose an output format then select submit.
	hpv-web.lanl.gov /cgi-bin/find_pattern.cgi (142 words)

	Active Motif » Tools to Analyze Nuclear Function
		Active Motif » Tools to Analyze Nuclear Function
		The October 2007 issue of Active Motif's official newsletter, MotifVations, is now available.
		February 9, 2007 – Active Motif Sees Double-Digit Growth in TimeLogic Group, New Deals for AKS
	www.activemotif.com /home (387 words)

	A Family of Cyclin D Homologs from Plants Differentially Controlled by Growth Regulators and Containing the Conserved ...
		A Family of Cyclin D Homologs from Plants Differentially Controlled by Growth Regulators and Containing the Conserved Retinoblastoma Protein Interaction Motif -- Soni et al.
		Phosphorylation of Retinoblastoma-Related Protein by the Cyclin D/Cyclin-Dependent Kinase Complex Is Activated at the G1/S-Phase Transition in Tobacco
		A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants
	www.plantcell.org /cgi/content/abstract/7/1/85 (1636 words)

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