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Topic: Threading protein sequence

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G protein coupled receptors

Protein data bank

G protein

protein folding

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	THREADER Info Page (Site not responding. Last check: 2007-11-05)
		Threading is an approach to fold recognition which used a detailed 3-D representation of protein structure.
		The idea was to physically "thread" a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential.
		Threading is one of the very few methods available which can predict the fold for a protein in the absence of an evolutionary relationship, though if there is an evolutionary link between the target protein and a protein of known structure then there are better methods available e.g.
	bioinf.cs.ucl.ac.uk /threader/threader.html (454 words)

	Protein threading (Site not responding. Last check: 2007-11-05)
		Massive amounts of protein sequence datamay be derived from modern large-scale DNA sequencing efforts of, for example, the Human Genome Project.
		Homology modelling is based on the reasonableassumption that two homologous proteins will share very similar structures.Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in thesolved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.
		Protein threading scans the amino acid sequence ofan unknown structure against a database of solved structures.
	www.therfcc.org /protein-threading-124789.html (465 words)

	BioMed Central \| Full text \| An approach to large scale identification of non-obvious structural similarities between ...
		Such genes and their corresponding proteins would usually have distinct sequences from those of the molecule they mimic, but would typically have evolved to imitate, at least in part, the shape and critical chemical groups on the surface of the functional homologues.
		Threading attempts to assign folds for a protein of unknown structure by sampling it onto each member of a library of known folds using pseudo-energy as a measure of fit [15-20].
		If a set of threading scores against a standard library is indeed sequence specific, then for proteins with known structures we should be able to observe a defined relationship between coefficients of threading scores correlation and parameters of protein 3D structural similarity.
	www.biomedcentral.com /1471-2105/5/61 (4662 words)

	Citations: An Empirical Energy Function for Threading Protein Sequence through Folding Motif - Bryant, Lawrence ... (Site not responding. Last check: 2007-11-05)
		Sequence structure alignment For sequence structure alignment (or threading) the estimate of fitness is mostly based on some kind of pseudo energy function.
		On the Approximation of Protein Threading - Akutsu, Miyano (1997)
		In inverse folding, given an amino acid sequence and a set of protein structures (structural patterns) a structure into which the sequence is most likely to fold is computed.
	citeseer.ist.psu.edu /context/261961/0 (2620 words)

	PP Help 09: Hints
		When interpreting predictions for a particular protein it is often instructive to mark the 30% of the residues you suspect to be falsely predicted.
		The exact number of sequences needed for a 'good prediction' cannot be given, as it depends on the variation and on characteristics of the particular protein family.
		Problematic cases are proteins with many cysteine bridges that stabilise the particular protein structure, or proteins for which the structure is stabilised by functional constraints (co-factors).
	www.cmbi.kun.nl /bioinf/predictprotein/doc/help_09.html (2710 words)

	Sisyphus and protein structure prediction
		Currently, databases for protein sequence (Bairoch and Apweiler, 1997) and protein structure (Bernstein et al., 1977) are expanding rapidly due to large scale sequencing projects (Oliver et al., 1992; Fleischmann et al., 1995; Fraser et al., 1995; Goffeau et al., 1996; Johnston et al., 1996) and improvements in experimental determination of 3D structures (Lattman, 1994).
		Accuracy of homology modelling is proportional to the level of pairwise sequence identity between the protein of unknown structure and its target of known structure.
		Thus, the precise pattern of amino acid exchanges observed in a multiple sequence alignment of a protein family is highly indicative of the particular structure.
	www.embl-heidelberg.de /~rost/Papers/sisyphus.html (8205 words)

	AN EFFICIENT POTENTIAL FOR PROTEIN SEQUENCE DESIGN (Site not responding. Last check: 2007-11-05)
		While this may be a problem for threading applications, for inverse folding the tessellations of the target structure as well as the collection of reference structures needed for computing the zscore have to be computed only once and can be kept in memory.
		Table 1: zscores of native and misfolded structures For five pairs of proteins with the same sequence length zscores were calculated for the native sequence on its respective structure and with sequence and structure swapped.
		In addition, Zhang and Skolnick [14] recently estimated that the zscore of a protein of 100 residues should be better than 15, significantly larger than the scores of native sequencestructure pairs obtained from currently available potentials.
	www.bioinfo.de /isb/gcb99/talks/weberndorfer/main.html (1571 words)

	Protein Fold Recognition Score Functions: Unusual Construction Strategies (ResearchIndex) (Site not responding. Last check: 2007-11-05)
		21 Identification of native protein folds amongst a large numbe..
		14 The FSSP database of structurally aligned protein fold famil..
		Protein Sequence Threading, the Alignment Problem and a Two..
	citeseer.ist.psu.edu /ayers99protein.html (570 words)

	Sequence Alignments (Site not responding. Last check: 2007-11-05)
		While ssearch reports only the best alignment between the query sequence and the library sequence, lalign and plalign will report a specified number of alignments (the default is 10) between the two sequences.
		Sequences in the alignment are gathered into sub-groups on the basis of sequence similarity, functional similarity, or other criteria.
		Protein structure prediction methods via threading have been extended to EST assemblies to allow for EST translation and fold prediction in one integrated procedure.
	www.rna.icmb.utexas.edu /linxs/seq-info/alignments.html (899 words)

	PredictProtein: structure prediction and sequence analysis (Site not responding. Last check: 2007-11-05)
		PredictProtein is a service for sequence analysis, and structure prediction.
		PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure (brief introduction, data flowchart).
		submit a protein sequence for prediction (default, advanced, expert)
	www.embl-heidelberg.de /predictprotein/predictprotein.html (119 words)

	[No title] (Site not responding. Last check: 2007-11-05)
		A comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.
		A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of OWL.
		A protein database with emphasis on the physical and functional properties of the yeast proteins.
	www.secsg.org /biolinks.htm (655 words)

	Protein Multiple Sequence Analysis
		The Match-Box multiple sequence alignment method circumvents the gap penalty requirement: in the Match-Box method the gaps are the result of the alignment and not a governing parameter of the matching procedure.
		The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics.
		A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences.
	www.biologie.uni-hamburg.de /b-online/library/genomeweb/GenomeWeb/prot-mult.html (800 words)

	Fold recognition methods and links (Site not responding. Last check: 2007-11-05)
		Ab initio prediction of protein 3D structures is not possible at present, and a general solution to the protein folding problem is not likely to be found in the near future.
		However, it has long been recognised that proteins often adopt similar folds despite no significant sequence or functional similarity and that nature is apparently restricted to a limited number of protein folds.
		Methods of protein fold recognition attempt to detect similarities between protein 3D structure that are not accompanied by any significant sequence similarity.
	www.bmm.icnet.uk /people/rob/CCP11BBS/foldrec.html (1522 words)

	Representation And Data Structure Of Genetic Algorithms For Protein Threading (ResearchIndex) (Site not responding. Last check: 2007-11-05)
		Abstract: Despite many years of efforts, a direct prediction of protein structure from sequence is still not possible.
		How to identify and align a sequence to the fold with which it is most compatible, a process called Threading.
		17 Threading a database of protein cores (context) - Bryant, Madej et al.
	citeseer.ist.psu.edu /yadgari97representation.html (323 words)

	SAM: UCSC's Sequence Alignment and Modeling System
		A linear hidden Markov model is a sequence of nodes, each corresponding to a column in a multiple alignment.
		Using a match state indicates that the sequence has a character in that column, while using a delete state indicates that the sequence does not.
		standard methods of sequence search is their ability to characterize an entire family of sequences.
	www.cse.ucsc.edu /research/compbio/sam.html (1181 words)

	Week 8: Protein Sequence Analysis
		The SAPS (statistical analysis of protein sequences) algorithm provides amino acid composition, charge distribution, hydrophobicity, and information pertaining to transmembrane regions and repetetive stretches.
		Profiles are a numerical representation of a multiple sequence alignment which are used to construct a position-specific scoring table (PSST).
		Thermodynamic calculations must be made to determine the most energetically favorable structure of the unknown sequence in comparison to the known target sequence.
	userpages.umbc.edu /~gurumurt/1116lec1.html (2040 words)

	FORCASP - CASP Forums Site - Protein structure prediction using intermediate resolution off-lattice protein model ... (Site not responding. Last check: 2007-11-05)
		Protein structure prediction using intermediate resolution off-lattice protein model (Refiner) and public accessible threading and comparative modeling tools.
		The prediction path combining off-lattice intermediate resolution protein model and public accessible tools for threading and comparative modeling, was described.
		At first protein sequence was submitted to meta-server.
	www.forcasp.org /print/2192 (155 words)

	HUBI : Protein sequence analysis
		The Protein Colourer : is a tool for colouring a personal protein sequence (each given amino acid class is associated with a choosen colour).
		Protein secondary structure prediction : SSP method (Segment-oriented prediction, prediction of a-helix and b-strand segments of globular proteins) or NNSSP method (Nearest-neighbor prediction, prediction of protein secondary sturcture by combining nearest-neighbor algorithms and multiply sequence alignments) (BCM)
		Protein Sequence Analysis : secondary structure prediction consensus from Gibrat, de Levin, double prediction, Phd and SOPM methods (Self optimized prediction method).
	www.biocenter.helsinki.fi /bi/rnd/biocomp/PROG3.HTM (1441 words)

	References
		Bowie, J.U., Luthy, R., and Eisenberg, D. A method to identify protein sequences that fold into a known three dimensional structure.
		Rey, A. and Skolnick, J. Efficient algorithm for the reconstruction of a protein backbone from the alpha-carbon coordinates.
		Richardson, J.S. and Richardson, D.C. Principles and Patterns of Protein Conformation in: Prediction of Protein Structure and the Principles of Protein Conformation.
	www.unc.edu /~ivaisman/delaunay/refer.htm (431 words)

	Internet Resources for Biological Sciences (Site not responding. Last check: 2007-11-05)
		It is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
		The homologous sequences found by PredictProtein can then be used as input to a phylogenetics program (at the ETH Computational Server - next link!) in order to construct PAM matrices, phylogenetic trees and more.
		It allows you to retrieve citations and records in the area of molecular biology from the databases of the National Center for Biotechnology Information which include MEDLINE (database of biomedical articles), protein sequence databases and GenBank DNA sequence databank.
	www.clarku.edu /~chem/classes/Spring2002/protein/link.htm (450 words)

	threading: 123D+ (Site not responding. Last check: 2007-11-05)
		Threading a sequence through a set of structures
		123D+ is a program which combines sequence profiles, secondary structure prediction, and contact capacity potentials to thread a protein sequence through the set of structures.
		Fast protein fold recognition via sequence to structure alignment and contact capacity potentials.
	123d.ncifcrf.gov /123D+.html (117 words)

	[No title] (Site not responding. Last check: 2007-11-05)
		* We are developing methods to thread newly discovered protein sequences through core folding motifs from the Protein Data Bank, as a means to find the three-dimensional structure most likely for a protein with that sequence.
		The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions.
		The width and coloring of cylinders indicates the strength of a pairwise residue interaction, according to an empirical potential developed for "threading" protein sequences through alternative folding motifs.
	www.nih.gov /sigs/SBC/csb/bryant.html (274 words)

	CUBIC papers: abstract for 'Pitfalls of protein sequence analysis' (Site not responding. Last check: 2007-11-05)
		Imagine you have a protein sequence, either sequenced in your own lab or pulled down from genome projects of EST production.
		You decide to let theoretical biology assist you in finding a priori information about your protein that may be useful to accelerate and design experiments.
		If no sequence homologue is found in PDB, there still is a chance to predict 3D structure by threading, i.e., by remote homology modelling (<25% sequence identity).
	cubic.bioc.columbia.edu /papers/1996_pitfalls/abstract.html (332 words)

	Links to the Genetic World: 1
		Human Proteome Organisation International group formed to further the understanding of human proteins and to realize the benefits of proteomics by encouraging cooperation among scientific, governmental, and financial communities.
		ProtoMap+ hierarchical classification of all SWISSPROT and TrEMBL proteins
		Structural Classification of Proteins database of structural and evolutionary relationships among proteins
	www.ornl.gov /sci/techresources/Human_Genome/links.shtml (2355 words)

	CITIDEL: Viewing 'An anytime algorithm for gapped block protein threading with pair interactions' (Site not responding. Last check: 2007-11-05)
		Crippen, G.M. Failures of inverse folding and threading with gapped alignment.
		Lathrop, R.H. The protein threading problem with sequence amino acid interaction preferences is NP-complete.
		Xu, Y., Uberbacher, C.E. A polynomial-time algorithm for a class of protein threading prob- Ictus.
	www.citidel.org /?op=getobj&identifier=oai:ACMDL:articles.299488 (532 words)

	Skolnick Group Publications (Site not responding. Last check: 2007-11-05)
		Milik, A. Kolinski and J. Skolnick, An algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates.
		Vieth, A. Kolinski, C. Brooks III, and J. Skolnick, A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants.
		Vieth, A. Kolinski, C. Brooks III and J. Skolnick, Prediction of quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.
	www.bioinformatics.buffalo.edu /current_buffalo/skolnick/publications.html (5054 words)

	NCBI Structure - THREADING
		We are working on methods for the assertion of homology by comparing sequences to structural templates.
		If structural similarity between target and template is sufficiently large, their relationship may be detected even in the absence of statistically significant sequence similarity.
		Download PKB and Threading from the NCBI FTP-site (requires Splus).
	www.ncbi.nlm.nih.gov /Structure/RESEARCH/threading.shtml (179 words)

	Services at MBCR and throughout the world (Site not responding. Last check: 2007-11-05)
		Here is a collection of services that will analyze your sequence and return the results of the analysis to you.
		Many are unique services that cannot be duplicated locally, while other utilities are provided for those without access to a good package of sequence analysis programs.
		Procrustes forces genomic DNA sequence to fit into a related target protein (also test mode)
	condor.bcm.tmc.edu /services.html (457 words)

	CrystaLinks - Structure/Sequence Searches
		Christine Orengo's scheme for identifying and classifying protein fold
		Protein comparison by alignment of distance matrices (Holm and Sander, 1993)
		Interpro combined search of sequence and motif databases
	www.bmsc.washington.edu /CrystaLinks/databases_1.html (108 words)

	[No title]
		Rish, I and Frost, D. (1997) Statistical analysis of backtracking on inconsistent CSPs, to appear in Proceedings of CP97, Austria.
		P. Smyth, 'Clustering sequences with hidden Markov models,' in Advances in Neural Information Processing 9, M. Mozer, M.
		and Smith, T.F. Global optimum protein threading with gapped alignment and empirical pair potentials.
	www.ics.uci.edu /~mlearn/MLPapers.html (4014 words)

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