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Topic: Backbone chain

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	Polypeptide-based Drug Design
		Side chain substitution is when scientists will substitute a different side chain in for either the methyl or the carboxyl group.
		Backbone replacement is the replacement of the backbone the runs throughout the peptide.
		If the backbone is replaced with something that is not a component of an amino acid (N, H, or C) then the peptide becomes a pseudopeptide.
	www.louisville.edu /~mjwell04/peptide.htm (198 words)

	Database Fields: (Site not responding. Last check: 2007-10-21)
		The default structure is the L isomer with two, unbranched saturated hydrocarbon chains esterified to the C1 and C2 positions on a glycerol backbone with the headgroup covalently attached through a phosphodiester group at the C3 position of glycerol.
		The two chain lengths, in units of carbon atoms (and with the first carbon of the chain defined to be that which is bonded through an oxygen atom to the glycerol backbone) are given, each to the left of a colon (":").
		Unless the sphingolipid backbone is specifically identified as being sphingosine, the letters "Spd" are attached via a hyphen to the name of the source of a biologically-derived lipid preparation and to synthetic lipid preparations, where necessary, to denote a generic sphingoid base.
	www.lipidat.chemistry.ohio-state.edu /data_fields.stm (2618 words)

	ANWENDUNGEN (Site not responding. Last check: 2007-10-21)
		The silicon backbones are in the all-trans zigzag conformation, the dihedral angle of the silicon backbone chain is proposed to be perpendicular on the graphite substrate.
		As concluded from the intensity modulation of the backbone chains the orientation of the polysilanes with respect to the base axis of the graphit hexagon is different for each of the polysilanes.
		Because of the delocalization of s-electrons, the silicon backbone chains may be considered as semiconducting "molecular wires", the hydrocarbon side groups as the "insulator" of the wire.
	www.ccc.uni-erlangen.de /clark/info/anwend_semi_ai.html (3209 words)

	Proteins are polypeptides
		The backbone of the protein chain is highly polar with the amino (-NH-) group a strong donor of hydrogen bonds and the carbonyl (-CO-) group an acceptor of hydrogen bonds.
		However, since the backbone is highly polar, and prefers contact with water, it creates a problem because part of the backbone also has to be buried along with the hydrophobin sied-chains.
		-helix: (a) is a ribbon diagram showing schematically the backbone chain, (b) shows the hydrogen bonds (shown as red springs) between the C' atom of the carbonyl group and the -NH- group, (c) shows the real conformation of the backbone chain, and (d) shows the residues (in pink) sticking out from the helix.
	www.uic.edu /classes/phys/phys461/phys450/ANJUM05 (1901 words)

	Proteins are polypeptides
		The backbone of the protein chain is highly polar with the amino (-NH-) group a strong donor of hydrogen bonds and the carbonyl (-CO-) group an acceptor of hydrogen bonds.
		However, since the backbone is highly polar, and prefers contact with water, it creates a problem because part of the backbone also has to be buried along with the hydrophobin sied-chains.
		-helix: (a) is a ribbon diagram showing schematically the backbone chain, (b) shows the hydrogen bonds (shown as red springs) between the C' atom of the carbonyl group and the -NH- group, (c) shows the real conformation of the backbone chain, and (d) shows the residues (in pink) sticking out from the helix.
	tigger.uic.edu /classes/phys/phys461/phys450/ANJUM05 (1901 words)

	RSG: Features: The Towers of Backbone.
		Unfortunately, whilst mentioning a role for Backbone in both civil defence and air defence he assumed that the system linked “secret sites”, a belief founded on the mistaken, but perhaps understandable assumption that the civil defence sites the government said it would provide existed but because they could not be seen they must be secret.
		As many people have pointed out “backbone” is a common term in communications technology to simply mean a central carrying system, there are references from as early as 1909 to “backbone trunk telephone circuits”.
		Backbone would consist of 14 radio stations each situated at least 10 miles from a likely target running south to north up the country with spurs to Grantham and Shrewsbury.
	www.subbrit.org.uk /rsg/features/backbone/index.shtml (4149 words)

	2-Carb-17 (Site not responding. Last check: 2007-10-21)
		A double bond between a carbon atom of the backbone chain and an atom outside that chain, or a double or triple bond between two carbon atoms outside the backbone chain, will be treated according to the normal rules of organic nomenclature [13,14].
		Monosaccharide derivatives having a double bond between two contiguous carbon atoms of the backbone chain are named by inserting, into the name for the corresponding fully saturated derivative, the infix 'x-en'.
		Monosaccharide derivatives having a triple bond or cumulative double bonds in the backbone chain are named by the methods of 2-Carb-17.2, with the infix 'n-yn' for a triple bond and infixes such as 'i,j-dien' for cumulative double bonds.
	www.chem.qmw.ac.uk /iupac/2carb/noGreek/17.html (468 words)

	Glossary
		In a graft copolymer, the distinguishing feature of the side chains is constitutional, i.e., the side chains comprise units derived from at least one species of monomer different from those which supply the units of the main chain.
		Disproportionation is a method of terminating chain polymerization which involves a free radical stripping a hydrogen atom from another free radical, so that one chain stabilizes with the hydrogen, and the other with a double bond.
		A polymer liquid crystal in which the mesogens are attached to the side of the main chain and not a part of the main chain itself.
	plc.cwru.edu /tutorial/enhanced/files/glossary/glossary.htm (5322 words)

	One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations -- Marshall et al. 14 (5): ...
		The key distinctions between the two methods are as follows: The exact calculation uses the protein backbone and all of the side chains in the protein to define the dielectric boundary, while in the one-body method, the dielectric boundary is defined by the backbone and a single side chain only.
		The key distinctions between the exact, one-body, and two-body methods are as follows: The exact calculation uses the protein backbone and all of the side chains in the protein to define the dielectric boundary, and a single calculation is used to determine the folded-state solvation energy.
		The key distinctions between the exact and two-body methods are as follows: The exact calculation uses the protein backbone and all of the side chains in the protein to define the dielectric boundary, while the two-body calculation uses the protein backbone and only two side chains to define the dielectric boundary.
	www.proteinscience.org /cgi/content/full/14/5/1293 (5591 words)

	2-Carb-17
		A double bond between a carbon atom of the backbone chain and an atom outside that chain, or a double or triple bond between two carbon atoms outside the backbone chain, will be treated according to the normal rules of organic nomenclature [13,14].
		Monosaccharide derivatives having a double bond between two contiguous carbon atoms of the backbone chain are named by inserting, into the name for the corresponding fully saturated derivative, the infix 'x-en' followed by 'o' for euphony before a consonant.
		Monosaccharide derivatives having a triple bond or cumulative double bonds in the backbone chain are named by the methods of 2-Carb-17.2, with the infix 'n-yn' for a triple bond and infixes such as 'i,j-dien' for cumulative double bonds.
	www.chem.qmul.ac.uk /iupac/2carb/17.html (476 words)

	U.S. Patent: 6008058 - Cyclic peptide mixtures via side chain or backbone attachment and solid phase synthesis - ...
		One of the amino acid constituents, either a bifinctional or trifunctional amino acid, is attached to the solid support using either a side chain functional group or through its amine group forming in the latter case a secondary amine with the characteristics of proline, a well-known cyclization inducing amino acid.
		A further advantage of using the amine group for attachment of the peptide chain is that this aids in the cyclization of the linear peptide mixtures thus produced through the well-known "pseudo-proline" effect.
		This improvement effectively eliminates the major disadvantage of side chain coupled amino acids in that virtually all amino acids, including a-amino acids, 6-amino acids, and a wide variety of other unusual amino acids, synthetic or naturally occurring, may be used to attach the first amino acid to the solid support.
	www.everypatent.com /comp/pat6008058.html (14044 words)

	backbone \| \| Dictionary & Translation by Babylon
		Backbone may mean:Vertebral column, of a vertebrate organismBackbone chain, in polymer chemistry, the framework of the moleculeBackbone Entertainment, a video game development companyBackbone network, the top level of a hierarchical networkInternet backbone
		In de Internet-terminologie is een backbone een stelsel van zeer snelle computerverbindingen waarlangs het gegevensverkeer loopt van de netwerken die op de backbone zijn aangesloten.
		Een aangesloten netwerk kan zelf ook weer een backbone hebben.Het Nederlandse woord voor backbone is 'ruggengraat'.Een voorbeeld is het Abilene-netwerk, dat fungeert als de backbone in het Internet2-project.
	www.babylon.com /definition/backbone/All (269 words)

	Advantages of fine-grained side chain conformer libraries -- Shetty et al. 16 (12): 963 -- Protein Engineering Design ... (Site not responding. Last check: 2007-10-21)
		the backbone is held fixed in the native conformation.
		chain conformations are enumerated for the DCRL and the PRL,
		and the backbone is in a native or near-native conformation.
	peds.oxfordjournals.org /cgi/content/full/16/12/963 (3753 words)

	Forthcoming Paper (Site not responding. Last check: 2007-10-21)
		In this study, we generated and analyzed the side-chain conformational potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide.
		The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory.
		backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds.
	www.edpsciences.org /articles/epjd/forth/abstracts/koo.html (175 words)

	Adjuvant for chemical mechanical polishing slurry - Patent 20060141741
		The adjuvant according to claim 1, which is obtained by a method comprising the steps of: (i) polymerizing at least one sub-monomer to obtain a macromonomer that forms the side chain of the graft type polymer; and (ii) copolymerizing the macromonomer with a monomer that forms the backbone of the graft type polymer.
		The adjuvant according to claim 2, which is obtained by a method comprising the steps of: (i) polymerizing at least one sub-monomer to obtain a macromonomer that forms the side chain of the graft type polymer; and (ii) copolymerizing the macromonomer with a monomer that forms the backbone of the graft type polymer.
		When comparing a graft type polyelectrolyte with a linear polyelectrolyte under the same molecular weight range, a backbone chain length of the graft type polyelectrolyte is shorter than the chain length of the linear polyelectrolyte, resulting in minimization of an agglomeration phenomenon.
	www.freepatentsonline.com /20060141741.html (6184 words)

	β Structure: The Anatomy & Taxonomy of Protein Structure
		Since both sides of the sheet are covered by other main chain (as is almost always true for parallel sheet), side groups pointing in both directions are predominantly hydrophobic except at the ends of the strands.
		These close side chain pairs on neighboring strands show preferences for having hydrophobic groups together, unlike charges together, and branched β-carbons next to unbranched β-carbons (in antiparallel sheet), but none of these preferences are stronger than 2 to 1.
		Essentially every one of the crossover connections in the known protein structures regardless of the length or conformation of the connecting loop, is right-handed (Richardson, 1976; Sternberg and Thornton, 1977a).
	kinemage.biochem.duke.edu /~jsr/html/anatax.2b.html (3148 words)

	Assignment 2: Performing Rotations
		The easiest orientation is that used for the sequence of a protein, where the backbone is defined as the chain starting at the N atom of the first aminoacid of the sequence and ending at the C atom of the last aminoacid of the sequence.
		If you need to identify one atom as your anchor atom, with the default backbone orientation, your anchor atom is the N of the very first aminoacid (the very first atom of the chain).
		Please answer Q2 When you rotated a dihedral bond in the middle of the backbone until you reached a conformation that had collisions, you verified the presence of steric clashes by visualizing the conformation.
	cnx.org /content/m11624/latest (2468 words)

	Department of Biological Chemistry - Johns Hopkins University
		On the experimental side, staphylococcal nuclease and eglin C are used as simple systems for characterizing the residual structure that persists in the ensemble of conformations known as the denatured states.
		Beginning with fragments of length 4 to 8 residues lacking side chain atoms beyond CG, larger fragments are assembled in a hierarchical fashion, using a variety of statistical potentials to enforce protein-like interactions between elements of secondary structure.
		In the final step, heavy atoms are added to form complete side chains, and several high resolution all atom potential, including one to quantify solvation, are used as fitness functions in a genetic algorithm-based conformational search.
	biolchem.bs.jhmi.edu /members/facultydetail.asp?PersonID=637 (669 words)

	Saturday NYC March: Peace,Justice Democracy- Backbone vs Chain Gang \| The Agonist
		The Backbone Campaign will launch the "Bush and Co. Chain Gang" at the Saturday, April 29 March for Peace, Justice and Democracy in New York City.
		The Backbone Campaign, a leader in the use of political theater as metaphor and spectacle, is a grassroots effort to embolden citizens and elected officials to stand up for progressive values.
		The backbone symbolizes an interlocking agenda, a coalition, and the personal courage necessary to fight for a future worthy of our children.
	agonist.org /nymole/20060429/saturday_nyc_march_peace_justice_democracy_backbone_vs_chain_gang (889 words)

	New LIPIDAT Database Design
		A chain is connected to a specific backbone with the connection specified by the Backbone_Number.
		There is an ordering of the chains connected to a specific backbone.
		In this case the lipids may all have a single headgroup or backbone, in which case this information is also recorded.
	www.cse.ohio-state.edu /~doug/Lipidat/LIPIDAT_new/DBdesigns/DatabaseDesign.htm (2596 words)

	BioMed Central \| Full text \| Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the ...
		The backbone of the peptides is predominantly extended.
		A value of 1 means the long axis of the Trp side chain is aligned with the normal of the membrane, a value of -0.5 means the long axis of the Trp side chain is perpendicular to the normal of the membrane.
		Although this overall trend is visible in the distributions of the side chains at the water/phospholipids interface, the intrinsic motions of both lipids and the peptide at this interface are too slow to obtain accurate convergence on a 50 ns time scale of hydrophobicity.
	www.biomedcentral.com /1471-2091/6/30 (4866 words)

	Backbone Campaign
		The Backbone Campaign is leading the way by providing imagery to help the American people "Visualize Impeachment." We are raising funds and organizing the building of a fun group of characters we fondly refer to as the "Chain Gang." These cartoonish figures/costumes are already booked to visit Crawford, Texas, with Cindy Sheehan this summer.
		She has been nominated for three positions on the Backbone Cabinet and we thought that on this 100th anniversary of Columbus Day, we would be providing a valuable service to the movement to elicit Ms.
		Phyllis Bennis (bio), a leading nominee for Progressive Ambassador to the UN in the Backbone Cabinet is a fellow at both the Institute for Policy Studies and the Transnational Institute in Amsterdam.
	www.backbonecampaign.org /storylisto.cfm?name=news (7717 words)

	Congen V2.1.2178 - Conformational Search
		The backbone search of an N residue segment begins by using backbone degrees of freedom to sample the free torsions of N-3 residues and then using the chain closure degree of freedom to close the chain.
		The N-terminus of the internal segment is anchored on the peptide nitrogen; the C-terminus is anchored on the alpha carbon.
		The procedure analogous to the backbone generation procedure would result in a series of nested iterations over each chi torsion angle with the number of levels being equal to the sum of the free torsions in all the side chains of the peptide segment.
	www.congenomics.com /congen/congen_13.html (12848 words)

	Silicone Implants
		The backbone is a chain of alternating silicon and oxygen atoms.
		But when they were discovered it was thought that they had "silicone" groups in the backbone chain.
		Silicone fluids are usually linear chain of polydimethylsiloxane (PDMS), which have a wide range of chain lengths and molecular masses.
	www.eng.buffalo.edu /Courses/ce435/2001ZGu/Silicon_Implants/SiliconImplantsReport.htm (2668 words)

	Model Backbone (Site not responding. Last check: 2007-10-21)
		When the backbone dihedrals are changed one end of the protein chain can remain in the same position but the moving end of the protein chain could potentially move a significant distance thorough space.
		By default when the backbone torsions are changed the whole of the non-fixed terminal of the segment beyond the rotated bonds will move with the rotation.
		After remodelling the protein backbone by copying coordinates from a database fragment it is advisable to remodel the side chains.
	scv.bu.edu /SCV/HelpPages/quantadocs/protein/10_Model_Backbone.html (2088 words)

	Backbone - AOL Music
		Vertebral column, of a vertebrate organism; Backbone chain, in polymer chemistry, the framework...
		This is a small look at the backbone of the Internet.
		Watch or listen to Backbone music videos, songs, live performances, concerts and more on AOL Music.
	music.aol.com /artist/backbone/289466/main (110 words)

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