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Three dimensional structure

Following the hierarchical nomenclature of protein structure, RNA tertiary structure represents a more global layout than secondary structure alone. The kissing loops motif is a prime example of an RNA tertiary structure contact not regularly seen in secondary structure [12]. In sequence and in secondary structure, the two loops of the motif may be distant. In the tertiary structure, the loops are seen to be close in space and form a hydrogen bond. Hence, the [Pg.518]

Coarse-grained (CG) models are poised to mediate this conflict of computational expense by discretizing the RNA molecule. In a CG model, the nucleotides are not represented at the atomic resolution, but are instead represented by a parameterized set of beads or pseudoatoms. The number of pseudoatoms is less than the full set of [Pg.519]


Fischer projection A method of representing three-dimensional structures in two-dimensional drawings in which the chiral atom(s) lies in the plane of the paper. The two enantiomeric forms of glyceraldehyde are represented as... [Pg.175]

In traditional Fan-Beam CT the radiation emitted from the X-ray tube is collimated to a planar fan, and so most of the intensity is wasted in the collimator blades (Fig. 2a). Cone-Beam CT, where the X-rays not only diverge in the horizontal, but also in the vertical direction, allows to use nearly the whole emitted beam-profile and so makes best use of the available LINAC photon flux (Fig. 2b). So fast scanning of the samples three-dimensional structure is possible. For Cone-Beam 3D-reconstruction special algorithms, taking in consideration the vertical beam divergence of the rays, were developed. [Pg.493]

Bdhm H-J 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J. Comp.-Aided Mol. Design 8 243-56... [Pg.2850]

In ice, there is an infinite three-dimensional structure in which the... [Pg.269]

Abstract. This paper presents results from quantum molecular dynamics Simula tions applied to catalytic reactions, focusing on ethylene polymerization by metallocene catalysts. The entire reaction path could be monitored, showing the full molecular dynamics of the reaction. Detailed information on, e.g., the importance of the so-called agostic interaction could be obtained. Also presented are results of static simulations of the Car-Parrinello type, applied to orthorhombic crystalline polyethylene. These simulations for the first time led to a first principles value for the ultimate Young s modulus of a synthetic polymer with demonstrated basis set convergence, taking into account the full three-dimensional structure of the crystal. [Pg.433]

Such a fundamental theory does exist for chemistry quantum mechanics. The dependence of the property of a compound on its three-dimensional structure is given by the Schrodinger equation. Great progress has been made both in the de-... [Pg.6]

Many problems in force field investigations arise from the calculation of Coulomb interactions with fixed charges, thereby neglecting possible mutual polarization. With that obvious drawback in mind, Ulrich Sternberg developed the COSMOS (Computer Simulation of Molecular Structures) force field [30], which extends a classical molecular mechanics force field by serai-empirical charge calculation based on bond polarization theory [31, 32]. This approach has the advantage that the atomic charges depend on the three-dimensional structure of the molecule. Parts of the functional form of COSMOS were taken from the PIMM force field of Lindner et al., which combines self-consistent field theory for r-orbitals ( nr-SCF) with molecular mechanics [33, 34]. [Pg.351]

As mentioned above, HMO theory is not used much any more except to illustrate the principles involved in MO theory. However, a variation of HMO theory, extended Huckel theory (EHT), was introduced by Roald Hof nann in 1963 [10]. EHT is a one-electron theory just Hke HMO theory. It is, however, three-dimensional. The AOs used now correspond to a minimal basis set (the minimum number of AOs necessary to accommodate the electrons of the neutral atom and retain spherical symmetry) for the valence shell of the element. This means, for instance, for carbon a 2s-, and three 2p-orbitals (2p, 2p, 2p ). Because EHT deals with three-dimensional structures, we need better approximations for the Huckel matrix than... [Pg.379]

The physical, chemical cind biological properties of a molecule often depend critically upo the three-dimensional structures, or conformations, that it can adopt. Conformational analysi is the study of the conformations of a molecule and their influence on its properties. Th development of modem conformational analysis is often attributed to D H R Bcirton, wh showed in 1950 that the reactivity of substituted cyclohexanes wcis influenced by th equatoricil or axial nature of the substituents [Beirton 1950]. An equcilly important reaso for the development of conformatiorml analysis at that time Wcis the introduction c analytic il techniques such as infreired spectroscopy, NMR and X-ray crystaillograph] which actucilly enabled the conformation to be determined. [Pg.473]

A particularly important application of molecular dynamics, often in conjunction with the simulated annealing method, is in the refinement of X-ray and NMR data to determine the three-dimensional structures of large biological molecules such as proteins. The aim of such refinement is to determine the conformation (or conformations) that best explain the experimental data. A modified form of molecular dynamics called restrained moleculai dynarrdcs is usually used in which additional terms, called penalty functions, are added tc the potential energy function. These extra terms have the effect of penalising conformations... [Pg.499]

I J, J C Cole, J P M Lommerse, R S Rowland, R Taylor and M L Verdonk 1997. Isostar A Libraij )f Information about Nonbonded Interactions. Journal of Computer-Aided Molecular Design 11 525-531. g G, W C Guida and W C Still 1989. An Internal Coordinate Monte Carlo Method for Searching lonformational Space. Journal of the American Chemical Scociety 111 4379-4386. leld C and A J Collins 1980. Introduction to Multivariate Analysis. London, Chapman Hall, ig C-W, R M Cooke, A E I Proudfoot and T N C Wells 1995. The Three-dimensional Structure of 1 ANTES. Biochemistry 34 9307-9314. [Pg.522]

Bioinformatics is a relatively new discipline that is concerned with the collection, organisatic and analysis of biological data. It is beyond our scope to provide a comprehensive overvie of this discipline a few textbooks and reviews that serve this purpose are now available (s the suggestions for further reading). However, we will discuss some of the main rnethoc that are particularly useful when trying to predict the three-dimensional structure and fum tion of a protein. To help with this. Appendix 10.1 contains a limited selection of some of tf common abbreviations and acronyms used in bioinformatics and Appendix 10.2 lists sorr of the most widely used databases and other resources. [Pg.529]

As more protein structures became available it was observed that some contained more that one distinct region, with each region often having a separate function. Each of these region is usually known as a domain, a domain being defined as a polypeptide chain that can folc independently into a stable three-dimensional structure. [Pg.531]

A number of structured databases have been developed to classify proteins according to the three-dimensional structures. Many of these are accessible via the World Wide Web, T1 protein databanlc (PDB [Bernstein d al. 1977]) is the primary source of data about the stru tures of biological macromolecules and contains a large number of structures, but many i these are of identical proteins (complexed with different ligands or determined at differet resolutions) or are of close homologues. [Pg.555]

A sequence alignment establishes the correspondences between the amino adds in th unknown protein and the template protein (or proteins) from wliich it will be built. Th three-dimensional structures of two or more related proteins are conveniently divided int structurally conserved regions (SCRs) and structurally variable regions (SVRs). Ihe structural conserved regions correspond to those stretches of maximum sequence identity or sequenc... [Pg.555]

Domain Sequence of a polypeptide chain that can independently fold into a stable three-dimensional structure... [Pg.569]

Bowie J U, R Liithy and D Eisenberg 1991. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure Science 253 164-170. [Pg.574]


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Activities Structures: Three-Dimensional Works

Approaches to Three-Dimensional Quantitative Structure—Activity Relationships

Aromaticity three dimensional structures

Azurin three-dimensional structure

Biopolymers three-dimensional structure

Bond-line structures three-dimensional

Catalysis/catalysts three-dimensional structures

Cellulose three-dimensional structure

Chapman-Jouguet detonations three-dimensional structures

Charge compensating cations three-dimensional structures

Chymosin Three-dimensional structure

Computer-generated three-dimensional structure

Conformations 7 Three-dimensional Structure Generation

Crystal structure three-dimensional

Crystal structures, polymers three dimensional

Databases three-dimensional structure searching

Descriptors Based on Three-Dimensional Structure

Descriptors from the Three-Dimensional Structure

Determination of three-dimensional structure

Domains three-dimensional structures

Effects of three-dimensional structures

Fold into Complex Three-Dimensional Structures

G protein three-dimensional structures

G three-dimensional structure

GABA three-dimensional structure

Glycosyltransferases three-dimensional structures

Green fluorescent protein three-dimensional structure

Hemoglobins three-dimensional structure

Human growth hormone three-dimensional structure

INDEX three-dimensional structure

Inhibitor binding three-dimensional structure

Inorganic compounds three-dimensional structural databases

Integrins three-dimensional structure

Interleukin three-dimensional structure

Lactoferrin three-dimensional structure

Lipophilicity Fields An Enhancement of Three-Dimensional Quantitative Structure-Activity Relationships

Manganese three-dimensional structures

Methods three-dimensional structure

Methylmalonyl-CoA mutase three-dimensional structure

Molecular representations three-dimensional bond-line structures

Molecular structure The three-dimensional

Molecular structure The three-dimensional arrangement of atoms in a molecule

Molecular structure data, three-dimensional

Molecules three-dimensional structure

Monellin three-dimensional structure

Muscle, three-dimensional structure

Nanofibrous structure three-dimensional

Naturally occurring three-dimensional structure

Neutron diffraction studies three-dimensional structure

Nicotinic acetylcholine receptors three-dimensional structure

Notexin Three dimensional structure

Nuclear magnetic resonance three-dimensional structure elucidation

Other Representations of Three-Dimensional Molecular Structure

Papain three-dimensional structure

Penicillopepsin three-dimensional structure

Pepsin three-dimensional structure

Peptides three-dimensional structures

Polymers three-dimensional structures

Primary and three-dimensional structure

Protein affinity chromatography three-dimensional structures

Protein three-dimensional structure

Proteins integral three-dimensional structure

QSAR (Quantitative structure-activity three-dimensional

Quantitative structure-activity relationship three-dimensional descriptors

Quantitative structure-activity relationships three-dimensional

RRNA 5S, three-dimensional structure

RRNA three-dimensional structure

Renaturation three-dimensional structure

Ribosome three-dimensional structure

Searching Databases of Three-Dimensional Structures

Self-assembly three-dimensional "spherical" structures

Services three-dimensional protein structures

Sheet forming three-dimensional structure

Sialidase three-dimensional structure

Similarity of Small Molecules Based on Three-Dimensional Structure

Spinel Structure Materials (three dimensional)

Structural formulae three-dimensional

Structure data, three-dimensional

Structure databases three-dimensional

Structure generation three-dimensional, automation

Structure of Three-dimensional Polymeric Networks as Biomaterials

Structure three-dimensional interphase

Structure three-dimensional reinforcement

Structure three-dimensionally connected

Structure with three-dimensional boron networks

Structure, three-dimensional 3-sheet

Structure, three-dimensional chaperones

Structure, three-dimensional electrostatic interactions

Structure, three-dimensional folding, forces

Structure, three-dimensional hairpin loop

Structure, three-dimensional hydrogen bonds

Structure, three-dimensional hydrophobic interactions

Structure, three-dimensional molten globule state

Structure, three-dimensional motifs, structural

Structure, three-dimensional oligomers

Structure, three-dimensional pleated-sheet

Structure, three-dimensional protein-folding pathways

Structure, three-dimensional subunits

Structure, three-dimensional summary

Structure, three-dimensional topological diagrams

Structure, three-dimensional torsional angles

Structure-activity relationships three-dimensional-ligand-based

Structure-activity relationships three-dimensional-protein-based

Structure-based drug design three-dimensional

Structures Systems Three Dimensional

Substrate inhibition three-dimensional structure

TOPICAL three-dimensional structure

Tetrahedral frameworks Three- or two-dimensional structures

The Protein Data Bank, Three-Dimensional Structures, and Computation

The Three-Dimensional Structure of Insulin

The Three-Dimensional Structure of Protein Molecules in Aqueous Solution

The Three-Dimensional Structures of Proteins

The three-dimensional structure of Bacillus subtilis ferrochelatase

Theoretical and Practical Aspects of Three-Dimensional Quantitative Structure-Activity Relationships

Thioredoxin three-dimensional structure

Three Dimensional (3D) Structure

Three Dimensional Structures Searching

Three Dimensional Structures Searching Willett, Peter

Three dimensional multilayer structure

Three dimensionally ordered porous structures

Three structures

Three-Dimensional Biological Structures

Three-Dimensional Molecular Structure Tables

Three-Dimensional Silicon-oxygen Structures

Three-Dimensional Structure Database Searches

Three-Dimensional Structure Representation

Three-Dimensional Structure Search Methods

Three-Dimensional Structure of Biopolymers

Three-Dimensional Structure of the Protein Portion

Three-Dimensional Structures of Molecules

Three-dimensional artworks structures

Three-dimensional braided fabric structures

Three-dimensional chemical structures

Three-dimensional electrode structures

Three-dimensional geometry, transition structure

Three-dimensional honeycomb structure

Three-dimensional lattice structure

Three-dimensional lattice structure sphere model

Three-dimensional ligand-based models structure-activity relationships

Three-dimensional model phases structure

Three-dimensional molecular structures

Three-dimensional molecular structures in solution

Three-dimensional molecular structures superconductivity

Three-dimensional periodic structures

Three-dimensional periodic structures fabrication

Three-dimensional polymeric networks structural characteristics

Three-dimensional quantitative structure

Three-dimensional quantitative structure activity relationships conformation

Three-dimensional quantitative structure activity relationships superposition

Three-dimensional quantitative structure-activity relationship drug design

Three-dimensional quantitative structure-activity relationship example

Three-dimensional quantitative structure-activity relationship methods

Three-dimensional quantitative structure-activity relationship models

Three-dimensional spectroscopy protein structure determination

Three-dimensional structural analysis, Patterson

Three-dimensional structural data bases

Three-dimensional structural diagrams

Three-dimensional structural keys

Three-dimensional structural notations

Three-dimensional structure determination

Three-dimensional structure determination oligosaccharide

Three-dimensional structure elucidation using

Three-dimensional structure generation

Three-dimensional structure glycans

Three-dimensional structure immunoglobulins

Three-dimensional structure modeling

Three-dimensional structure of individual

Three-dimensional structure of microcystins

Three-dimensional structure of nodularins

Three-dimensional structure of proteins

Three-dimensional structure poly resist

Three-dimensional structure searching conformational flexibility

Three-dimensional structure searching types

Three-dimensional structure series

Three-dimensional structure synthesis

Three-dimensional structure transferrins

Three-dimensional structure, compounds

Three-dimensional structure, of biomolecules

Three-dimensional structure, photonic

Three-dimensional structure, relationship

Three-dimensional structure, relationship biological activity

Three-dimensional structure/substructure searching

Three-dimensional structures Bchl b molecules

Three-dimensional structures D-amino acid oxidase

Three-dimensional structures Volume

Three-dimensional structures a-amylase, pancreatic

Three-dimensional structures aconitase

Three-dimensional structures actin filament

Three-dimensional structures adenylate kinase

Three-dimensional structures aldehyde oxido-reductase

Three-dimensional structures and projections

Three-dimensional structures aspartate aminotransferase

Three-dimensional structures aspartate carbamyltransferase

Three-dimensional structures aspartate chemoreceptor

Three-dimensional structures bacteriophage

Three-dimensional structures bacteriorhodopsin

Three-dimensional structures cadherin

Three-dimensional structures calmodulin

Three-dimensional structures carbonic acid anhydrase

Three-dimensional structures carboxypeptidase

Three-dimensional structures catalase

Three-dimensional structures catalytic intermediates

Three-dimensional structures cholera toxin

Three-dimensional structures chymotrypsin

Three-dimensional structures citrate synthase

Three-dimensional structures conotoxin

Three-dimensional structures cutinase

Three-dimensional structures cyclosporin

Three-dimensional structures cytochrome

Three-dimensional structures cytochrome c oxidase

Three-dimensional structures dehydrogenase

Three-dimensional structures dihydrofolate reductase

Three-dimensional structures elastase

Three-dimensional structures enolase

Three-dimensional structures ferredoxin

Three-dimensional structures ferritin

Three-dimensional structures glutathione reductase

Three-dimensional structures glyceraldehyde phosphate

Three-dimensional structures hydrogenase

Three-dimensional structures inorganic compounds

Three-dimensional structures insulin

Three-dimensional structures insulin receptor

Three-dimensional structures isomers

Three-dimensional structures lysozyme

Three-dimensional structures organic compounds

Three-dimensional structures pectate lyase

Three-dimensional structures plastocyanin

Three-dimensional structures projections

Three-dimensional structures pyruvate dehydrogenase

Three-dimensional structures rhinovirus

Three-dimensional structures subtilisin

Three-dimensional structures tissue factor

Three-dimensional structures trypsin

Three-dimensional structures tubulin

Three-dimensional structures vanadium phosphates

Three-dimensional structures virus

Three-dimensional structures with zinc finger protein

Three-dimensional structures, animating

Three-dimensional structures, drawing

Three-dimensional structures, how

Three-dimensional textile structures

Unknown Three-Dimensional Structures

Watson-Crick three-dimensional structure

X-ray diffraction Three-dimensional structures

Xylose three dimensional structure

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