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Topic: Protein structure

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In the News (Mon 18 Dec 17)

  Proteins   (Site not responding. Last check: 2007-10-14)
The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom).
The tertiary structure of a protein molecule, or of a subunit of a protein molecule, is the arrangement of all its atoms in space, without regard to its relationship with neighbouring molecules or subunits (IUPAC-IUB, 1970).
The degree to which the three-dimensional structure of a protein may differ from the native state may vary from a change in a single noncovalent bond or side-chain orientation to the case where almost no atom exist in the same spatial relationship to others except for the constraints of the primary structure.
www.friedli.com /herbs/phytochem/proteins.html   (11287 words)

 Protein structure prediction   (Site not responding. Last check: 2007-10-14)
Protein structure prediction is one of the most significant tasks tackled in computational structural biology.
Given the usefulness of known protein structures in such valuable tasks as rational drug design, this is a highly active field of research.
The output of experimentally determinedprotein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behindthe output of protein sequences.
www.therfcc.org /protein-structure-prediction-9147.html   (465 words)

 Peptides and Proteins
The spontaneous folded state of globular proteins is a reflection of a balance between the opposing energetics of H-bonding between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups.
Proteins of opposite charge to the resin are retained as a solution of proteins is passed through the column.
Proteins are layered atop the gradient in an ultracentrifuge tube then subjected to centrifugal fields in excess of 100,000 x g.
web.indstate.edu /thcme/mwking/protein-structure.html   (3144 words)

 AllRefer.com - protein : Protein Structure (Biochemistry) - Encyclopedia
The term primary structure denotes the precise linear sequence of amino acids that constitutes the polypeptide chain of the protein molecule.
The precise three-dimensional structure of a protein molecule is referred to as its native state and appears, in almost all cases, to be required for proper biological function (especially for the enzymes).
If the tertiary or quaternary structure of a protein is altered, e.g., by such physical factors as extremes of temperature, changes in pH, or variations in salt concentration, the protein is said to be denatured; it usually exhibits reduction or loss of biological activity.
reference.allrefer.com /encyclopedia/P/protein-protein-structure.html   (439 words)

 ipedia.com: Protein structure prediction Article   (Site not responding. Last check: 2007-10-14)
The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences.
Given the amino acid sequence of a unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.
Protein threading scans the amino acid sequence of an unknown structure against a database of solved structures.
www.ipedia.com /protein_structure_prediction.html   (542 words)

 ScienceDaily: First Glimpse Of Protein Structure Holds Promise For New Way To Fight AIDS
Wedekind is an expert in structural biology, the branch of molecular biology concerned with the study of the molecular shape and properties of proteins and nucleic acids, the molecules that make up the body's structures and carry out its life functions.
In seeking to determine the structure of A3G, however, the team was unable to use standard methods to start.
Messenger RNAs, copies of DNA that serve as a templates for the building of proteins, thus, may be natural regulators of whether A3G remains active or not.
www.sciencedaily.com /releases/2006/11/061101150714.htm   (1197 words)

 Protein Structure Literature
A "new view" of proteins is presented based on the notion that conformational diversity for a single sequence may support multifunctionality, and that this in turn fosters relatively rapid evolution of function from existing folds.
The evolutionary relationships of domains in proteins of known structure are described in the Structural Classification of Proteins (SCOP) database.
Membrane proteins are greatly underrepresented in the Protein Data Bank because they are less amenable to the classical methods of X-ray crystallography and solution NMR.
molvis.sdsc.edu /protexpl/favlit.htm   (2153 words)

Approximately one-third of all residues in globular proteins are contained in turns that serve to reverse the direction of the polypeptide chain.Three types of turns are designated I, II, and III are known.
Many proteins contain 2 or more different polypeptide chains that are held in association by the same non-covalent forces that stabilize the tertiary structures of proteins.
This change of a single amino acid alters the structure of hemoglobin molecules in such a way that the deoxygenated proteins polymerize and precipitate within the erythrocyte, leading to their characteristic sickle shape.
www.med.unibs.it /~marchesi/proteins.html   (1338 words)

 Protein Structure   (Site not responding. Last check: 2007-10-14)
Proteins consist of a polypeptide backbone with attached side chains.
Each type of protein differs in its sequence and number of amino acids; therefore, it is the sequence of the chemically different side chains that makes each protein distinct.
The amino acid sequence of a protein is always presented in the N to C direction, reading from left to right.
www.accessexcellence.org /AB/GG/prot_Struct.html   (136 words)

 Biopharmaceutical protein structure glossary
The conformation into which a proteinfolds.” For proteins consisting of only one polypeptide chain, it is the tertiary structure that is usually referred to by the term “the 3D structure of a protein.
Protein folding is a particularly good target for the application of molecule methods because its complexity and stochastic nature make it difficult to study using ensemble methods.
The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily.
www.genomicglossaries.com /content/protein_structure_glossary.asp   (2741 words)

 3.4 Primary through Quartenary structure   (Site not responding. Last check: 2007-10-14)
This is a molecule of hexokinase, a metabolic protein found in almost all living organisms.
This protein is composed of approximately 6000 atoms and weighs 48 kiloDaltons (kDA).
Protein secondary structure refers to certain common repeating structures found in proteins.
web.mit.edu /esgbio/www/lm/proteins/structure/structure.html   (512 words)

 Review: Protein Structure
A domain with a particular structure and function may be part of the structure of several otherwise distinct proteins.
For example, an enzyme's primary structure may include a segment that folds to produce an active site with particular catalytic activity, plus other segments that may mediate regulation of the enzyme or binding of the enzyme to a membrane.
Quaternary structure tends to be stabilized mainly by weak interactions between residues exposed on surfaces polypeptides within a complex.
www.rpi.edu /dept/bcbp/molbiochem/MBWeb/mb1/part2/protein.htm   (1123 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).
In the absence of known structures with significant sequence identity to a protein of interest, predictions of residue solvent accessibility can be used to investigate function, and to suggest which residues to mutate to facilitate crystallisation or to reduce aggregation.
Native 3D structures of proteins are encoded by a linear sequence of amino acid residues.
www.embl-heidelberg.de /~rost/Papers/sisyphus.html   (8205 words)

 Vegetarians in Paradise/Protein Basics/Vegetarian Protein /Protein Charts/Vegan Protein/Protein Sources
During pregnancy and breastfeeding, protein needs can easily be met by adding a little extra of the foods higher in protein, such as enriched soymilk, beans, tofu, tempeh, nuts, and nut butters in addition to a wide variety of fruits and vegetables.
While the focus on protein is important, the leafy green vegetables such as collards, kale, mustard greens, turnip greens, and spinach are also necessary for their high content of folate known to prevent neural tube defects such as spina bifida.
Those who believe plant protein is inferior to animal protein may be surprised to learn that plant proteins contain the same 23 amino acids as animal proteins.
www.vegparadise.com /protein.html   (1502 words)

 Science Functional Genomics Resources: Protein Structure and Function
Protein Data Bank (PDB) -- databank of 3D protein structures primarily determined experimentally by X-ray crystallography and NMR
Structural Classification of Proteins (SCOP) -- aims to describe structural and evolutionary relationships between proteins whose structure is known.
ProtoMap -- Hierarchical classification of proteins in the SWISSPROT and TrEMBL databases
www.sciencemag.org /feature/plus/sfg/resources/res_protein.dtl   (1465 words)

 UB Reporter: UB researchers win top spots in global "protein structure Olympics"
In the Sixth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP), three of the 17 winning predictor teams were from UB, and two of them are affiliated with UB's New York State Center of Excellence in Bioinformatics and Life Sciences.
In the biennial competition, several dozen protein amino-acid sequences are provided to bioinformatics scientists who compete with one another—and with automated computer servers using algorithms written by humans—to complete the three-dimensional structures of the same mystery protein.
At stake is a far greater understanding of proteins, how they interact and cause disease, and how new drugs might be developed rationally to fight them.
www.buffalo.edu /reporter/vol36/vol36n45/articles/ProteinOlympics.html   (610 words)

 IUL Biotechnology Series, Protein Structure Prediction, edited by Igor F. Tsigelny
Chapters on concepts of protein structure prediction discuss areas such as a Bayesian approach to protein fold recognition, three-dimensional structure prediction using simplified structure models and Bayesian block fragments, and protein structure prediction using hidden Markov model structural libraries.
Chapters on methods of structure and sequence alignment outline methods such as the PCONS consensus approach, and discuss new insights into protein fold space and sequence-structure relationships.
field of protein structure prediction, where new approaches to fold recognition, structural alignment and threading continue to appear at a rate that leaves the individual investigator at a loss of which way to turn to solve any particular problem.
www.iul-press.us /Books/BBT03-Prediction/prediction.html   (453 words)

 Sandor Pongor: ICGEB Protein Structure and Bioinformatics
Both the structural organization and the moelcular interactions of proteins can be described as specific and robust networks.
We study the proteins of the notch signalling network and its involvement in genetic diseases.
In particular, we look at the formation of disulfide bonds in proteins; evolution of network stability and systems biology; prediction of protein structure and function using machine learning approaches, and aspects of protein chemistry including synthesis of modified peptides and pharmaceutical applications.
www.icgeb.org /RESEARCH/TS/ProtStructBioinformatics.htm   (270 words)

 Statistical geometry of protein structure   (Site not responding. Last check: 2007-10-14)
In this work the Delaunay tessellation is applied for the first time for the analysis of protein structure.
By representing amino acid residues in protein chains by Ca atoms, the protein structure is described as a set of points in three- dimensional space.
The Delaunay tessellation of a protein structure generates an aggregate of space-filling irregular tetrahedra, or Delaunay simplices.
www.unc.edu /~ivaisman/proteins.htm   (239 words)

 The PSIPRED protein structure prediction server
It is important to realise, however, that due to the small sample sizes, the results from CASP are not statistically significant, although they do give a rough guide as to the current "state of the art".
The method was benchmarked on a test set of 86 transmembrane proteins of known topology.
GenTHREADER is a fast and powerful fold recognition method, which can be applied to either whole, translated genomic sequences (proteomes) as in the case of the GTD or individual protein sequences as in the case of the PSIPRED server.
bioinf.cs.ucl.ac.uk /psipred   (691 words)

 NCBI Structure Group
MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis.
Each protein chain and 3D domain from MMDB is compared with all the others using the VAST (Vector Alignment Search Tool) algorithm.
CDD, the Conserved Domain Database, a protein annotation resource, which consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.
www.ncbi.nlm.nih.gov /Structure   (205 words)

 [No title]   (Site not responding. Last check: 2007-10-14)
Proteins and peptides are biopolymers composed of amino acid residues interlinked by amide bonds.
with similar proteins (say from different organisms) structure tends to be more conserved than the exact sequence of amino acids.
although sequence must determine structure, it is not yet possible to predict the entire structure from sequence accurately.
bmbiris.bmb.uga.edu /wampler/tutorial/prot0.html   (177 words)

 Protein Structure Prediction Center
Our goal is to help advance the methods of identifying protein structure from sequence.
The Center has been organized to provide the means of objective testing of these methods via the process of blind prediction.
CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused.
predictioncenter.org   (174 words)

 PSA Structure Prediction
The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Since we expect Web results to be more popular, we have made this the default for the "Return results via:" choice on the submission page; the standard e-mail delivery technique is still available as the other option for this choice.
Analysis of full-length amino acid sequences that are assumed to be monomeric globular, water-soluble proteins consisting of a single domain.
bmerc-www.bu.edu /psa   (196 words)

 Protein Structure Prediction
The PSA server analyzes amino acid sequences to predict secondary structures and folding classes.
Single sequence-based prediction for coiled-coil regions using statistical patterns of coiled-coil proteins in the database.
Prediction-based threading detecting the fold type and aligning a protein of unknown structure and a protein of known structure for low levels of sequence identity (< 25%).
cmgm.stanford.edu /WWW/www_predict.html   (443 words)

 CE Home Page -- Combinatorial Extension   (Site not responding. Last check: 2007-10-14)
Structural similarity between Acetylcholinesterase and Calmodulin found using CE (Tsigelny et al, Prot Sci, 2000, 9:180)
Shindyalov IN, Bourne PE (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
This service is not funded as part of the Protein Data Bank (PDB).
cl.sdsc.edu /ce.html   (141 words)

 RCSB Protein Data Bank
RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
narrated tutorial illustrates how to search, navigate, browse, generate reports and visualize structures using this new site.
Glucose is a major source of energy in your body, but unfortunately, free glucose is relatively rare in our typical diet.
www.rcsb.org /pdb   (361 words)

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