Tools for peptides

PESTfind - Identification of PEST regions at EMBnet Austria

HLA_Bind - Prediction of MHC type I (HLA) peptide binding

PEPVAC - Prediction of supertypic MHC binders

RANKPEP - Prediction of peptide MHC binding

SYFPEITHI - Prediction of MHC type I and II peptide binding

ProtScale - Amino acid scale representation (Hydrophobicity, other conformational parameters, etc.)

Drawhca - Draw an HCA (Hydrophobic Cluster Analysis) plot of a protein sequence

Protein Colourer - Tool for coloring your amino acid sequence

Three To One - Tool to convert a three-letter coded amino acid sequence to single letter code

Colorseq - Tool to highlight (in red) a selected set of residues in a protein sequen

Protein identification and characterization

Identification and characterization with peptide mass fingerprinting data

Aldente - Identify proteins with peptide mass fingerprinting data. A new, fast and powerful tool that takes advantage of Hough transformation for spectra recalibration and outlier exclusion

FindMod - Predict potential protein post-translational modifications and potential single amino acid substitutions in peptides. Experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot entry or from a user-entered sequence, and mass differences are used to better characterize the protein of interest.

FindPept - Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage

GlycoMod - Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses (can be used for free or derivatized oligosaccharides and for glycopeptides)

The Peptide Bond

The peptide bond links the carbonyl carbon of one amino acid residue to the amino nitrogen of another. Learn the characteristics of the peptide bond and how to interpret Ramachandran plots in this webcast.

Peptide bond formation - Biofundamentals

A short introduction into peptide bond formation and polypeptide structure

http://trade.1111.com.tw/web/peptide

Peptide - definition

Peptide
From Wikipedia, the free encyclopedia
"Peptides" redirects here. For the journal, see Peptides (journal).

A tetrapeptide (example Val-Gly-Ser-Ala) with green marked amino end (L-Valine) and blue marked carboxyl end (L-Alanine).

Peptides (from Gr. πεπτός, "digested", derived from πέσσειν, "to digest") are short chains of amino acid monomers linked by peptide (amide) bonds, the covalent chemical bonds formed when the carboxyl group of one amino acid reacts with the amino group of another. Peptides are distinguished from proteins on the basis of size, and as a benchmark can be understood to contain approximately 50 amino acids or less[citation needed]. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a single peptide bond, followed by tripeptides, tetrapeptides, etc. A polypeptide is a long, continuous, and unbranched peptide chain. Hence,peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligo- and polysaccharides, etc.

Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule (DNA, RNA, etc.), or to complex macromolecular assemblies. Finally, while aspects of the techniques that apply to peptides versus polypeptides and proteins differ (i.e., in the specifics of electrophoresis, chromatography, etc.), the size boundaries that distinguish peptides from polypeptides and proteins are not hard and fast: long peptides such as amyloid beta have been referred to as proteins, and smaller proteins like insulin have been consideredpeptides.

Amino acids that have been incorporated into peptides are termed "residues"; all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide (as shown for the tetrapeptide in the image).

http://en.wikipedia.org/wiki/Peptide

Peptide Classes

Peptide classes

Here are the major classes of peptides, according to how they are produced:

Ribosomal peptides 

Are synthesized by translation of mRNA. They are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules. Some lower organisms produce peptides as antibiotics, such as microcins.^[1] Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome. However, these peptides frequently have posttranslational modifications, such as phosphorylation, hydroxylation, sulfonation, palmitylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed.<ref.Pons M, Feliz M, Antònia Molins M, Giralt E (1991). "Conformational analysis of bacitracin A, a naturally occurring lariat". Biopolymers 31 (6): 605–12. PMID 1932561.</ref> More exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom.^[2]

Nonribosomal peptides 

These peptides are assembled by enzymes that are specific to each peptide, rather than by the ribosome. The most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms.^[3] Other nonribosomal peptides are most common in unicellular organisms, plants, and fungi and are synthesized by modular enzyme complexes called nonribosomal peptide synthetases.^[4] These complexes are often laid out in a similar fashion, and they can contain many different modules to perform a diverse set of chemical manipulations on the developing product.^[5] These peptides are often cyclic and can have highly-complex cyclic structures, although linear nonribosomal peptides are also common. Since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. Oxazoles, thiazoles often indicate that the compound was synthesized in this fashion.^[6]

Peptones 

Are derived from animal meat digested by proteolases. The resulting material is used as a source of proteins in nutrient media for growing bacteria and fungi.^[7]

Peptide Fragments 

Refer to fragments of proteins which used to identify or quantify the source protein.^[8] Often these are the products of enzymatic degradation performed in the laboratory on a controlled sample, but can also be forensic or paleontological samples which have been degraded by natural effects.^[9][10]

Info:http://www.wikidoc.org/index.php/Peptide

More Info about Peptide 

Peptide - Wikidoc

Peptide

Peptides (from the Greek πεπτίδια, "small digestibles") are short polymers formed from the linking, in a defined order, of α-amino acids. The link between one amino acid residue and the next is known as an amide bond or a peptide bond.

Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. There are several different conventions to determine these, all of which have flaws.

Conventions

One convention is that those peptide chains that are short enough to be made synthetically from the constituent amino acids are called peptides rather than proteins. However, with the advent of better synthetic techniques, peptides as long as hundreds of amino acids can be made, including full proteins like ubiquitin. Native chemical ligation has given access to even longer proteins, so this convention seems to be outdated.

Another convention places an informal dividing line at approximately 50 amino acids in length (some people claim shorter lengths). However, this definition is somewhat arbitrary. Longpeptides, such as the amyloid beta peptide linked to Alzheimer's disease, can be considered proteins; and small proteins, such as insulin, can be considered peptides.

Info:http://www.wikidoc.org/index.php/Peptide

More Info about Peptide