Protein sequence secondary

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

In this paper we develop a new method for finding the three-dimensional space that surrounds a substrate/ligand. This space, which is the chemical equivalent of the receptor, is represented as a protein structure, referred herein as a "pseudo-receptor". A variety of computational tools are used to create the pseudo-receptor. A molecular mechanics and dynamics program, CHARMm(l), is used to calculate the energy and conformational features of the pseudo-receptor. The program QUANTA(l) is used to define the preliminary protein sequence, secondary structure, graphically examine molecular interactions, interface with CHARMm, and model amino-acid mutations in the protein sequence. 

Role of the Amino Acid Sequence in Protein Structure Secondary Structure in Protein.s Protein Folding and Tertiary Structure Subunit Interaction.s and Quaternary Structure... 

Primary structure is determined, as we ve seen, by sequencing the pTotein. Secondary, tertiary, and quaternary structures are determined by X-ray crystallography (Chapter 22 Focus On) because it s not yet possible to predict computationally how a given protein sequence will fold. 

Proteins have four levels of structure. Primary structure describes a protein s amino acid sequence secondary structure describes how segments of the protein chain orient into regular patterns—either a-helix or /3-pleated sheet tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape and quaternary structure describes how individual protein molecules aggregate into larger structures. 

Starting from the protein sequence (primary structure) several algorithms can be used to analyze the primary structure and to predict secondary structural elements like beta-strands, turns, and helices. The first algorithms from Chou and Fasman occurred already in 1978. The latest algorithms find e.g., that predictions of transmembrane... 

Fig. 2 Illustration of protein structure levels. Shown are primary structure (amino acid sequence), secondary structure (local order of protein chain, a-helix shown as an example), tertiary structure (assembly of secondary structure elements), and quaternary structure (relationship of different protein chain in multisubunit protein). (From Ref. 66.)...

A number of tools have been around for several years that aim to predict likely areas of secondary structure from a primary protein sequence or based on an RNA sequence [50]. These models have varying degrees of accuracy of prediction, with some of the best reaching up to 70% accuracy [57]. 

The systematic characterization of secondary protein modifications is different from sequencing a protein. For a systematic analysis of protein modifications, the complete protein sequence should be covered by the investigation. This is difficult to achieve since the enzymatic digestion of a protein is not homogeneous. The sequence coverage depends on the nature of the protein, its quantity, and the enzyme used. Typical... 

The secondary identifier is the "PROTEIN ID," which stands for the Protein Sequence Identifier. In nucleotide sequence entries, it is a string stored, in a qualifier called protein id, which is tagged to every CDS in the nucleotide database. Example ... 

Submit a protein sequence and you will receive secondary structure prediction via e-mail. 

It has also been demonstrated that the neural network approaeh ean be utihsed to predict the 3-D backbone folding of a protein related to the proteins the neural network has been trained upon (Bohr et al, 1990). A neural network is trained upon matehing pairs of protein sequences and secondary stractrrre as well as C a distance eorrstraints (i.e. the distance between 2 residue Ca-atoms larger or smaller than a seleeted threshold... 

The presence of RNA in the cytoplasm had been linked to protein synthesis by experiments done in the early 1940s. After the discovery of the double helix, the concept followed quickly that DNA was the master "blueprint" from which secondary blueprints or transcripts of RNA could be copied. The RNA copies, later identified as messenger RNA (mRNA), provided the genetic information for specifying protein sequence. The flow of information from DNA to RNA to proteins could be symbolized as in Eq. 26-1. 

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