Pdb-L Mailing List August 14, 2008
Posted by nhabibi in Bioinformatics, Internet.3 comments
I don’t have so much experiment with mailing lists, but this one is great! A number of knowledgeable and helpful people in the field, around the world.
Special thanks to Dr. Kevin Karplus, professor of Bioinformatics at University of California, Santa Cruz, for his useful and detailed responses.
Protein Contact Map Prediction November 28, 2007
Posted by nhabibi in Bioinformatics.4 comments
Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.
(Source: Wikipedia)
As the definition indicates, bioinformatics is an interdisciplinary field, hard but interesting.
The studies in bioinformatics are categorized in three groups: Genomics, Proteomics and Transcriptoemics. (Now we have some biology, You would like it! Skip, if your not interested. 
)
Genomics is the study of an organism’s entire genome. the genome of an organism is its whole hereditary information and is encoded in the DNA. This includes both the genes and the non-coding sequences of the DNA. More precisely, the genome of an organism is a complete DNA sequence of one set of chromosomes.
Proteomics is the large-scale study of proteins, particularly their structures and functions. The proteome of an organism is the set of proteins produced by it during its life, and its genome is its set of genes.
The transcriptome is the set of all messenger RNA (mRNA) molecules, or “transcripts”, produced in one or a population of cells. Unlike the genome, which is roughly fixed for a given cell line (excluding mutations), the transcriptome can vary with external environmental conditions. Because it includes all mRNA transcripts in the cell, the transcriptome reflects the genes that are being actively expressed at any given time. The study of transcriptomics examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology.
Proteins are large organic compounds made of amino acids arranged in a linear chain. Proteins are essential parts of organisms and participate in every process within cells.
A protein contact map represents the distance between every two amino acids of a three-dimensional protein structure in a two-dimensional matrix. It can be used to describe the similarity between protein structures and prediction of tertiary structure. These maps are either predicted from protein sequence or calculated from a given structure.
Contact map prediction is a problem in bionformatics. Several approaches have been proposed, each one with a degree of success. We are working now on the subject. You can take a look at my seminar report and presentation, both in Persian.
More information:
- Computational Methods for Protein Structure Prediction and Modeling: Volume 1: Basic Characterization – Chapter 8
PS: Can you guess Why my “Blogroll” is empty?
