Computer biologists

MQ Zhang. Large-scale gene expression data analysis A new challenge to computational biologists. Genome Res 9 681-688, 1999. 

One of the crucial steps in this transformation will be training a new generation of biologists who are both computational scientists and laboratory scientists. This major challenge requires both vision and hard work vision to set an appropriate agenda for the computational biologist of the future and hard work to develop a curriculum and textbook. 

In 1965, Jacques Monod stated in his Nobel lecture that the ambition of molecular biology is to interpret the essential properties of organisms in terms of molecular structures [1]. Similarly, it would be no exaggeration to say that most computational biologists naturally believe that the ambition of computational molecular biology is to interpret the essential functions of organisms in terms of molecular dynamics. ... 

The "Computer Biologists are able to predict which oncogene will strike and how. How to counteract the invasion of the oncogenes (no sarcasm meant). External interventions with radiation and chemicals may decimate the new colonists (and harm the host as well), however resistant new mutants of the new colonists arise to re-occupy the host. The extraordinary resistance of the primordial ancestors to... 

Caetano-Anoiys, Gustavo Computational biologist who developed a molecular clock to date the invention of different protein activities. 

Air pollution control statistical planners, agricultural biologists, biologists, computer specialists, economists, management analysts, mathematicians, microbiologists, ph)rsicists, phytotoxicologists, researchers, research analysts, research scientists, research specialists, scientists (environmental and unspecified), statisticians, and statistical analysts. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

Along with code breakers, weather forecasters, and molecular biologists, chemists are now among the heaviest users of computers, which they use to calculate the detailed electronic structures of atoms and molecules (see Major Technique 5, following Chapter 13). 

Today, computers are so ubiquitous in pharmaceutical research and development that it may be hard to imagine a time when there were no computers to assist the medicinal chemist or biologist. A quarter-century ago, the notion of a computer on the desk of every scientist and company manager was not even contemplated. Now, computers are absolutely essential for generating, managing, and transmitting information. The aim of this chapter is to give a... 

In an outreach to the medicinal chemists at Lilly, a one-week workshop was created and taught in the research building where the organic chemists were located. (The computational chemists were initially assigned office space with the analytical chemists and later with the biologists.) The workshop covered the basic and practical aspects of performing calculations on... 

More recently, a group in England led by a structural biologist compiled a list of marketed medicines that came from SBDD [133]. These are labeled SBDD in Table 1.2. It can be seen that there is only a little overlap between the two compilations (CADD and SBDD). It can also be seen that the number of pharmaceuticals from SBDD is very impressive. Computer-based technologies are clearly making a difference in helping bring new medicines to patients. 

The days in which IP (intellectual property) strategists were separated into groups of pharmacologists (chemists or biologists) and other groups of computer scientists are slowly passing—in the same manner in which the tech-... 

Molecular biologist Leroy Hood anticipates that people will carry credit-card type strips that contain computer readouts of their personal genome. Your entire genome and medical history will be on a credit card .12... 

Kauffman s conclusions arise only from computer simulations, and this is also the main reason for criticism, in particular for biologists. Even though extensive mathematical deliberations and sophisticated computer simulations could show that networks containing many elements can tend towards transitions which give systems of organized complexity, some important factors which lead to a living system are still missing. 

As we have already pointed out, the theoretical basis of free energy calculations were laid a long time ago [1,4,5], but, quite understandably, had to wait for sufficient computational capabilities to be applied to molecular systems of interest to the chemist, the physicist, and the biologist. In the meantime, these calculations were the domain of analytical theories. The most useful in practice were perturbation theories of dense liquids. In the Barker-Henderson theory [13], the reference state was chosen to be a hard-sphere fluid. The subsequent Weeks-Chandler-Andersen theory [14] differed from the Barker-Henderson approach by dividing the intermolecular potential such that its unperturbed and perturbed parts were associated with repulsive and attractive forces, respectively. This division yields slower variation of the perturbation term with intermolecular separation and, consequently, faster convergence of the perturbation series than the division employed by Barker and Henderson. 

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... 

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