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General
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Protein
structure prediction is one of the most important goals pursued by
bioinformatics and theoretical chemistry. Its aim is the prediction of the
three-dimensional structure of proteins from their amino acid sequences,
sometimes including additional relevant information such as the structures
of related proteins.
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The
complexes of two or more proteins, where the structures of the proteins are
known or can be predicted with high accuracy, protein-protein docking
methods can be used to predict the structure of the complex.
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Protein
threading scans the amino acid sequence of an unknown structure against a
database of solved structures. In each case, a scoring function is used to
assess the compatibility of the sequence to the structure, thus yielding
possible three-dimensional models. This type of method is also known as
3D-1D fold recognition.
Process
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Crystallography plays a major role in current efforts towards protein
structure determination. Building a protein model from crystallographic
data, however, is a complex and time-consuming process, which is somewhat
assisted by the use of computer graphics for tracing the polypeptide chains,
and for viewing and improving the resulting model.
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The
wire-bender of Rubin and Richardson is a convenient tool for constructing
carbon models of proteins. It has been used in laboratories for building
protein backbone models which helped us establish the existence of
continuous regions of peptide chain in globular proteins.
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X-ray
crystallography is the main method for structure determination of proteins.
This can be a time-consuming process, and it will succeed only if it is
possible to find suitable conditions for growing crystals.
Application
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Protein
structure prediction is of high importance in medicine and biotechnology.
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Homology-based rational drug design is a useful tool for the pharmaceutical
industry.
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The
application of the techniques of molecular biology, transgenics, knockouts
and antisense have led to many advances in our understanding of drug action,
and indeed to the development of new drugs.
Report
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Knowledge
of the three-dimensional (3D) structure of protein-protein complexes
provides a valuable systems. The rate of protein structure
determination is increasing rapidly. Today there are some 5,000 entries in
the Brookhaven Protein Data Bank (PDB).
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The
development of a new drug, or medicine, is a challenge of tremendous
complexity and of truly multi-disciplinary character. It is currently also
of a dual nature. Typical trialand error processes are carried out
simultaneously with the most advanced biochemical synthetic and
computational procedures.
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In recent
years two new techniques have received great interest from medicinal
chemists: protein crystallography and computer graphics.
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