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Micro-Biology Homology Modeling via Protein Threading Paper Presentation & Seminar.
Researchers attempting to solve a protein's structure start their a study with little more than a protein sequence. Initial steps may include performing a PSI-BLAST or PatternHunter search to locate a similar sequences with a known structure in the Protein Data Bank (PDB). If there are highly similar sequences with known structures, there is a high probability that this protein's structure will be very similar to those known structures as well as functions. If there is no homology found, the researcher must perform either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, both of which require considerable time and resources to yield a structure. Where these techniques are too expensive, time-consuming or limited in scope, researchers can use protein threading software, such as RAPTOR to create a highly reliable model of the protein.
Protein threading is more effective than homology modeling, especially for proteins which have few homologs detectable by sequence alignment. The two methods both predict protein structure from a template. Given a protein sequence, protein threading first aligns (threads) the sequence to each template in a structure library by optimizing a scoring function that measures the fitness of a sequence-structure alignment. The selected best template is used to build the structure model. Unlike homology modeling, which selects template purely based on homology information (sequence alignments), the scoring function used in protein threading utilizes both homology and structure information (sequence structure alignments).
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