摘要: The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching) has a limited applicability on intermediate stages of solution process, when secondary cannot be reliably computed due to structural incompleteness or fragmented mainchain. In this study, we describe new algorithm for alignment and comparison protein structures CCP4, which was designed overcome SSM's limitations but retain its quality speed. algorithm, named GESAMT (General Efficient Structural Alignment Macromolecular Targets), employs old idea deriving global similarity from promising set locally similar short fragments, uses few technical solutions that make it considerably faster. A comparative sensitivity selectivity analysis revealed an unexpected significant improvement fold recognition properties also makes useful applications bioinformatics domain. tool is included Suite starting version 6.3.
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