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CCP4 Program Suite ProSMART (version 0.8) Documentation Pre-distribution version, for Linux, Mac OS X and Windows. Contact for more information. This software is under development - if any aspect of the functionality/implementation is considered undesirable, or if any bugs, strange behavior or unexpected results are encountered, please email - any comments, questions and suggestions are very much appreciated. Sony drx 830u driver. Contents: • • • • • • • • • • Summary: ProSMART ( Procrustes Structural Matching Alignment and Restraint Tool) is a software tool designed for the conformation-independent structural comparison of protein chains. At current, ProSMART has two components: • ProSMART ALIGN - for the alignment, superposition, and scoring of protein chains; • ProSMART RESTRAIN - for the generation of external restraints for use in the crystallographic refinement of protein structures.
ProSMART ALIGN allows the pairwise alignment of chain-pairs, and also allows the batch-processing of multiple pairwise alignments. Similarity is based on the conservation of local structure, and is consequently independent of global conformation. For each chain-pair, multiple superpositions may be provided: a global superposition based on the achieved alignment, and a superposition for each identified common rigid substructure (e.g. Domain), if any are identified. Output includes residue-based, sidechain-based and global similarity scores, thus providing a multi-resolution view of chain similarity.
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Residue-based and sidechain-based scores may be viewed in color, using the graphics software. Experimental ProSMART analysis features are under development and available in the latest versions of. ProSMART RESTRAIN uses the results from ProSMART ALIGN in order to generate restraints for a target protein, based on one (or multiple) other homologous protein structures. Restraints may also be generated for individual fragments (e.g. Secondary structure elements). The use of restraints from ProSMART is intended to improve refinement.
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