The collection of known protein structures contains a wealth of information, not only about small building blocks of proteins, but also about the way these elements assemble in real structures. Both types of information can be valuable to the modeler or crystallographer. With the software known as LORE, we provide substructure search and coordinate manipulation tools that place a wide variety of different types of structural information at the user's fingertips. Substructure, varying in complexity from small segments to complicated elements of a protein fold, can be identified and used in a wide range of applications, from density interpretation to protein engineering. To our knowledge, no other database modeling software provides such generalized coordinate manipulation capabilities. We have found the software to be a valuable addition to our molecular modeling tools.
Bibliographical noteFunding Information:
This work was supported by the Swedish Natural Science Research Council and Uppsala University. The many fruitful discussions with other crystallographers in Uppsala, with Dr. Eleanor Dodson (York) and the other members of the EU-funded Biotech group, the participants in the York meeting on statistical validators in protein crystallography,6 and in particular Dr. Axel Brtinger (Yale, New Haven, CT) are gratefully acknowledged. We also thank Dr. Jonas Uppenberg (Uppsala) for providing us with lipase B-Tween 80 data.
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