Cavity programs: Difference between revisions
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*A '''channel''' connects two entrances<ref name="caverweb" />. | *A '''channel''' connects two entrances<ref name="caverweb" />. | ||
*A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | *A '''pore''' may mean a trans-membrane channel through an integral membrane protein<ref name="moleonline" /> | ||
*Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>. | *Some cavities are buried with no entrances (example: [[3drf]]). These buried cavities are sometimes called '''voids'''<ref name="moleonline" /><ref name="void">The [http://sts.bioe.uic.edu/castp/background.html CASTp server] uses the term '''void'''.</ref>. | ||
Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing the catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | Nearly all proteins have irregular surfaces with shallow pockets, mostly with no known functions. Some proteins have deep pockets, for example the catalytic anionic gorge in acetylcholinesterase (e. g. [[1vot]]). Such a pocket can also be termed a tunnel accessing the catalytic site<ref name="damborsky3" /><ref name="kingsley" />. | ||
The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. Programs are listed alphabetically. | The '''example illustrated below''' is the membrane-proximal cavity of [[SARS-CoV-2 spike protein priming by furin|SARS-CoV-2 spike protein]] ([[6zgi]]). The membrane-proximal cavity is a [[SARS-CoV-2 spike protein fusion transformation|potential target for drugs to prevent membrane fusion]], and thus prevent infection. Programs are listed alphabetically. | ||
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==CASTp== | ==CASTp== | ||
<table align="right" width="570" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td> | <table align="right" width="570" cellpadding="5" hspace="8" style="border: 1px solid black; border-collapse:collapse;padding-left:8px;"><tr><td> | ||
