Cavity programs: Difference between revisions
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[http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref>In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>) | [http://sts.bioe.uic.edu/castp/index.html CASTp]: '''C'''omputed '''A'''tlas of '''S'''urface '''T'''opography of '''p'''roteins. "CASTp is based on recent theorectical and algorithmic results of Computational Geometry. It has many advantages: 1) pockets and cavities are identified analytically, 2) the boundary between the bulk solvent and the pocket is defined precisely, 3) all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points." (See Comparison Note<ref>In contrast with CASTP, PACUPP uses grid points. Therefore, its cavity boundaries are slightly different when the grid points are offset by half of the spacing between points -- an option it offers. See ''Offset: Hit or Miss & Cavity Volume'' in [http://molviz.org/pacupp/1-How-To-Use-PACUPP.pdf How To Use PACUPP].</ref>) | ||
CASTp 3.0 published summer, 2018<ref>PMID: 29860391</ref>. | CASTp 3.0 published summer, 2018<ref>PMID: 29860391</ref>. Available as a web server, and a PyMOL plugin. | ||
==Jmol== | ==Jmol== | ||
