http:\/\/corysimon.github.io\/articles\/uniformdistn-on-sphere\/<\/a>
\nThis correction results in different RAMD trajectories but tests have so far not shown any significant difference in results for a set of RAMD simulations or use of the tauRAMD procedure to compute relative residence times. The biggest effect might be expected in cases with a dependence on the z-axis, e.g. for a binding pocket in a protein channel along the z-axis. <\/p>\nDescription<\/h3>\n
t-random acceleration molecular dynamics (tRAMD) is a protocol for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanism.
\nThe approach is based on the RAMD method in which, during a standard molecular dynamics simulation of the bound complex, a small additional randomly oriented force is applied to the compound to facilitate its unbinding. Note, that in the previous RAMD versions acceleration (instead of the force) was used as an input parameter.<\/p>\n
tRAMD protocol includes:<\/p>\n
(i) system minimization and equilibration<\/p>\n
(ii) generation of a set of starting replicas using standard MD simulations with NAMD software<\/p>\n
(iii) simulations of RAMD trajectories starting from different replicas<\/p>\n
(iv) statistical analysis of the RAMD dissociation times using an R script, which yields relative residence times of compounds<\/p>\n
Important notice<\/h3>\n
The RAMD license prohibits commercial use of the code. For testing and using RAMD on a commercial basis you need to negotiate a commercial license by\u00a0contacting us<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"If you are a member of an academic institution and you use this software solely for research purposes, you can download …<\/p>\n","protected":false},"author":2,"featured_media":0,"template":"","edd-categories":[1181],"edd-tags":[1067],"hits-research-group":[],"class_list":["post-22082","download","type-download","status-publish","hentry","download_category-ramd","download_tag-academic","edd-download","edd-download-cat-ramd","edd-download-tag-academic"],"acf":[],"yoast_head":"\n
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