The GPCRDOCK 2013 contest hosted by Scripps Institute was finished months ago with the released of 5HT1B and 5HT2B crystal structures bound with agonist molecule Ergotamine. I also attended this event and compared my models with the crystal structure. My models were built in Modeller templ ...
In the late 1800's, E. Overton discovered that substances that dissolve in lipids pass more easily into the cell than those that dissolve in water. This was some of the first evidence that cells were surrounded by a lipid membrane. The phospholipid membrane of cells can greatly modify the p ...
Structure of the human smoothened receptor bound to an antitumour agent Chong Wang,Huixian Wu,Vsevolod Katritch,Gye Won Han,Xi-Ping Huang,Wei Liu,Fai Yiu Siu,Bryan L. Roth,Vadim Cherezov Raymond C. Stevens Nature(2013) doi:10.1038/nature12167 Received15 January 2013 Accept ...
This new version finally update VIPARR tool from 3.x into 4.x which can handle NBFIX terms in CHARMM 36 protein FF and latest CHARMM 36 LIPIDS FF parameter sets. ____ &nbs ...
In most people's minds, modeling and simulation work can only be released in journal with IF 3-5 such as: J Chem Inf Model or PLOS Computational Biology and so on. However, if the work is good enough, it is still possible to be accepted by nowadays so called "CNS (CELL, Nature and Science)". He ...
The Desmond .dms file, which can be converted from Schrodinger Maestro file format .cms with command mae2dms, is quite difficult to modify by text editor. However, the .dms file actually is a SQLite database file, and w ith Sqlite3 command or SQLite Manager we can easily handle .dms file. Thanks ...
Compiling Desmond from source code seems to be the most challenging work that I've ever found especially the latest V3.4. Fortunately, it was successfully compiled these days. During the sampling test, 2 CPU can even get up to 4 ns /day with NVE ensemble for a typical membrane system which is real ...
As the most widely used MD analysis tool, VMD isdistributedthe pre-compiled version for almost all kinds of platform. However, if we would like to use advanced module of VMD such as running python script or render scene with alternative engine, the pre-compiled versions are most likely ...
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