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分享 Desmond Configuration in Cluster
袁曙光 2011-7-16 13:17
Configure the schrodinger.hosts in /home/user/.schrodinger folder 1. with multiple nodes in the same host name: 32a host: myhost queue: PBS qargs:&n ...
个人分类: 科研笔记|2916 次阅读|没有评论
分享 Membrane Protein Simulation with Desmond
热度 1 袁曙光 2011-6-25 02:59
Membrane Protein Simulation with Desmond
Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle-mesh-based Ewald techniques.Constraints can be enforced using the M-SHAKE algorithm. These approaches can be used in combination w ...
个人分类: 科研笔记|6097 次阅读|1 个评论 热度 1
分享 humor at conference
热度 2 袁曙光 2011-5-24 21:22
Recently, I am attendinga conference in Utrecht, Netherlands. Some speakers (PhD student)made mistakes during the presentation. Although scientists are quit serious for most cases, they still have humors: 1. one speaker madespellingmistakes for his institut ...
个人分类: 科研笔记|2069 次阅读|6 个评论 热度 2
分享 Science Arts
热度 3 袁曙光 2011-5-22 20:11
Science Arts
Protein-ligand interaction Membrane protein Induced Fit docking
个人分类: 科研笔记|3461 次阅读|1 个评论 热度 3
分享 Is 5Å big enough for your docking grid box?
袁曙光 2011-5-12 03:04
Is 5Å big enough for your docking grid box?
Recently, I am preparing a manual script for previous work. When someone read it he claimed in the email: "your gird box for docking is too small to include the whole molecule. I measure the distance between two atoms in the ligand and it is11 Å , but you defined y ...
个人分类: 科研笔记|2035 次阅读|没有评论
分享 Potential Molecular Modelling Journal IF
热度 1 袁曙光 2011-4-26 22:25
PLOS COMPUTATIONAL BIOLOGY PLOS COMPUT BIOL 5.8 CHEMISTRY-A EUROPEAN JOURNAL  CHEM-EUR J 5.3 CURRENT MEDICINAL CHEMISTRY CURR MED CHEM &nbs ...
个人分类: 科研笔记|1989 次阅读|1 个评论 热度 1
分享 Another Ramachandra Plot
热度 4 袁曙光 2011-4-11 14:55
Another Ramachandra Plot
个人分类: 科研笔记|2358 次阅读|5 个评论 热度 4
分享 a self rendered figure
袁曙光 2011-2-28 02:14
a self rendered figure
个人分类: 科研笔记|2338 次阅读|没有评论
分享 [转载]Rosetta Commons 3.2 released
袁曙光 2011-2-4 21:41
Download http://www.rosettacommons.org/software/ Forum : http://www.rosettacommons.org/forum New features of the current release (Rosetta 3.2) Comparative Modeling: This application build structural models of proteins using one or more known structures as templates for mode ...
个人分类: 科研笔记|4091 次阅读|没有评论
分享 homology modelling of GPCR with modeller
热度 1 袁曙光 2011-1-29 17:06
homology modelling of GPCR  with modeller
R ecent work on GPCR homology modelling found that the modelling of GPCR is different from these cytoplasm protein owing to the low sequence identity with its homology patenters. Model building by Modeller usually lead to satisfied models based on the protocol provided from Modeller ...
个人分类: 科研笔记|3400 次阅读|1 个评论 热度 1

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