Science Blog of Dr. Yuan分享 http://blog.sciencenet.cn/u/albumns This blog is mainly on Molecular molecular modelling and simulations

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homology modelling of GPCR with modeller
热度 1 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|4683 次阅读|1 个评论 热度 1
Protein-Protein Docking in Rosetta
热度 2 2010-12-26 11:08
The protein-protein docking workflow in Rosetta could be described as following: 1. Low resolution docking command: docking_protocol.linuxgccrelease @flags docking.log This step will create large number of initial pose e.g. 10,000 for full sampling. To faste ...
个人分类: 科研笔记|6178 次阅读|1 个评论 热度 2
monomer, dimer or tetramer?
2010-10-27 23:12
Dimerand tetramer are often found in crystal structures and this sometimes confuses many people owing to the crystal symmetry in which the smallest subunit of a protein displays. Different structrual biologists have different habits: someone will display the whole mutime ...
个人分类: 科研笔记|5461 次阅读|没有评论
MODELLER 9v8 user manual
2010-7-2 21:20
Andrej ˇSali with help from Ben Webb, M.S. Madhusudhan, Min-Yi Shen, Marc A. Mart?-Renom, Narayanan Eswar, Frank Alber, Maya Topf, Baldomero Oliva, Andr´as Fiser, Roberto S´anchez, Bozidar Yerkovich, Azat Badretdinov, Francisco Melo, John P. Overington, and Eric Feyfant email: modeller-c ...
个人分类: 科研笔记|5588 次阅读|没有评论
One self rendered 3D figure
2010-6-28 12:55
个人分类: 科研笔记|3054 次阅读|2 个评论
Amber11+AmberTools 1.4并行安装
2010-5-28 15:42
系统:SUSE Linux Enterprise 10 Sp3 Desktop X86 编译器:Intel ifort 11.1 Intel MKL 10.2 Intel ICC 11.1 并行工具:mpich2-1.2.1 先安装编译器和并行工具,然后配置编译器环境变量: #Amber11 setenv AMBERHOME /soft/amber11 set path=($AMBERHOME $p ...
个人分类: 科研笔记|5982 次阅读|没有评论
Gromacs 4.0.7并行 含QM/MM功能安装
热度 1 2010-4-11 04:17
Gromacs 4.0.7并行带QM/MM安装 平台 SUSE Linux Enterprise Desktop 10 SP3 gcc4.1.2 mpich2-1.2.1p1 ifrot 10.1 fftw 3.2.2 解压缩mpich2-1.2.1p1.tar.gz进入此目录,运行: ./configure make make install 运行 touch /etc/mpd.conf ...
个人分类: 科研笔记|8850 次阅读|3 个评论 热度 1

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