iFold：一个用于蛋白质交互式折叠模拟的平台。
iFold: a platform for interactive folding simulations of proteins.
作者信息
Sharma Shantanu, Ding Feng, Nie Huifen, Watson Daniel, Unnithan Aditya, Lopp Jameson, Pozefsky Diane, Dokholyan Nikolay V
机构信息
Department of Biochemistry and Biophysics, University of North Carolina Chapel Hill, NC 27599, USA.
出版信息
Bioinformatics. 2006 Nov 1;22(21):2693-4. doi: 10.1093/bioinformatics/btl460. Epub 2006 Aug 29.
UNLABELLED
We built a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and p(fold) analysis using DMD and coarse-grained protein model with structure-based Gō-interactions between amino acids.
AVAILABILITY
未标注
我们构建了一个基于网络的新型平台，用于对蛋白质进行离散分子动力学模拟。计算机模拟蛋白质折叠涉及在广阔的构象空间中寻找最小化的挫折感。传统的蛋白质折叠模拟方法在解决理解潜在生物分子现象所需的相关时间和长度尺度下的模拟问题上并不充分。离散分子动力学（DMD）提供了一个弥合尺寸和时间尺度差距并揭示实验上无法检测到的蛋白质动力学的结构和生物学特性的机会。iFold服务器支持使用DMD和具有基于结构的氨基酸间Gō相互作用的粗粒度蛋白质模型对蛋白质折叠、热变性、热力学扫描、模拟退火和p（折叠）分析进行大规模模拟。
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