Determining protein loop conformation using scaling-relaxation techniques

Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.

We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled con...

using game theory techniques in self-organizing maps training

شبکه خود سازمانده پرکاربردترین شبکه عصبی برای انجام خوشه بندی و کوانتیزه نمودن برداری است. از زمان معرفی این شبکه تاکنون، از این روش در مسائل مختلف در حوزه های گوناگون استفاده و توسعه ها و بهبودهای متعددی برای آن ارائه شده است. شبکه خودسازمانده از تعدادی سلول برای تخمین تابع توزیع الگوهای ورودی در فضای چندبعدی استفاده می کند. احتمال وجود سلول مرده مشکلی اساسی در الگوریتم شبکه خودسازمانده به حسا...

DNA relaxation by human topoisomerase I occurs in the closed clamp conformation of the protein.

In cocrystal structures of human topoisomerase I and DNA, the enzyme is tightly clamped around the DNA helix. After cleavage and covalent attachment of the enzyme to the 3' end at the nick, DNA relaxation requires rotation of the DNA helix downstream of the cleavage site. Models based on the cocrystal structure reveal that there is insufficient space in the protein for such DNA rotation without...

Using Relaxation Techniques to Evaluate Queries in Deductive Databases

Characterizing protein conformation space

In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms are not in selfcollision. Unlike energy based methods, this approach allows efficient exploration and remains general – the benefits of characterization of the space apply to...