ITR: A Global Optimization Package for Protein Structure Prediction

科罗拉多大学的Richard Byrd和Robert Schnabel以及加州大学伯克利分校的Teresa Head-Gordon和Silvia Crivelli通过信息技术研究计划得到化学部门的支持，开发了一个用于蛋白质结构预测的全球优化软件包。他们的方法结合了数值计算的优化研究、计算生物物理学的能量建模研究和计算机科学的并行计算研究。本研究的主要特点包括一种新的水溶液表示，结合二级结构预测和能量平滑模型以提高准确性和效率。在给定氨基酸序列的情况下，预测蛋白质的三维形状或天然状态是现代科学的基本挑战之一。蛋白质结构知识是理解蛋白质功能的基础，对许多生物医学和生物材料的应用都很重要。该研究将推动大规模和并行数值计算、计算生物物理学模型和预测方法的发展。

Richard Byrd and Robert Schnabel of U. Colorado, and Teresa Head-Gordon and Silvia Crivelli of UC-Berkeley are supported by the Chemistry Divsion through the Information Technology Research Initiative to develop a global optimization package for protein structure prediction. Their approach combines optimization research from numerical computation, energy-modeling research from computational biophysics, and parallel computation research from computer science. Key features of this research include a novel representation of the aqueous solvent, incorporation of secondary structure prediction, and energy-smoothing models to increase accuracy and efficiency.The prediction of the three-dimensional shape, or native state, of a protein given its sequence of amino acids is one of the fundamental challenges of modern science. Protein structure knowledge is fundamental in understanding protein function, and important to many biomedical and biomaterial applications. This research will result in advances in large-scale and parallel numerical computation, and models and prediction methods for computational biophysics.