Simulating Protein Structures, Complexes, And Dynamics

我们对羧肽酶E的结构和功能的研究已经发表，我们对无序肽中环形成动力学的研究正在进行中。使用几种实验和建模技术设计稳定的四螺旋束蛋白质也在按下。 我们正在准备一份描述抗生素与二氢叶酸还原酶结合的手稿。我们继续完善我们的人类钙受体模型。 用量子力学和分子力学的联合势研究分支酸盐催化反应机理的两篇论文正在出版中。关于N-乙酰基转移酶的机制的手稿正在进行中。 一篇描述了分子动力学模拟研究醛糖还原酶及其抑制剂托司他之间氢键相互作用的论文已被接受出版。 本文采用量子化学方法研究了抗癌药物格尔德霉素与热休克蛋白90的结合方式。还进行了量子化学计算，以量化丙二醇和水分子之间的相互作用能。对A-β淀粉样蛋白探针的分子建模研究也正在进行，以建立结构-活性关系。 最大熵方法与非线性相结合的混合算法 最小二乘拟合被开发用于分析动力学数据。蛋白质折叠的荧光研究进行了分析。这个名为MemExp的计算机程序可以在网上找到。一份介绍这项工作的文件已经发表，该软件的后续扩展正在印刷中。

Our investigation of the structure and function of carboxypeptidase E was published, and our study of the dynamics of loop formation in disordered peptides is in press. The design of a stable four-helix bundle protein using several experimental and modeling techniques is also in press. We are preparing a manuscript characterizing antibiotic binding to dihydrofolate reductase. We continue to refine our model of the human calcium receptor. Two papers on the catalytic mechanism of chorismate mutase studied using the combined potentials of quantum mechanics and molecular mechanics are in press. A manuscript on the mechanism of N-actyltransferase is in progress. A paper that describes the simulation of molecular dynamics to investigate the hydrogen bonding interactions between aldose reductase and its inhibitor tolrestat has been accepted for publication. Quantum chemical calculations are being carried out to invesigate the binding mode of the anti-cancer agent geldanamycin to hsp90. Quantum chemical calculations are also being carried out to quantify the interaction energy between propanediol and water molecules. Molecular modeling studies on the A-beta amyloid probes are also being carried out to establish a structure-activity relationship. A hybrid algorithm combining the maximum entropy method and nonlinear least-squares fitting was developed to analyze kinetics data. Fluorescence studies of protein folding were analyzed. The computer program, called MemExp, is available online. A paper describing this work was published, and a follow-up extension to the software is in press.