Schrödinger药物虚拟筛选流程模块在大学生物和化学信息学教学中的应用

介绍了Schr?dinger药物虚拟筛选的基本原理和流程,结合大学生物和化学信息学课程的相关教学内容,分别描述了蛋白受体的预处理、类药性五原则、毒药物动力学(ADME)、泛筛选干扰化合物(PAINS)、高通量虚拟筛选、标准精度筛选、高精度筛选和MM/GBSA的打分排序原理和使用方法。该软件可以在大学生物和化学信息学的教学中演示,有助于提高学生对蛋白结构、分子构象、药物虚拟筛选和计算机辅助分子设计的理解,该软件有很好的图形界面,可以给学生直观的体验,大大丰富了大学课堂的教学内容。此外,该软件在药物设计领域里面也有很好的应用价值,大大节约了药物筛选的成本,提高了药物发现的效率。     

基于结构虚拟筛选发现蛋白质精氨酸甲基转移酶5抑制剂

蛋白质精氨酸甲基转移酶5(PRMT5)是蛋白质甲基转移酶家族(PRMTs)的重要一员,其主要生理功能是催化精氨酸单对称二甲基化。PRMT5的上调发生在不同类型的肿瘤中,并与不良预后密切相关,已被视为肿瘤治疗中的潜在靶点。近年来,已有多种PRMT5抑制剂进入临床试验,但目前尚未有药物获批上市。本研究基于Glide对接的虚拟筛选和生物活性实验,发现化合物8018-1271对PRMT5酶的抑制活性IC₅₀值为13.56±0.86μmol/L,并通过分子动力学揭示其与PRMT5蛋白结构域的相互作用模式。本研究所得化合物8018-1271可作为进一步改造的先导化合物,为新型PRMT5抑制剂的发现提供参考。     

基于WebGL的舰船模拟训练虚拟三维技术应用

由于目前国内的舰船模拟训练系统大多均为岸基模拟器,和半实物半仿真的应用模式,受制于该传统方式下系统通用性、可扩展性差,成本高等局限性;提出一种基于WebGL的舰船模拟训练虚拟三维环境,采用其应用框架Three.js图形引擎库在网页中绘制3D虚拟交互界面,可直接通过浏览器登录系统,从而给出了可跨平台免插件高效的舰船模拟训练界面;结果表明该方法在人机交互界面的友好性、监控的直观性、训练操作的便捷性、较强的沉浸性等方面具有优势,亦可推广应用于其他模拟训练领域。     

基于Unity 3D的船舶压缩空气系统的虚拟设计

针对目前船舶空气压缩仿真训练系统大多采用半物理仿真与二维软件界面仿真相结合方式训练效果不佳的问题,将虚拟现实技术引入到船舶压缩空气系统的仿真设计;设计一套基于Unity 3D的船舶压缩空气系统,实现虚拟仿真程序和三维虚拟场景的实时交互,生成一个逼真的三维视觉、听觉、触觉的感官世界,加强培训人员的沉浸感,从而获得一种置身于真实环境中的感受;系统可供学员无限制反复训练,节省系统的维护费用,规避实物操作设备中可能出现的各种风险,提高训练效果。     

基于虚拟仪器技术和网络的综合实验控制系统设计

为实现大型物理实验现场复杂多样的仪器控制,分析了物理实验的特点、过程、环境及仪器控制功能需求,利用虚拟仪器技术、计算机网络技术和数据库技术,建立了一套集成硬件和软件的综合控制管理信息系统,实现记录系统中示波器状态远程批量设置及波形数据自动采集、控制探测系统的高压电源并发加压或退压、保障各测试项目间测试仪器之间时间关联、监控UPS电量和远端现场图片或视频状态。给出了系统的关键的设计思路,列举了某型示波器控制的通用控制代码。结果表明,系统达到了一人总控或多人分权控制实验过程中多种多台仪器的目标,方便快捷地实现不同品牌不同类型示波器的相同功能。     

Influence of electronic and steric effects on stability constants and electrochemical reversibility of divalent ion complexes with glycine and sarcosine. A glass electrode potentiometric, sampled direct current polarographic, virtual potentiometric, and molecular modelling study

Cd^II complexes with glycine (gly) and sarcosine (sar) were studied by glass electrode potentiometry, direct current polarography, virtual potentiometry, and molecular modelling. The electrochemically reversible Cd^II–glycine–OH labile system was best described by a model consisting of M(HL), ML, ML₂, ML₃, ML(OH) and ML₂(OH) (M = Cd^II, L = gly) with the overall stability constants, as log β, determined to be 10.30 ± 0.05, 4.21 ± 0.03, 7.30 ± 0.05, 9.84 ± 0.04, 8.9 ± 0.1, and 10.75 ± 0.10, respectively. In case of the electrochemically quasi-reversible Cd^II–sarcosine–OH labile system, only ML, ML₂ and ML₃ (M = Cd^II, L = sar) were found and their stability constants, as log β, were determined to be 3.80 ± 0.03, 6.91 ± 0.07, and 8.9 ± 0.4, respectively. Stability constants for the ML complexes, the prime focus of this work, were thus established with an uncertainty smaller than 0.05 log units. The observed departure from electrochemical reversibility for the Cd–sarcosine–OH system was attributed mainly to the decrease in the transfer coefficient . The MM2 force field, supplemented by additional parameters, reproduced the reported crystal structures of diaqua-bis(glycinato-O,N)nickel(II) and fac-tri(glycinato)-nickelate(II) very well. These parameters were used to predict structures of all possible isomers of (i) [Ni(H₂O)₄(gly)]⁺ and [Ni(H₂O)₄(sar)]⁺; and (ii) [Ni(H₂O)₃(IDA)] and [Ni(H₂O)₃(MIDA)] (IDA = iminodiacetic acid, MIDA = N-methyl iminodiacetic acid) by molecular mechanics/simulated annealing methods. The change in strain energy, ΔU_str, that accompanies the substitution of one ligand by another (ML + L′ → ML′ + L), was computed and a strain energy ΔU_str = +0.28 kcal mol⁻¹ for the reaction [Ni(H₂O)₄(gly)]⁺ + sar → [Ni(H₂O)₄(sar)]⁺ + gly was found. This predicts the monoglycine complex to be marginally more stable. By contrast, for the reaction [Ni(H₂O)₃IDA] + MIDA → [Ni(H₂O)₃MIDA] + IDA, ΔU_str = −0.64 kcal mol⁻¹, and the monoMIDA complex is predicted to be more stable. This correlates well with (i) stability constants for Cd–gly and Cd–sar reported here; and (ii) known stability constants of ML complex for glycine, sarcosine, IDA, and MIDA.     

悬浮法生产可发性聚苯乙烯(EPS)虚拟仿真实验平台的设计与开发

为实现我校高分子材料与工程专业人才培养目标,即培养高素质工程应用型人才,弥补教学过程中实际操作的缺陷与不足,我们开发了基于实际工业生产的悬浮法生产可发性聚苯乙烯的虚拟仿真实验平台.详述了该平台的设计开发思路与理念,平台主题结构,以及实验主控界面设计思路和主要内容.实践证明,该平台不仅包含工程应用的相关知识,而且极大的提...     

用于解决大规模波长路由光网中路由和波长分配问题的新启发式算法

本文提出了一种新的启发式算法,它将路由和波长分配问题分解为两个子问题分别进行优化求解,并以最小化波长需求作为目标函数。在不同通信负荷的情况下,我们以NSF网为例,分析了波长通道(WP)和虚波长通道(VWP)路由方案之间在波长需求方面的差别。同时还研究了网络波长重用度的问题。数值结果表明所提出的算法可有效地应用于大规模波长路由光网。     

C–H dipolar recoupling under very fast magic-angle spinning using virtual pulses

A new solid-state NMR pulse sequence for recoupling ¹³C–¹H dipolar interactions under magic-angle spinning is proposed, which works under a spinning speed of a few to several tens kilohertz. The sequence is composed of two different frequency switched Lee–Goldburg sequences, and the modulation of the spin part of the ¹³C–¹H dipolar interaction is introduced by a virtual pulse sequence consisting of unitary operators connecting the rotating frame and the tilted rotating frame. When the cycle time of the spinning is equal to or twice the cycle time of the sequence, the ¹³C–¹H dipolar interactions can be recoupled. The sequence is insensitive to experimental imperfections such as rf inhomogeneity or frequency offset, and the resulting lineshape can be represented by a simple analytical equation based on the zeroth-order average Hamiltonian. Experimental results for [2-¹³C] -valine·HCl are reported.