非键相互作用对于生物体系中的分子识别和结合过程起着关键作用。然而,传统的方法并不能在残基水平自动批量计算非键相互作用。近年来,已经发展了一些方法和工具进行非键相互作用的计算分析。该文研究发展了一种可以自动计算残基间非键...非键相互作用对于生物体系中的分子识别和结合过程起着关键作用。然而,传统的方法并不能在残基水平自动批量计算非键相互作用。近年来,已经发展了一些方法和工具进行非键相互作用的计算分析。该文研究发展了一种可以自动计算残基间非键相互作用的方法,即用Perl脚本调用Discovery Studio 2.0(DS 2.0,Accelrys Inc.)底层模块中的非键相互作用协议,实现了直接利用命令行批量计算非键相互作用能量,而无需通过DS2.0的图形界面。该方法扩展了DS2.0的计算模块,并于近期运用到了复合结构的研究分析中。展开更多
Discovery Studio是BIOVIA公司研发的一款药物发现计算模拟平台。在Discovery Studio 2017中新增拉伸分子动力学模块,拉伸分子动力学模块的功能包括研究配体(药物分子)与受体的结合方式、蛋白质的去折叠构象变化、拉伸配体(药物分子)通...Discovery Studio是BIOVIA公司研发的一款药物发现计算模拟平台。在Discovery Studio 2017中新增拉伸分子动力学模块,拉伸分子动力学模块的功能包括研究配体(药物分子)与受体的结合方式、蛋白质的去折叠构象变化、拉伸配体(药物分子)通过通道蛋白等。本文介绍Discovery Studio 2017的拉伸分子动力学功能。展开更多
利用分子对接技术,探究实验室获得的35个黄酮类化合物与乙型肝炎病毒相关蛋白的结合模式与相互作用关系,筛选其中具有抗乙肝病毒可能性的黄酮类化合物,为新型抗乙肝病毒药物的研究及后续实验提供一定的理论依据。应用分子对接软件Discov...利用分子对接技术,探究实验室获得的35个黄酮类化合物与乙型肝炎病毒相关蛋白的结合模式与相互作用关系,筛选其中具有抗乙肝病毒可能性的黄酮类化合物,为新型抗乙肝病毒药物的研究及后续实验提供一定的理论依据。应用分子对接软件Discovery Studio 2.5中的Dock Ligand(Libdock)模块,将临床使用较为广泛的三种抗乙肝病毒药物恩替卡韦、拉米夫定、阿德福韦酯与乙型肝炎病毒蛋白进行分子对接,获得对接比分Libdock Score,并确定乙肝病毒蛋白潜在活性位点;再将实验室获得的35个黄酮类化合物与乙型肝炎病毒蛋白进行对接模拟计算,将两部分对接结果进行比较与分析,进一步筛选出来具有潜在可能性抗乙肝病毒的活性黄酮类化合物。将部分结果可视化,发现黄酮类化合物与三种药物作用的蛋白残基大致相同,并推测出PHE23、LEU140、PRO25、PRO134可能为乙型肝炎病毒蛋白的活性位点残基。采用分子对接技术筛选药物的方案是具有一定可行性的,能为新型药物开发提供理论基础。展开更多
Actinorhizal plants contain numerous antioxidants that may play a crucial role in preventing the formation of tumors.H-Ras p21,a member of the Ras-GTPase family,is a promising target to treat various kinds of cancers....Actinorhizal plants contain numerous antioxidants that may play a crucial role in preventing the formation of tumors.H-Ras p21,a member of the Ras-GTPase family,is a promising target to treat various kinds of cancers.An in silico docking study was carried out to identify the inhibitory potential of compounds of these plants against H-Ras by using Discovery Studio 3.5 and by using Autodock 4.2.Docking studies revealed that four compounds,isorhamnetin-7-rhamnoside,quercetin-3-glucoside-7-rhamnoside（present in H.rhamnoides）,zeaxanthin,and translutein（present in H.salicifolia） significantly bind with binding energies-17.1534,-14.7936,-10.2105 and-17.2217 Kcal/mol,respectively,even though they slightly deviate from Lipinski＇s rule.Absorption,distribution,metabolism,excretion and toxicity（ADME/tox） analyses of these compounds and their stereoisomers showed that they were less toxic and non-mutagenic.Amongst them,isorhamntein-7-rhamnoside showed hepatotoxicity.Hence,these compounds can be further investigated in vivo to optimize their formulation and concentration and to develop potential chemical entities for the prevention and treatment of cancers.展开更多
Calcitonin receptor-like receptor(CRLR)is a human protein,that produces a calcitonin gene-related peptide receptor(CGRP)when associates with human receptor activity-modifying protein-1(HRAMP1).CGRP is believed to be i...Calcitonin receptor-like receptor(CRLR)is a human protein,that produces a calcitonin gene-related peptide receptor(CGRP)when associates with human receptor activity-modifying protein-1(HRAMP1).CGRP is believed to be involved in triggering of migraine.Many strategies were employed to design antimigraine drug using various CGRP antagonist/ligands but most of them have failed due to their inability to reach the target“CGRP receptor”as they get metabolized before conferring their pharmacological action and exhibit toxic effect to the liver.The present study,evaluated the binding of 13 phyto-chemical compounds of“Abrus precatorius”identified through GCMS analysis against the protein CGRP using“Discovery Studio software”.The molecular docking study and ADME/T properties prediction were performed with the compounds using C-DOCKER module.The results showed that five lead compounds of A.precatorius may act as good inhibitors for migraine headache and the compounds can be re-designed and synthesized for better antimigraine activity.展开更多
文摘非键相互作用对于生物体系中的分子识别和结合过程起着关键作用。然而,传统的方法并不能在残基水平自动批量计算非键相互作用。近年来,已经发展了一些方法和工具进行非键相互作用的计算分析。该文研究发展了一种可以自动计算残基间非键相互作用的方法,即用Perl脚本调用Discovery Studio 2.0(DS 2.0,Accelrys Inc.)底层模块中的非键相互作用协议,实现了直接利用命令行批量计算非键相互作用能量,而无需通过DS2.0的图形界面。该方法扩展了DS2.0的计算模块,并于近期运用到了复合结构的研究分析中。
文摘Discovery Studio是BIOVIA公司研发的一款药物发现计算模拟平台。在Discovery Studio 2017中新增拉伸分子动力学模块,拉伸分子动力学模块的功能包括研究配体(药物分子)与受体的结合方式、蛋白质的去折叠构象变化、拉伸配体(药物分子)通过通道蛋白等。本文介绍Discovery Studio 2017的拉伸分子动力学功能。
文摘利用分子对接技术,探究实验室获得的35个黄酮类化合物与乙型肝炎病毒相关蛋白的结合模式与相互作用关系,筛选其中具有抗乙肝病毒可能性的黄酮类化合物,为新型抗乙肝病毒药物的研究及后续实验提供一定的理论依据。应用分子对接软件Discovery Studio 2.5中的Dock Ligand(Libdock)模块,将临床使用较为广泛的三种抗乙肝病毒药物恩替卡韦、拉米夫定、阿德福韦酯与乙型肝炎病毒蛋白进行分子对接,获得对接比分Libdock Score,并确定乙肝病毒蛋白潜在活性位点;再将实验室获得的35个黄酮类化合物与乙型肝炎病毒蛋白进行对接模拟计算,将两部分对接结果进行比较与分析,进一步筛选出来具有潜在可能性抗乙肝病毒的活性黄酮类化合物。将部分结果可视化,发现黄酮类化合物与三种药物作用的蛋白残基大致相同,并推测出PHE23、LEU140、PRO25、PRO134可能为乙型肝炎病毒蛋白的活性位点残基。采用分子对接技术筛选药物的方案是具有一定可行性的,能为新型药物开发提供理论基础。
文摘Actinorhizal plants contain numerous antioxidants that may play a crucial role in preventing the formation of tumors.H-Ras p21,a member of the Ras-GTPase family,is a promising target to treat various kinds of cancers.An in silico docking study was carried out to identify the inhibitory potential of compounds of these plants against H-Ras by using Discovery Studio 3.5 and by using Autodock 4.2.Docking studies revealed that four compounds,isorhamnetin-7-rhamnoside,quercetin-3-glucoside-7-rhamnoside（present in H.rhamnoides）,zeaxanthin,and translutein（present in H.salicifolia） significantly bind with binding energies-17.1534,-14.7936,-10.2105 and-17.2217 Kcal/mol,respectively,even though they slightly deviate from Lipinski＇s rule.Absorption,distribution,metabolism,excretion and toxicity（ADME/tox） analyses of these compounds and their stereoisomers showed that they were less toxic and non-mutagenic.Amongst them,isorhamntein-7-rhamnoside showed hepatotoxicity.Hence,these compounds can be further investigated in vivo to optimize their formulation and concentration and to develop potential chemical entities for the prevention and treatment of cancers.
文摘Calcitonin receptor-like receptor(CRLR)is a human protein,that produces a calcitonin gene-related peptide receptor(CGRP)when associates with human receptor activity-modifying protein-1(HRAMP1).CGRP is believed to be involved in triggering of migraine.Many strategies were employed to design antimigraine drug using various CGRP antagonist/ligands but most of them have failed due to their inability to reach the target“CGRP receptor”as they get metabolized before conferring their pharmacological action and exhibit toxic effect to the liver.The present study,evaluated the binding of 13 phyto-chemical compounds of“Abrus precatorius”identified through GCMS analysis against the protein CGRP using“Discovery Studio software”.The molecular docking study and ADME/T properties prediction were performed with the compounds using C-DOCKER module.The results showed that five lead compounds of A.precatorius may act as good inhibitors for migraine headache and the compounds can be re-designed and synthesized for better antimigraine activity.
