MDL数据库与虚拟筛选技术跨平台对接技术研究与应用
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摘要
本文深入研究了当前化学信息管理系统和虚拟筛选系统的发展现状及其存在的问题,分析了现有的化学信息学软件技术及虚拟筛选工作流程,针对现如今新药研究周期长、效率低这一现状,采用Java软件技术,集中研究并实现了基于TCP的Socket的跨平台数据通讯通方法,从而为现有化学信息管理系统MDL ISIS/BASE与LINUX集群上的虚拟筛选系统DOCK/Pocket搭建了一条可靠、有效的跨平台数据通讯通道,并在Windows平台下构建了易于被用户操作的可视化平台——ChemManager系统,从而使分布在Unix、Linux和Windows等不同操作系统平台下的化学信息学软件能协同工作,将虚拟筛选的操作过程Dock、Pocket整合到Windows下,实现了MDL数据、DOCK和Pocket虚拟筛选过程的可视化管理,方便化学科研人员的操作过程,提高了计算机药物辅助过程的可靠性和工作效率,方便研究工作的开展。
In this paper, in-depth study of the current chemical information management systems and virtual screening system and the development of the existing problems, analysis of the existing chemical informatics software technology and virtual screening process for new drug research is now Long, low efficiency of the current situation, the use of Java software technology, and focus on the achievement based on TCP Socket cross-platform data communication method for existing chemical information management system MDL ISIS / BASE and LINUX clusters on the Virtual screening system DOCK / Pocket build a reliable and effective cross-platform data communication channels, and under the Windows platform built by easy-to-user visualization platform—ChemManager System, so that in Unix, Linux and Windows operating system and other platforms Under the Chemical Informatics software can work together to the virtual screening process Dock, Pocket integrated into Windows, the realization of the MDL data, DOCK and Pocket virtual visualization of the selection process to facilitate chemical operations staff to improve Drug computer-assisted process of the reliability and efficiency to facilitate the research work carried out.
In this paper, in-depth study of the current chemical information management systems and virtual screening system and the development of the existing problems, analysis of the existing chemical informatics software technology and virtual screening process for new drug research is now Long, low efficiency of the current situation, the use of Java software technology, and focus on the achievement based on TCP Socket cross-platform data communication method for existing chemical information management system MDL ISIS / BASE and LINUX clusters on the Virtual screening system DOCK / Pocket build a reliable and effective cross-platform data communication channels, and under the Windows platform built by easy-to-user visualization platform—ChemManager System, so that in Unix, Linux and Windows operating system and other platforms Under the Chemical Informatics software can work together to the virtual screening process Dock, Pocket integrated into Windows, the realization of the MDL data, DOCK and Pocket virtual visualization of the selection process to facilitate chemical operations staff to improve Drug computer-assisted process of the reliability and efficiency to facilitate the research work carried out.
引文
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[2]Gasteiger J.Chemoninfomatics:a new field with a long tradition.Anal Bioanal Chem,2006,384:57-64
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[8]Chen,HM;Liu,BF;Huang,HL;Hwang,SF;Ho,SY.SODOCK:Swarm optimization for highly flexible proteinligand docking.Jornal of Computational Chemistry.2007,28(26).
[9]Junhyong kim,Etsuko N.Moriyama,Coral G.Warr,Petter J.Clyne and John R.Carlson,(2000),Identification of novel multi-transmembrance proteins from genomic database using quasi-periodic structure properties,Bioinformatics,2000,16:767-775.
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[11]Georg C.Terstappen and Angelo Reggiani,In silico research in drug discovery,Trend in Pharm.Sci.2001,22(1):23-26.
[12]urgen Drews,Drug Discovery:A historical perspective,Science,2000,287:1960-1964
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[15]MDL ISIS/Base Database Maintenance.MDL Information Systems,Inc.2002,9
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[18]潘俊强.实验室环境下Windows和Linux的资源共享.实验室研究与探索.2000(03)
[19]文自勇,廖亮.基于OpenSSH实现Windows 与 Linux平台间的安全文件传输.成都信息工程学院学报.2005(04)
[20]王立宾.基于ssh的终端绑定的设计与实现:[硕士学位论文].北京:北京邮电大学.2008(10)
[21]凌以珂.Linux与Windows资源共享实现方法简析.电脑知识与技术(学术交流).2006(08)
[22]王强.Linux与Windows资源共享的安全控制.网络与信息.2006(05)
[23]Baliga,Girish Bantwal.A middleware framework for networked control systems.University of lllinois at Urbana-Champaign.2005
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[26]李勇.进程间通信的分布式实现:[硕士学位论文].吉林:吉林大学.2004.
[27]陈鹤鸣,周文胜,陈雄.Windows下的进程间通信.南京邮电大学学报(自然科学版).2000(02)
[28]彭银球.多平台问网络通信的实现方案.计算机丁程与设计.2004(06)
[29]李扬,耿昌宇,张丽芬.基于Socket 通讯模式下的跨平台数据同步.北京理工大学学报.2002,5(01)
[30]王静,曲凤娟.基于Socket的多用户并发通信的设计.福建电脑.2007(3):164-165
[31]李峰.利用流式Socket编程实现Windows与Linux的通信.微计算机信息.2006,12(03)
[32]姚晖,李定主,卢宁.Linux和Windows系统之间网络通信程序的开发.电脑开发与应用.2002,12(03)
[33]何世明.利用Java在Windows与Linux建立数据通讯的方法.计算机应用.2001,12(10)
[34]Shao,Yongliang.Object-based,distributed online real-time communication system modeling and development.University of Windsor(Canada).2000
[35]Mandadi,Sanjay Reddy.The design and implementation of a simple master/slave interprocess -communicatin module.University of Washington.2000
[36]Heymans,Louis;Vander Beken,Tony etal.Testing Techniques for the Cross-platform Migration of Very Large Interactive Applications.Software Maintenance and Reengineering(CSMR),European Conference on.2007.
[37]王晓鹏.TCP/IP下的Socket及Windows通信机制.航空计算技术.2004(02).
[38]梁立哲,时武略.TCP/IP跨平台通信的研究.电脑知识与技术(学术交流).2006(06).
[39]徐小东.基于socket技术的数据交换平台的设计与实现.[硕士学位论文].上海:上海交通大学.2007,09,14.
[40]赵文清,姜波.基于Socket的Java语言网络通讯机制和程序设计.华北电力大学.2002(7)
[41]Taleb,M,Seffah,A.Patterns-Oriented Design Applied to Cross-Platform Webbased Interactive Systems.Information Reuse and Integration.2007IEEE International Conference on.2007
[42]周坤.计算机远程终端监控系统:[硕士学位论文].南京:南京信息工程大学.2008(09).
[43](美)希尔德(Schildt,H.).Java参考大全(J2SE 5 Edition).北京:清华大学出版社,2006.
[44]www.cs.umanitoba.ca/~eclipse.An Eclipse GUI Builder.Department of ComputerScience University of Manitoba.
[2]Gasteiger J.Chemoninfomatics:a new field with a long tradition.Anal Bioanal Chem,2006,384:57-64
[3]李松,肖军海.后基因组时代创新药物研究战略—从基因到药物.2004年全国生化与生物技术药物学术年会论文集.2004:23-26.
[4]张礼和,王梅祥.化学生物学进展(精)/化学进展从书.北京:化学工业出版社.2005.第3章.
[5]赵丽琴,肖军海,李松.分予对接在基于结构药物设计中的应用.生物物理学报.2002,18(3).
[6]李松,肖军海.药物分子设计的关键技术.北京:军事医学科学院毒物药物研究所.军事医学科学出版社.2003
[7]Hann M and Green R..Chemoinfomatics—a new name for an old problem?.Curt OPin Chen Biol,1999,3:379-383.
[8]Chen,HM;Liu,BF;Huang,HL;Hwang,SF;Ho,SY.SODOCK:Swarm optimization for highly flexible proteinligand docking.Jornal of Computational Chemistry.2007,28(26).
[9]Junhyong kim,Etsuko N.Moriyama,Coral G.Warr,Petter J.Clyne and John R.Carlson,(2000),Identification of novel multi-transmembrance proteins from genomic database using quasi-periodic structure properties,Bioinformatics,2000,16:767-775.
[10]Collen M.Masimirembwa,Richard Thompson and Tommy B.Andersson,Combinatorial Chemistry and High Throughput screening,2001,4:245-263.
[11]Georg C.Terstappen and Angelo Reggiani,In silico research in drug discovery,Trend in Pharm.Sci.2001,22(1):23-26.
[12]urgen Drews,Drug Discovery:A historical perspective,Science,2000,287:1960-1964
[13]http://www.mdl.com.
[14]MDL ISIS/Application Development Kit User' s Guide(Version2.5) MDL Information Systems,Inc 2002,12.
[15]MDL ISIS/Base Database Maintenance.MDL Information Systems,Inc.2002,9
[16]孔德信,张红雨.生物信息学和化学信息学网络研究平台的构建山东理工大学生命科学学院山东省生物信息工程技术研究中心.计算机与应用化学.2007(05).
[17]郑纬民,石威,汪东升等.Rajkumar Buyya High Performance Cluster Computing:Architectures and Systems,VOLUMEl.北京.电子工业出版社.2001.27.
[18]潘俊强.实验室环境下Windows和Linux的资源共享.实验室研究与探索.2000(03)
[19]文自勇,廖亮.基于OpenSSH实现Windows 与 Linux平台间的安全文件传输.成都信息工程学院学报.2005(04)
[20]王立宾.基于ssh的终端绑定的设计与实现:[硕士学位论文].北京:北京邮电大学.2008(10)
[21]凌以珂.Linux与Windows资源共享实现方法简析.电脑知识与技术(学术交流).2006(08)
[22]王强.Linux与Windows资源共享的安全控制.网络与信息.2006(05)
[23]Baliga,Girish Bantwal.A middleware framework for networked control systems.University of lllinois at Urbana-Champaign.2005
[24]Du,Wei.Advanced middleware support for distributed data-intensive applications.The OHIO State University.2005
[25]赵东生,王小磊,毛逸清等.利用SFU开发Windows和Linux异构环境下的分布式生物信息学应用.军事医学科学院院刊.2006,6(04)
[26]李勇.进程间通信的分布式实现:[硕士学位论文].吉林:吉林大学.2004.
[27]陈鹤鸣,周文胜,陈雄.Windows下的进程间通信.南京邮电大学学报(自然科学版).2000(02)
[28]彭银球.多平台问网络通信的实现方案.计算机丁程与设计.2004(06)
[29]李扬,耿昌宇,张丽芬.基于Socket 通讯模式下的跨平台数据同步.北京理工大学学报.2002,5(01)
[30]王静,曲凤娟.基于Socket的多用户并发通信的设计.福建电脑.2007(3):164-165
[31]李峰.利用流式Socket编程实现Windows与Linux的通信.微计算机信息.2006,12(03)
[32]姚晖,李定主,卢宁.Linux和Windows系统之间网络通信程序的开发.电脑开发与应用.2002,12(03)
[33]何世明.利用Java在Windows与Linux建立数据通讯的方法.计算机应用.2001,12(10)
[34]Shao,Yongliang.Object-based,distributed online real-time communication system modeling and development.University of Windsor(Canada).2000
[35]Mandadi,Sanjay Reddy.The design and implementation of a simple master/slave interprocess -communicatin module.University of Washington.2000
[36]Heymans,Louis;Vander Beken,Tony etal.Testing Techniques for the Cross-platform Migration of Very Large Interactive Applications.Software Maintenance and Reengineering(CSMR),European Conference on.2007.
[37]王晓鹏.TCP/IP下的Socket及Windows通信机制.航空计算技术.2004(02).
[38]梁立哲,时武略.TCP/IP跨平台通信的研究.电脑知识与技术(学术交流).2006(06).
[39]徐小东.基于socket技术的数据交换平台的设计与实现.[硕士学位论文].上海:上海交通大学.2007,09,14.
[40]赵文清,姜波.基于Socket的Java语言网络通讯机制和程序设计.华北电力大学.2002(7)
[41]Taleb,M,Seffah,A.Patterns-Oriented Design Applied to Cross-Platform Webbased Interactive Systems.Information Reuse and Integration.2007IEEE International Conference on.2007
[42]周坤.计算机远程终端监控系统:[硕士学位论文].南京:南京信息工程大学.2008(09).
[43](美)希尔德(Schildt,H.).Java参考大全(J2SE 5 Edition).北京:清华大学出版社,2006.
[44]www.cs.umanitoba.ca/~eclipse.An Eclipse GUI Builder.Department of ComputerScience University of Manitoba.